jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Johanna Reich | Sebastian Kaiser | Ueli Heiz | Jan‐Dierk Grunwaldt | Manfred M. Kappes | Friedrich Esch | Barbara A. J. Lechner
Source: Topics in Catalysis (article, 2024-04-04)
Field: Materials Science — Materials Chemistry

A Critical View on the Quantification of Model Catalyst Activity Abstract The conversion of reactants, reaction rate referred to catalyst mass, and turnover frequency (TOF) are values typically employed to compare the activity of different catalysts. However, experimental parameters have to be chosen carefully when systems of different complexity are compared. In order to characterize UHV-based model systems, we use a highly sensitive sniffer setup which allows us to investigate the catalytic activity by combining three different measurement modes: temperature-programmed desorption, continuous flow, and pulsed-reactivity experiments. In this article, we explore the caveats of quantifying catalytic activity in UHV on the well-studied and highly defined reference system of CO oxidation on Pt(111), which we later compare to the same reaction on Pt 19 clusters deposited on Fe 3 O 4 (001). We demonstrate that we can apply fast heating ramps for TOF quantification, thus inducing as little sintering as possible in the metastable clusters. By changing the reactant ratio, we find transient reactivity effects that influence the TOF, which should be kept in mind when comparing catalysts. In addition, the TOF also depends on the surface coverage that itself is a function of temperature and pressure. At a constant reactant ratio, in the absence of transient effects, however, the TOF scales linearly with total pressure over the entire measured temperature range from 200 to 700 K since the reaction rate is dependent on both reactant partial pressures with temperature-dependent reaction order. When comparing the maximum TOF at this particular reactant ratio, we find a 1.6 times higher maximum TOF for Pt 19 /Fe 3 O 4 (001) than for Pt(111). In addition, pulsed-reactivity measurements help identify purely reaction-limited regimes and allow for a more detailed investigation of limiting reactants over the whole temperature range. Catalysis ; Environmental science ; Chemistry ; Organic chemistry Catalytic Processes in Materials Science ; Catalysis and Oxidation Reactions ; Catalysis and Hydrodesulfurization Studies
Authors: Yuanjin Zhang | Zhonglin Liu | Marsha Hirschi | Oleg Brodsky | Eric F. Johnson | Sang Joon Won | Asako Nagata | Matthew D. Petroski | Jaimeen D. Majmudar | Sherry Niessen | Todd VanArsdale | A. Gilbert | Matthew M. Hayward | Al Stewart | Andrew R. Nager | Bruno Melillo | Benjamin F. Cravatt
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-01-20)
Field: Chemistry — Organic Chemistry

Expanding the ligandable proteome by paralog hopping with covalent probes More than half of the ~20,000 protein-encoding human genes have at least one paralog. Chemical proteomics has uncovered many electrophile-sensitive cysteines that are exclusive to a subset of paralogous proteins. Here, we explore whether such covalent compound-cysteine interactions can be used to discover ligandable pockets in paralogs that lack the cysteine. Leveraging the covalent ligandability of C109 in the cyclin CCNE2, we mutated the corresponding residue in paralog CCNE1 to cysteine (N112C) and found through activity-based protein profiling (ABPP) that this mutant reacts stereoselectively and site-specifically with tryptoline acrylamides. We then converted the tryptoline acrylamide-N112C-CCNE1 interaction into a NanoBRET-ABPP assay capable of identifying compounds that reversibly inhibit both N112C- and WT-CCNE1:CDK2 complexes. X-ray crystallography revealed a cryptic allosteric pocket at the CCNE1:CDK2 interface adjacent to N112 that binds the reversible inhibitors. Our findings thus provide a roadmap for leveraging electrophile-cysteine interactions to extend the ligandability of the proteome beyond covalent chemistry. Cysteine ; Proteome ; Covalent bond ; Electrophile ; Chemistry ; Computational biology ; Biochemistry ; Combinatorial chemistry ; Biology ; Enzyme Click Chemistry and Applications ; Peptidase Inhibition and Analysis ; Chemical Synthesis and Analysis
Authors: А. В. Журавлев | Viktor Gavrilyuk | Xin Chen | V. V. AKSENOV | Hartmut Kühn | Igor Ivanov
Source: International Journal of Molecular Sciences (review, 2024-11-09)
Field: Chemistry — Organic Chemistry

