jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Xi Xue | Xiangying Liu | Xue Liu | Hanyu Sun | Shize Li | Kai Chen | Hanmiao Xu | Liangning Li | Chengxia Mao | Jingjie Yan | Peng Yang | Baolian Wang | Tingjun Hou | Tingting Du | Xiaojian Wang
Source: JACS Au (article, 2025-11-03)
Field: Chemistry — Organic Chemistry

One-Shot Rational Design of Covalent Drugs with CovalentLab Targeted covalent drugs have demonstrated remarkable potential in disease treatment over the past decades. However, existing methods for covalent drug design are often limited to serine and cysteine, ignoring other potentially ligandable binding sites. Statistical analyses indicate that over 95% of binding pockets contain covalent-binding residues, suggesting that all ligands that targeting these pockets possess the potential to be modified into covalent ligands. To achieve this goal, we introduced CovalentLab, an interactive computational platform that integrates ligand-based and warhead-based strategies into a unified workflow for the rational design of covalent ligands. Leveraging a covalent binding site prediction model constructed on ESM-2 with LoRA fine-tuning, CovalentLab enables the prediction and ranking of nine classes of covalent-binding residues in proteins according to their reactivity and facilitates systematic warhead attachment to ligands using 210 electrophilic groups or user-defined warheads. Using this platform, a comprehensive library of more than 100,000 covalent molecules across 95 targets was generated. Notably, CovalentLab has been successfully applied to various essential real-world targets, identifying wet-laboratory-validated bioactive compounds ranging from TRK orthosteric inhibitors to GAC allosteric inhibitors. By bridging gaps in covalent drug discovery, CovalentLab offers a versatile, publicly accessible resource to expand the druggable targets and accelerate the development of targeted covalent therapies. Covalent bond ; Druggability ; Rational design ; Covalent binding ; Drug discovery ; Small molecule ; Allosteric regulation ; Drug design ; Drug development Click Chemistry and Applications ; Protein Degradation and Inhibitors ; Biochemical and Structural Characterization
Authors: Ling Liang | Kai-Yue Liu | Guang Yang | Zeng-Min Xue | Wen-Xuan Zhao | Hongtao Lin | Shuhai Chen | Chuan‐Zeng Wang | M.R.J. Elsegood | Simon J. Teat | Ming Wang | Takehiko Yamato
Source: Journal of Molecular Structure (article, 2025-01-09)
Field: Materials Science — Materials Chemistry

Achieving tuneable, asymmetrical, pyrene-based luminogens for latent fingerprint extraction and flexible light source fabrication Chemistry ; Fingerprint (computing) ; Pyrene ; Fabrication ; Extraction (chemistry) ; Chromatography ; Nanotechnology ; Organic chemistry ; Artificial intelligence Luminescence and Fluorescent Materials ; Forensic Fingerprint Detection Methods ; Polydiacetylene-based materials and applications
Authors: Saravanakumar Natarajan | Latha Ganesapandian | P. Santhoshkumar | Anantha Krishnan Dhanabalan | Bangalore Rajanikanth Rakshith | Venkatasubramanian Ulaganathan | Palaniswamy Suresh
Source: Chemistry & Biodiversity (article, 2025-08-29)
Field: Chemistry — Organic Chemistry

Chiral 1,3,5‐Triazines as Potential EGFR Inhibitors: Pharmacophore Modeling, Synthesis, Molecular Docking, Molecular Dynamics Simulation, and Anticancer Evaluation To target epidermal growth factor receptor (EGFR) signaling in breast (MCF-7) and lung (A549) cancers, a library of chirally functionalized 1,3,5-triazine scaffolds was designed by a ligand-based drug design approach. An optimized synthetic protocol employing sequential chlorine replacement on cyanuric chloride delivered enantiomerically pure chiral-1,3,5-triazine derivatives. Through systematic structural modifications, fine-tuned physicochemical properties and optimal ADME profiles are achieved. The synthesized compounds were evaluated for anticancer activity against MCF-7 (breast) and A549 (lung) cancer cell lines using the MTT assay. Molecular docking studies at the ATP-binding site of EGFR-TK demonstrate that compounds with the best docking score exhibit strong in vitro EGFR inhibitory activity, confirming a correlation between computational and experimental findings. A common pharmacophore hypothesis derived from established EGFR inhibitors enabled virtual screening of the synthesized library, yielding six top candidates. Among these, analogue (R)-4-((4-(3-methoxyphenoxy)-6-(pyrrolidin-3-ylamino)-1,3,5-triazin-2-yl)amino)benzonitrile (13c) exhibited the strongest cytotoxicity, with IC<sub>50</sub> values of 8.04 and 12.24 µM against MCF-7 and A549 cell lines, respectively. These results highlight chiral 1,3,5-triazines as promising leads for EGFR-targeted cancer therapy. Pharmacophore ; Chemistry ; Docking (animal) ; EGFR inhibitors ; Epidermal growth factor receptor ; Virtual screening ; ADME ; Stereochemistry ; Cytotoxicity ; Triazine ; Molecular model ; MCF-7 ; A549 cell ; Combinatorial chemistry ; Pharmacology ; In vitro ; Biochemistry ; Receptor ; Cancer cell ; Cancer ; Organic chemistry ; Biology Synthesis and Characterization of Heterocyclic Compounds ; Click Chemistry and Applications ; DNA and Nucleic Acid Chemistry
Authors: Minghao Liu | Guojuan Liu | Qing Xu | Gaofeng Zeng
Source: Chemical Synthesis (article, 2025-01-08)
Field: Materials Science — Materials Chemistry

Decorating pore environment via cationic units of covalent organic frameworks for enhancing CO<sub>2</sub> reduction reaction The conversion performance for electrocatalytic CO2 reduction reaction (CO2RR) relies on the affinity of CO2 molecules. Ionic covalent organic frameworks (COFs) are promising platforms for CO2RR due to the accessible catalytic sites in the skeleton, high CO2 combination ability and the electronic conductivity. However, most ionic COFs are constructed via pre-functionalization of the monomers or post-modification of the skeleton, encountering incomplete loading or uneven distribution of the active sites. In this work, a cationic porphyrin-based COF using the (3-carboxypropyl)trimethylammonium and Co-porphyrin units is developed through the sub-stoichiometric bottom-up synthesis method to fine-tune the pore environment for modulating the binding ability of CO2. Compared to base COFs, the cationic COFs exhibit improved electronic conductivity, high CO2 adsorption uptakes and enhanced reducibility, further improving the electrocatalytic CO2RR performance. Notably, the cationic COF achieves a high CO selectivity of 93% and a partial current density of 24.6 mA·cm-2. This work not only offers considerable insights for improving the catalytic performance of COFs through the cationic groups but also provides a stoichiometry method to modulate the pore environment. Cationic polymerization ; Covalent bond ; Reduction (mathematics) ; Covalent organic framework ; Chemical engineering ; Chemistry ; Materials science ; Nanotechnology ; Organic chemistry ; Engineering Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; CO2 Reduction Techniques and Catalysts
Authors: Chengyue Yang | Yuanbo Sun | Bin Zhao | Ji Han | Benzheng Li | Peng Xue | Lei Xie | Jianshe Hu | Jingyi Wang
Source: Advanced Functional Materials (article, 2025-05-29)
Field: Materials Science — Materials Chemistry