Structural and Functional Biology of Mammalian ALOX Isoforms with Particular Emphasis on Enzyme Dimerization and Their Allosteric Properties The human genome involves six functional arachidonic acid (AA) lipoxygenase (<i>ALOX</i>) genes, and the corresponding enzymes (ALOX15, ALOX15B, ALOX12, ALOX12B, ALOXE3, ALOX5) have been implicated in cell differentiations and in the pathogenesis of inflammatory, hyperproliferative, metabolic, and neurological disorders. Humans express two different AA 15-lipoxygenating ALOX isoforms, and these enzymes are called ALOX15 (15-LOX1) and ALOX15B (15-LOX2). Chromosomal localization, sequence alignments, and comparison of the enzyme properties suggest that pig and mouse ALOX15 orthologs (leukocyte-type 12-LOX) on the one hand and rabbit and human ALOX15 orthologs on the other (reticulocyte-type 15-LOX1) belong to the same enzyme family despite their different reaction specificities with AA as a substrate. In contrast, human ALOX12 (platelet-type 12-LOX), as well as pig and mouse ALOX15 (leukocyte-type 12-LOX), belong to different enzyme families, although they exhibit a similar reaction specificity with AA as a substrate. The complex multiplicity of mammalian ALOX isoforms and the controversial enzyme nomenclatures are highly confusing and prompted us to summarize the current knowledge on the biological functions, enzymatic properties, and allosteric regulation mechanisms of mammalian ALOX15, ALOX15B, and ALOX12 orthologs that belong to three different enzyme sub-families. Allosteric regulation ; Gene isoform ; Enzyme ; Emphasis (telecommunications) ; Structural biology ; Allosteric enzyme ; Biology ; Biochemistry ; Computational biology ; Focus (optics) ; Chemistry ; Computer science ; Gene ; Physics Free Radicals and Antioxidants ; Microbial metabolism and enzyme function ; Eicosanoids and Hypertension Pharmacology
Authors: Chang Liu | Hui Zhang
Source: Expert Opinion on Drug Discovery (article, 2024-05-24)
Field: Chemistry — Spectroscopy

Data processing for high-throughput mass spectrometry in drug discovery The demand for automatic data processing in high-throughput mass spectrometry is driven by the need to keep pace with the accelerated speed of data acquisition. The seamless integration of processing capabilities with LIMS, efficient data review mechanisms, and the exploration of future features such as real-time feedback, automatic method optimization, and AI model training is crucial for advancing the drug discovery field. As technology continues to evolve, the synergy between high-throughput mass spectrometry and intelligent data processing will undoubtedly play a pivotal role in shaping the future of high-throughput drug discovery applications. Drug discovery ; Throughput ; Workflow ; Computer science ; Data acquisition ; Data processing ; Mass spectrometry ; Chemistry ; Database ; Chromatography ; Operating system Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Advanced Proteomics Techniques and Applications
Authors: Helen Forgham | Jiayuan Zhu | Taoran Zhang | Xumin Huang | Xiangke Li | Ao Shen | Heather Biggs | Gert Talbo | C. F. Xu | Thomas P. Davis | Ruirui Qiao
Source: Nanomedicine (article, 2024-04-09)
Field: Materials Science — Biomaterials

Fluorine-modified polymers reduce the adsorption of immune-reactive proteins to PEGylated gold nanoparticles <b>Aim:</b> To investigate the influence of fluorine in reducing the adsorption of immune-reactive proteins onto PEGylated gold nanoparticles. <b>Methods:</b> Reversible addition fragmentation chain transfer polymerization, the Turkevich method and ligand exchange were used to prepare polymer-coated gold nanoparticles. Subsequent <i>in vitro</i> physicochemical and biological characterizations and proteomic analysis were performed. <b>Results:</b> Fluorine-modified polymers reduced the adsorption of complement and other immune-reactive proteins while potentially improving circulatory times and modulating liver toxicity by reducing apolipoprotein E adsorption. Fluorine actively discouraged phagocytosis while encouraging the adsorption of therapeutic targets, CD209 and signaling molecule calreticulin. <b>Conclusion:</b> This study suggests that the addition of fluorine in the surface coating of nanoparticles could lead to improved performance in nanomedicine designed for the intravenous delivery of cargos. Colloidal gold ; Adsorption ; Nanoparticle ; PEGylation ; Polymer ; Protein adsorption ; Fluorine ; Materials science ; Chemical engineering ; Nanotechnology ; Chemistry ; Organic chemistry ; Metallurgy ; Composite material Nanoparticle-Based Drug Delivery ; Nanoplatforms for cancer theranostics ; Advanced Nanomaterials in Catalysis
Authors: Joana Gamboa | Pedro Lourenço | Carla Cruz | Eugénia Gallardo
Source: Pharmaceutics (review, 2024-04-14)
Field: Chemistry — Organic Chemistry

Aptamers for the Delivery of Plant-Based Compounds: A Review Natural compounds have a high potential for the treatment of various conditions, including infections, inflammatory diseases, and cancer. However, they usually present poor pharmacokinetics, low specificity, and even toxicity, which limits their use. Therefore, targeted drug delivery systems, typically composed of a carrier and a targeting ligand, can enhance natural product selectivity and effectiveness. Notably, aptamers-short RNA or single-stranded DNA molecules-have gained attention as promising ligands in targeted drug delivery since they are simple to synthesize and modify, and they present high tissue permeability, stability, and a wide array of available targets. The combination of natural products, namely plant-based compounds, with a drug delivery system utilizing aptamers as targeting agents represents an emerging strategy that has the potential to broaden its applications. This review discusses the potential of aptamers as targeting agents in the delivery of natural compounds, as well as new trends and developments in their utilization in the field of medicine. Aptamer ; Computational biology ; Nanotechnology ; Chemistry ; Computer science ; Biochemical engineering ; Biology ; Engineering ; Materials science ; Molecular biology Nanomaterials for catalytic reactions ; Catalysis for Biomass Conversion ; Mesoporous Materials and Catalysis
Authors: Saphia A. L. Matthew | F. Philipp Seib
Source: Advanced Therapeutics (article, 2024-10-30)
Field: Materials Science — Biomaterials

The Dawning Era of Anticancer Nanomedicines: From First Principles to Application of Silk Nanoparticles Abstract This review introduces nanomedicines and medical silks by addressing seminal and recent research within these fields. First, the successes of nanoparticles in improving the safety profiles and pharmacokinetic–pharmacodynamic properties are explored but also the concepts of threshold dosing and targeting of tumor‐associated macrophages. Current barriers to systemic delivery of nanomedicines are detailed and methods to overcome these barriers and increase tumor targeting are evaluated, namely: tuning the nanomedicine size and surface charge for enhanced tumor accumulation and penetration; non‐spherical nanomedicine morphologies for macrophage evasion and targeted delivery to endothelial cells; and, surface functionalization for stealth coatings and targeting receptor‐mediated endocytosis. The advantages of using silk as a nanomedicine with reference to its structure, composition, biological performance, and formulation are discussed. While batch methods for silk processing enable the formation of nano to microparticles, continuous technology can overcome bottlenecks of the deployed engineering methods such as low throughput and poor reproducibility. Finally, the chemical modification of silk using homogeneous and heterogenous chemistries is assessed within the nanomedicine context. Overall, this review covers silk nanomedicines from first principles to carrier design and on to areas of future development. SILK ; Nanotechnology ; Nanoparticle ; Nanomedicine ; Materials science ; Composite material Silk-based biomaterials and applications ; Nanoparticle-Based Drug Delivery ; Phytochemical compounds biological activities
Authors: Marcel Geppert | Kai Jellinek | Michael Linseis | Michael Bodensteiner | Jessica Geppert | Miriam M. Unterlass | Rainer F. Winter
Source: Inorganic Chemistry (article, 2024-07-30)
Field: Materials Science — Materials Chemistry

Dual Fluorescence and Phosphorescence Emissions from Dye-Modified (<i>NCN</i>)-Bismuth Pincer Thiolate Complexes We report the synthesis, characterization, and photophysical properties of four new dye-modified (<i>NCN</i>)Bi pincer complexes with two mercaptocoumarin or mercaptopyrene ligands. Their photophysical properties were probed by UV/vis spectroscopy, photoluminescence (PL) studies, and time-dependent density functional theory (TD-DFT) calculations. Absorption spectra of the complexes are dominated by mixed pyrene or coumarin π → π*/n(pS) → pyrene or coumarin π* transitions. While unstable toward reductive elimination of the corresponding disulfide under irradiation at room temperature, the complexes provide stable emissions at 77 K. Under these conditions, coumarin complexes <b>2</b> and <b>4</b> exhibit exclusively green phosphorescence at 508 nm. In contrast, the emissive properties of pyrene complexes <b>1</b> and <b>3</b> depend on the excitation wavelength and on sample concentration. Irradiation into the lowest-energy absorption band exclusively triggers red phosphorescence from the pyrenyl residues at 640 nm. At concentrations <i>c</i> < 1 μM, excitation into higher excited electronic states results in blue pyrene fluorescence. With increasing <i>c</i> (1-100 μM), the emission profile changes to dual fluorescence and phosphorescence emission, with a steady increase of the phosphorescence intensity, until at <i>c</i> ≥ 1 mM only red phosphorescence ensues. Progressive red-shifts and broadening of steady-state excitation spectra with increasing sample concentration suggest the presence of static excimers, as we observe it for concentrated solutions of pyrene. Crystalline and powdered samples of <b>1</b> indeed show intermolecular association through π-stacking. TD-DFT calculations on model dimers and a tetramer of <b>1</b> support the idea of aggregation-induced intersystem crossing (AI-ISC) as the underlying reason for this behavior. Chemistry ; Phosphorescence ; Fluorescence ; Bismuth ; Photochemistry ; Pincer movement ; Organic chemistry ; Catalysis Lanthanide and Transition Metal Complexes ; Organometallic Complex Synthesis and Catalysis ; Organic Light-Emitting Diodes Research
Authors: Peiwen Chen | Kuo Fu | Xiangyang Zhang | Sheng‐Yin Zhao | Hongwei Wu | Guofeng Liu
Source: Nano Research (article, 2024-12-16)
Field: Materials Science — Biomaterials