Debye Radius‐Guided Mercury Sequestration via Nanoconfinement by Adaptive Nano‐Ion Channels Abstract Rapid and targeted intervention during sudden mercury pollution incidents can significantly mitigate the harmful effects of mercury dissemination. Mesoporous metal–organic frameworks (MOFs) are demonstrated great promise for mercury wastewater purification, owing to their exceptional adsorption capacity. However, these materials often underperform at exceptionally high or low Hg(II) concentrations, limiting their use in emergencies. To address this issue, this study leverages nanostructure engineering techniques and, for the first time, fine‐tunes the proportion of surfactants to construct a thiol‐functionalized UiO‐66 MOF (Nic‐UiO‐66‐SH) with size‐adjustable nano‐ion channels for rapid Hg(II) pollution management in emergency contexts. The Nic‐UiO‐66‐SH, with a maximum adsorption capacity of 1695.87 mg g −1 , can quickly and effectively adsorb Hg(II) at extreme concentrations (10–600 mg L −1 ) within 2.5–105 min, bringing the concentration down to drinking water standards (&lt;0.002 mg L −1 ). This superior performance is attributed to the concentration‐specific adsorption mechanism of ions in adaptive nano‐ion channels based on Debye radius theory, which guides the precise control of channel size. Molecular simulations further validate the significant role of ion channels in optimizing Hg(II) diffusion and adsorption. This work establishes a theoretical foundation for the development of emergency wastewater purification materials and promotes their practical application in pollution response scenarios. Materials science ; Ion ; RADIUS ; Debye ; Mercury (programming language) ; Nano- ; Debye length ; Ionic radius ; Nanotechnology ; Condensed matter physics ; Engineering physics ; Chemical physics ; Physics ; Composite material ; Quantum mechanics ; Computer science Graphene research and applications ; Nanopore and Nanochannel Transport Studies ; Ion-surface interactions and analysis
Authors: Alehegn Eskemech | Hushan Chand | Rubi Bhakhar | Venkata Krishnan | Rik Rani Koner
Source: Advanced Sustainable Systems (article, 2025-07-28)
Field: Chemistry — Inorganic Chemistry

Zinc‐Based Metal–Organic Frameworks in Antibiotics Mitigation: From Detection to Decontamination Abstract Metal–organic frameworks (MOFs) are porous crystalline hybrid materials employed for various applications, starting from energy sectors and environmental remediation to catalysis. The designability, tunability, and robustness are key attributes of MOFs, making them materials of high pursuit. The detection and removal of antibiotics are of prime importance in the area of environmental remediation, where MOFs are increasingly utilized effectively. Antibiotic detection is vastly investigated using fluorescent MOFs, and the fluorescent behavior of MOFs originates from the linker, metal ions, or both. Fluorescent MOFs can be synthesized by systematic design and critical linkers and metal ions selection. In addition, their fluorescence attributes can be fine‐tuned by encapsulating various guest molecules within MOFs. On the other hand, the reduction of antibiotics via physical adsorption and photocatalytic degradation by using MOFs is another promising application to remediate wastewater and eliminate bacterial antibiotic resistance. Compiling state‐of‐the‐art progress and providing rational insights on detecting and removing antibiotics using Zn‐MOFs are of paramount interest in advancing this field. The recent advances of Zn‐based MOFs for detecting and removing antibiotics are emphasized. Additionally, future aspects, shortcomings, and scope for improvement in the detection and removal performance of Zn‐based MOFs are discussed. Human decontamination ; Metal-organic framework ; Zinc ; Antibiotics ; Waste management ; Materials science ; Environmental science ; Environmental chemistry ; Chemistry ; Metallurgy ; Organic chemistry ; Engineering ; Adsorption Metal-Organic Frameworks: Synthesis and Applications ; Covalent Organic Framework Applications ; Arsenic contamination and mitigation
Authors: Zhiwen Chen | Jipeng Xu | Mingyu Zhang | Yan Luo | Zicheng Cao | Yubin Hu | Yingwu Luo | Zheng Yang | Cheng Lian | Junjie Zhao
Source: Small (article, 2025-05-13)
Field: Materials Science — Materials Chemistry