Chirality inversion via van der Waals interactions to π–π stacking in non-equilibrium assembly within a narrow temperature range Understanding the dynamic control of supramolecular chirality is essential for the development of advanced chiral materials. This study presents a system where solvent-induced self-assembly of ortho-pyridine-azo-cholesterol (o-PAzPCC) and temperature-regulated co-assembly with Cu<sup>2+</sup> exhibit dynamic supramolecular chirality inversion. Dimethylsulfoxide (DMSO) and alcohol solvents induce the reverse assembly of o-PAzPCC monomers, leading to circular dichroism (CD) signal inversion. Notably, the chloro-bridged Cu<sup>2+</sup>/o-PAzPCC co-assembly system demonstrates temperature-regulated chirality inversion within a narrow range (283 to 293 K). At 283 K, van der Waals forces drive the formation of non-equilibrium nanosheet structures (Agg I) with positive CD absorption at 390 nm. At 293 K, π−π stacking interactions promote equilibrium nanoribbon structures (Agg III) with negative CD absorption at 440 nm wavelength. Increasing the temperature from 283 K can induce a transformation of the nanosheet structures to nanoflower structures (Agg II), characterized by positive CD absorption at 440 nm. The chirality inversion can be finely tuned by adjusting the concentrations and ultrasonication time. This work enhances our understanding of chiral assembly processes and their chirality transmission mechanisms, advancing the development of chiral supramolecular materials for applications in biological systems. van der Waals force ; Stacking ; Chirality (physics) ; Atmospheric temperature range ; Inversion (geology) ; Range (aeronautics) ; Materials science ; Chemical physics ; Chemistry ; Thermodynamics ; Physics ; Molecule ; Quantum mechanics ; Chiral symmetry ; Geology ; Organic chemistry Supramolecular Self-Assembly in Materials ; Surface Chemistry and Catalysis ; Synthesis and Properties of Aromatic Compounds
Authors: Ethan Richards | Luis Casarrubios | Jarryl M. D’Oyley | Henry S. Rzepa | Andrew J. P. White | Kristin Goldberg | Frederick W. Goldberg | James A. Bull | Silvia Díez‐González
Source: Advanced Synthesis & Catalysis (article, 2024-11-11)
Field: Chemistry — Organic Chemistry