Shielding CO <sub>2</sub> ‐Philic Sites in Trimmed Covalent Organic Framework Pores by Atomic Layer Deposition Strong adsorptive sites toward unwanted gas molecules in porous framework materials often lead to reversed sorption selectivity, creating tremendous challenges for enhancing the diffusion-driven membrane separations targeted at the weakly adsorbed species in the gas pair. While post-synthetic modification methods have been reported to downsize the pores in covalent organic frameworks (COFs), effective approaches to shield the highly adsorptive sites within the pores are rarely explored. Here, a solvent-less pore modification strategy is developed using atomic layer deposition (ALD). it is shown that controlled amounts of ZnO can be uniformly deposited into the COF pores, offering the ability to fine-tune the pore dimensions. Moreover, the Zn─O moieties grown into the COF pore are found to interact with the CO<sub>2</sub>-philic ketoenamine groups, and substantially reduce the CO<sub>2</sub> solubility by 72.4% in the COF membrane. Accordingly, the simultaneously increased diffusion selectivity and sorption selectivity for H<sub>2</sub>/CO<sub>2</sub> lead to a 330% improvement of the permselectivity in membrane separation, demonstrating the efficacy of the strategy for pore engineering in COFs. Covalent organic framework ; Selectivity ; Sorption ; Membrane ; Chemical engineering ; Covalent bond ; Atomic layer deposition ; Adsorption ; Materials science ; Solubility ; Porosity ; Metal-organic framework ; Gas separation ; Layer (electronics) ; Diffusion ; Deposition (geology) ; Nanotechnology ; Chemistry ; Organic chemistry ; Catalysis ; Composite material Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Membrane Separation and Gas Transport
Authors: Keizo Tsukamoto | Naoyuki Hirata | Masahide Tona | Y. Nemoto | Atsushi Nakajima
Source: Ultramicroscopy (article, 2025-09-16)
Field: Materials Science — Materials Chemistry

Evaluating atomic counts in metal nanoclusters via scanning transmission electron microscopy Nanoclusters ; Scanning transmission electron microscopy ; Metal ; Transmission electron microscopy ; Nanoscopic scale ; Platinum ; Atom (system on chip) ; Scanning electron microscope Nanocluster Synthesis and Applications ; Gold and Silver Nanoparticles Synthesis and Applications ; nanoparticles nucleation surface interactions
Authors: Muhammad Imran | Junpeng Deng | Zhaogang Nie | Zhengyan Liu | Lin Ma | Gloria Mazzone | Zheng Xie
Source: Dyes and Pigments (article, 2025-06-18)
Field: Chemistry — Physical and Theoretical Chemistry

Unveiling the effect of amino substitution on intramolecular electron/energy transfer and intersystem crossing in the naphthalimide-pyrene donor-acceptor dyad Intersystem crossing ; Intramolecular force ; Chemistry ; Substitution (logic) ; Photochemistry ; Pyrene ; Electron donor ; Electron transfer ; Acceptor ; Electron acceptor ; Stereochemistry ; Organic chemistry ; Singlet state ; Excited state ; Physics ; Catalysis Photochemistry and Electron Transfer Studies ; Electrochemical Analysis and Applications ; Luminescence and Fluorescent Materials
Authors: Ibrahim Ellithy | Mauricio Esguerra | R. Radhakrishnan
Source: IEEE Magnetics Letters (article, 2025-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