Bidentate NHC‐Containing Ligands for Copper Catalysed Synthesis of Functionalised Diaryl Ethers Abstract Diaryl and heteroaryl ethers are important and common motifs in drug discovery and agrochemicals. Here we present a catalytic system for the copper catalysed arylation of phenols with aryl halides. Bidentate N‐heterocyclic carbene ligands provide a well‐defined catalytic system that enable low loading of copper in effective coupling reactions (0.5 mol% Cu or lower). The reaction scope of aryl iodides and aryl bromides is developed, that is tolerant of functional groups and a library of biaryl ethers with lead‐like properties is prepared. The presence of excess ligand (in a 1:3 ratio) is shown to be optimal to prevent catalyst degradation, presumably by avoiding decomplexation of the ligand. This is also supported by the catalytic results obtained with pre‐formed copper complexes. The kinetics of the reaction are examined and shown to be first order in copper, supportive of a well‐defined catalyst species, first order in phenol and aryl iodide, and zero order in base under the developed conditions. Computational studies performed using Minnesota MN15‐L parametrisation method support an oxidative addition‐reductive elimination sequence with both steps having similar enegies and the reductive elimination occurring through an intimate ion pair intermediate. Chemistry ; Denticity ; Copper ; Combinatorial chemistry ; Catalysis ; Organic chemistry ; Polymer chemistry ; Metal Catalytic Cross-Coupling Reactions ; N-Heterocyclic Carbenes in Organic and Inorganic Chemistry ; Asymmetric Hydrogenation and Catalysis
Authors: Tra Huong | Van Tu Nguyen | Thi Nga Nguyen | Xuan Linh Ha | Nguyễn Quốc Dũng | Thi Kim Ngan Tran
Source: Applied Sciences (article, 2024-01-23)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Synthesis of Porous Carbon Nanomaterials from Vietnamese Coal: Fabrication and Energy Storage Investigations The choice of precursor and simple synthesis techniques have decisive roles in the viable production and commercialization of carbon products. The intense demand for developing high-purity carbon nanomaterials through inexpensive techniques has promoted the usage of fossil derivatives as a feasible source of carbon. In this study, Vietnamese-coal-derived porous carbon (PC) was used to fabricate coal-derived porous carbon nanomaterials (CDPCs) using the modified Hummers method. The resulting porous carbon nanomaterials achieved a nanoscale structure with an average pore size ranging from 3 to 10 nm. The findings indicate that CDPC exhibits well-developed micropores and mesopores. The presence of macropores and mesopores not only facilitates the complete immersion of the material in the electrolyte but also effectively shortens the ion diffusion pathways. CDPC boasts a high carbon content, constituting 80.88% by weight. Electrochemical impedance spectroscopy (EIS) Nyquist plot of electrodes made from CDPC showed good conductivity value with low charge-transfer resistance. This electrode worked well and stably with capacitance retention of 74.7% after 1000 cycles. The CDPC specific capacitance reached 236 F/g under a current density of 0.1 A using the constant current discharge method and then decreased as the current density increased. Based on the results of the electrochemical properties of the materials, the energy storage capacity of the CDPC material was good and stable. This investigation presents an eco-friendly methodology for the judicious utilization of coal in energy storage applications, specifically as electrodes for supercapacitors and anodes for Li-ion batteries. Materials science ; Coal ; Nanotechnology ; Waste management ; Engineering Supercapacitor Materials and Fabrication ; Advancements in Battery Materials ; Advanced Battery Technologies Research
Authors: Nouman Rasheed Jatoi | Muhammad Aslam Khan | Muhammad Hussain | Khaloud Mohammed Alarjani | Mohamed S. Elshikh | Dunia A. Al Farraj | Hadeel Salah Mansoor | Junaid Ihsan | Syed Ali Imran Bokhari
Source: Green Processing and Synthesis (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

A comparative study of <i>Fagonia arabica</i> fabricated silver sulfide nanoparticles (Ag <sub>2</sub> S) and silver nanoparticles (AgNPs) with distinct antimicrobial, anticancer, and antioxidant properties Abstract Silver sulfide (Ag 2 S) nanomaterials are important chalcogenides and have potential applications in photovoltaic cells, thermoelectric sensors, solar cell batteries, and infrared detectors. However, the biological properties of green synthesized silver sulfide nanoparticles (Ag 2 S-NPs) have been rarely explored as compared to the extensively studied silver nanoparticles (AgNPs). The current study thus investigates and compares Fagonia arabica synthesized Ag 2 S-NPs and AgNPs for multiple biological properties. Biosynthesis of the NPs is achieved using an aqueous extract of F. arabica , whereas physicochemical, structural, morphological, and optical characterization of the materials was undertaken using UV–Vis spectroscopy, Fourier transform infrared spectroscopy, X-ray diffractometer, scanning electron microscopy, energy dispersive spectroscopy, photoluminescence, and pH-responsive dispersion studies. Our result reveals that both the NPs exhibit excellent biological properties, yet Ag 2 S-NPs exhibit relatively enhanced antioxidant and in vitro anticancer potential against MCF-7 cells. However, AgNPs possess comparatively better antibacterial, antileishmanial, and antifungal properties. Most importantly, both the synthesized NPs are exceptionally well compatible with human blood cells, ensuring their safe and non-toxic properties. Being highly potent and compatible antimicrobial and anticancer materials, the F. arabica synthesized G-Ag 2 S-NPs and G-AgNPs can be further explored in in vivo studies. Silver nanoparticle ; Antimicrobial ; Nanoparticle ; Chemistry ; Silver sulfide ; Antioxidant ; Nuclear chemistry ; Nanotechnology ; Materials science ; Organic chemistry ; Inorganic chemistry Nanoparticles: synthesis and applications ; Moringa oleifera research and applications