High-Permeability Magnetic Composites With Cement, Asphalt, and Epoxy Binders for Enhanced Performance Across Diverse Applications As the global demand for energy transition and transport decarbonization intensifies, the development of advanced magnetizable materials becomes crucial for supporting large-scale applications. This study presents the optimization of MAGMENT composites, which are produced using recycled ferrite aggregates combined with binders such as cement, asphalt, or epoxy. These composites are engineered to achieve high magnetic permeability and low core losses, key characteristics for efficient energy systems. Our results demonstrate that by fine-tuning the aggregate size and volume fraction, permeability can be significantly enhanced, with volume fractions above 65% showing the most promise. Although cement workability imposes a 73% limit, the performance of these composites still surpasses industry benchmarks, notably the KH-HT 60μ from KEDA, by refining the particle size distribution. Adjusting the Nominal Maximum Aggregate Size (NMAS) from 4.5 to 19 mm changes permeability from 40 to 180. The superior magnetic performance of the MC60 grade, particularly its minimal core losses, underscores its potential as a leading material in the market. These advancements are for applications in wireless charging, both static and dynamic, and in high-power transmission systems, addressing critical needs in sustainable transport and energy infrastructure. The use of recycled materials further aligns with the global push for environmentally responsible technologies. Materials science ; Composite material ; Asphalt ; Epoxy ; Permeability (electromagnetism) ; Cement ; Membrane Magnetic Properties of Alloys ; Geomagnetism and Paleomagnetism Studies ; Supercapacitor Materials and Fabrication
Authors: Zhongbao Han | Zhongyu Zhao | Meiru Pan | Yong Qi | Liyan Liu | Dan Wang | Zhan Yu
Source: Analytical Chemistry (article, 2025-04-15)
Field: Chemistry — Spectroscopy

Rapid Screening of Illicit Drugs from Biofluid via Dried Blood/Urine Spot and Ultrasonic Desorption-Assisted Low-Temperature Arc Plasma Ionization Mass Spectrometry A novel method for rapid and sensitive illicit drug screening in biofluids has been developed by employing a paper-based sample collection coupled with ultrasonic desorption-assisted low-temperature plasma ionization mass spectrometry (PBS-LTPI-MS). For optimization, key experimental parameters, such as geometry coordinates, angle, and plasma intensity, were fine-tuned using ketamine as the representative analyte. The redissolution process, which encompasses the use of organic solvents and sample collection paper, underwent an evaluation to establish conditions conducive to efficient ionization. The proposed method demonstrated excellent analytical performance, with linear ranges exceeding <i>R</i><sup>2</sup> > 0.99, limits of detection ranging from 10 to 20 ng mL<sup>-1</sup>, and impressive recovery rates exceeding 91.16% in complex biofluid matrixes. Spiked recovery experiments revealed strong matrix tolerance and reliable performance, even in the presence of illicit drug mixtures. The robustness of the sampling device under varying storage temperatures and durations further confirmed the method's suitability for point-of-care testing and large-scale sample collection. With the ability to analyze samples within a mere 3 s, high-throughput potential, and environmental robustness, this method stands out as an invaluable instrument for rapid illicit drug screening and forensic analysis. Chemistry ; Chromatography ; Mass spectrometry ; Urine ; Dried blood ; Desorption ; Ultrasonic sensor ; Analytical Chemistry (journal) ; Adsorption ; Organic chemistry ; Biochemistry Mass Spectrometry Techniques and Applications ; Analytical chemistry methods development ; Forensic Toxicology and Drug Analysis
Authors: Dikran Tsitsekian | Γεράσιμος Δάρας | Anthi Panara | Anastasios Alatzas | Anastasia Koupa | Efstratios Kamargiakis | Panagiota Mylona | Νikolaos S. Τhomaidis | Stamatis Rigas
Source: Plant Cell Reports (article, 2025-11-27)
Field: Chemistry — Organic Chemistry

Molecular regulation of fatty acid biosynthesis and oil composition during olive drupe ripening Oleic acid ; Polyunsaturated fatty acid ; Fatty acid ; Linoleic acid ; Transcription factor ; Transcriptome ; Transcriptional regulation ; Metabolic pathway ; Metabolism Edible Oils Quality and Analysis ; Lipid metabolism and biosynthesis ; Plant Surface Properties and Treatments
Authors: Tony Ho‐Ching Fung | Nathan Man‐Wai Wu | Ziyong Chen | Ming‐Yi Leung | Vivian Wing‐Wah Yam
Source: Journal of the American Chemical Society (article, 2025-11-26)
Field: Materials Science — Materials Chemistry

Rational Molecular Design of Germole-Fused Dithienylethenes with Tunable Photochromic Response, Reaction Pathway, and Switching Efficiency A new series of photoswitchable organogermanium based on dithienylethenes with germole as the ethene bridge has been designed and synthesized. The rational designs of the germole-fused dithienylethene molecules allow fine-tuning of the optical band gaps, resulting in different photochromic responses upon photoexcitation at suitable wavelengths in the solution state and in PMMA thin films. The compounds exhibit robust photofatigue resistance with clean conversion between the open form and the closed form after 12 photoswitching cycles, as well as excellent thermal irreversibility with half-lives of up to 33 days even at 100 °C. High photoswitching efficiencies with balanced photocyclization and photocycloreversion quantum yields and a percentage conversion at photostationary state of up to 85% are also observed, rendering the germole-fused dithienylethenes attractive candidates as stable and efficient photoswitches for practical applications. Photochromism ; Photoexcitation ; Photostationary state ; Molecule ; Rational design ; Solid-state ; Thermal ; Diarylethene Photochromic and Fluorescence Chemistry ; Synthesis and Properties of Aromatic Compounds ; Polydiacetylene-based materials and applications
Authors: Olga Gorlová | Sára Pálková | Jaroslav Kocík | Zdeněk Tišler | Jiří Čmelík | Eliška Vyskočilová | Iva Paterová
Source: Applied Catalysis A General (article, 2025-06-21)
Field: Materials Science — Materials Chemistry

(Sn, Fe)/Mg/Zn/Al hydrotalcites as efficient catalysts for Baeyer-Villiger oxidation of aldehydes with cyclic structures: Role of composition and surface properties Chemistry ; Hydrotalcite ; Catalysis ; Composition (language) ; Baeyer–Villiger oxidation ; Heterogeneous catalysis ; Organic chemistry ; Inorganic chemistry Layered Double Hydroxides Synthesis and Applications ; Mesoporous Materials and Catalysis ; Catalysis for Biomass Conversion
Authors: Rajendra Prasad Nandi | Jingyao Zuo | Abhishek Shibu | Frieder Jaekle
Source: Angewandte Chemie International Edition (article, 2025-12-10)
Field: Chemistry — Organic Chemistry

B‐N Fused Anthracene as Functional Linker for π‐Extended Viologens: Near‐IR Emission and Electrochromism As prototypical organic electrochromic materials viologens have been extensively studied in display technologies, smart materials, and energy storage applications. Their properties can be fine-tuned by introducing different substituents on the pyridine rings, fusion with heteroatoms, or insertion of π-conjugated linkers. In this article we study the effect of B-N fused dipyridylanthracene (BDPA) as a novel linker unit in viologens on the electronic structure, optical properties, and electrochromic characteristics. Quaternization of pyridyl-functionalized BDPA (1Py) by N-methylation or complexation with B(C<sub>6</sub>F<sub>5</sub>)<sub>3</sub> as a powerful Lewis acid gives rise to two fundamentally different π-extended viologens, dicationic [1Py-Me](PF<sub>6</sub>)<sub>2</sub>, and the neutral complex 1Py-BCF. We investigate the effect of these different quaternization methods on the LUMO energy, band gaps, absorption and emission, and the self-sensitized reactivity toward oxygen. We also demonstrate facile electrochemical reduction to singly and multiply reduced species. Spectroelectrochemical and computational studies reveal formation of strongly colored doubly reduced species with a closed shell electronic configuration and prominent quinoidal delocalization. The corresponding radical anions give rise to absorptions in the near-IR. A prototype electrochromic device with 1Py-BCF as the redox-active material is also presented. Electrochromism ; Anthracene ; Linker ; Reactivity (psychology) ; HOMO/LUMO ; Pyridine ; Electrochemistry Organoboron and organosilicon chemistry ; Synthesis and Properties of Aromatic Compounds ; Luminescence and Fluorescent Materials