jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Hui Yu | C. D. Hu | Xuelin Wang | Ying Zhang | Nanhui Zhang | Pengxia Yu | Kai Lian | Jiaolong Huang | Peng Duan
Source: International Journal of Nanomedicine (review, 2025-11-01)
Field: Materials Science — Biomaterials

Is Emerging Nanomedicine a Friend or Foe to Germ Cells? Nanomaterials are increasingly applied in biomedicine and have significant potential in reproductive medicine. However, because they can impact germ cells, use of nanomaterials could represent a "double-edged sword", whose benefits must be balanced with the possible risks. Because of their excellent physicochemical properties, nanoparticles (NPs) can serve as multi-functional platforms for targeted drug delivery, enhancing outcomes in assisted reproductive technologies, refining in vitro culture systems, and improving the precision of diagnostic imaging. Nevertheless, accumulating evidence indicates that various NPs, including metallic and polymeric forms, can accumulate in reproductive tissues and induce detrimental effects, primarily through increased oxidative stress, DNA damage, and activation of apoptotic pathways. Moreover, NPs can directly compromise gamete quality and function: in oocytes, NP exposure can disrupt key processes, such as meiotic spindle assembly and chromosomal segregation; while in sperm, NPs can impair critical functions, such as histone-to-protamine exchange and mitochondrial integrity. The delicate balance between the benefits and risks of NP use are profoundly influenced by their physicochemical properties. This review critically assesses the "friend or foe" duality of NP use in reproductive medicine, by systematically analyzing their beneficial applications in contrast with their potential for NP-induced toxicity. Mechanistic pathways of NP toxicity are described, and the necessity of a safety-focused approach for the future development of reproductive nanomedicine is emphasised. Nanomedicine ; Biomedicine ; Nanotoxicology ; Drug delivery ; Germ cell ; Gamete Nanoparticle-Based Drug Delivery ; Nanoparticles: synthesis and applications ; Reproductive Biology and Fertility
Authors: Xumin He | J H Yi | Jianchen Yang | Genzoh Tanabe | Osamu Muraoka | Weijia Xie
Source: Molecules (article, 2025-07-04)
Field: Chemistry — Organic Chemistry

Design and Synthesis of Sulfonium and Selenonium Derivatives Bearing 3′,5′-O-Benzylidene Acetal Side Chain Structure as Potent α-Glucosidase Inhibitors A group of sulfonium and selenonium salts bearing diverse benzylidene acetal substituents on their side chain moiety were designed and synthesized. Compared with our previous study, structural modifications in this study focused on multi-substitution of the phenyl ring and bioisosteric replacements at the sulfonium cation center. In vitro biological evaluation showed that selenonium replacement could significantly improve their α-glucosidase inhibitory activity. The most potent inhibitor <b>20c</b> (10.0 mg/kg) reduced postprandial blood glucose by 48.6% (15 min), 52.8% (30 min), and 48.1% (60 min) in sucrose-loaded mice, outperforming acarbose (20.0 mg/kg). Docking studies of <b>20c</b> with ntMGAM presented a new binding mode. In addition to conventional hydrogen bonding and electrostatic interaction, amino residue Ala-576 was first identified to contribute to binding affinity through π-alkyl and alkyl interactions with the chlorinated substituent and aromatic ring. The selected compounds exhibited a high degree of safety in cytotoxicity tests against normal cells. Kinetic characterization of α-glucosidase inhibition confirmed a fully competitive inhibitory mode of action for these sulfonium salts. Sulfonium ; Chemistry ; Moiety ; Substituent ; Stereochemistry ; Side chain ; Alkyl ; Acarbose ; Acetal ; Residue (chemistry) ; Docking (animal) ; Enzyme ; Organic chemistry Carbohydrate Chemistry and Synthesis ; Synthesis and biological activity ; Click Chemistry and Applications
Authors: Hao Xu | Weimin Zhong | Xin Peng | Yiming Wang
Source: Chemical Engineering Science (article, 2025-12-30)
Field: Materials Science — Materials Chemistry

Generative transformer decoder-only model polyGT: Toward polymer informatics comprehension and target polymer inverse design Polymer ; Transformer ; Generative grammar ; Inverse ; Generative Design ; Polymer architecture Machine Learning in Materials Science ; Block Copolymer Self-Assembly ; Model Reduction and Neural Networks
Authors: Ronaldo C. Prati
Source: Journal of the Brazilian Chemical Society (article, 2025-01-01)
Field: Materials Science — Materials Chemistry

Recent Advances in Natural Language Processing in Chemistry and Materials Science Natural Language Processing (NLP) in chemistry and materials science enables computers to understand, analyze, and generate human-readable output related to chemical concepts and materials. With the latest advancements in NLP, text processing at a near-human level has become possible in various tasks. Large Language Models (LLMs) have demonstrated exceptional proficiency in text generation, leading to the redefinition of numerous specific NLP tasks as text generation problems. This review explores the recent progress in applying LLMs to specialized domains, such as chemistry and materials science. It was discussed how LLMs overcome limitations of traditional NLP methods (such as rigid rule-based systems and shallow statistical models) by enabling context-aware interpretation of unstructured literature, flexible entity recognition (e.g., compounds, reactions), and generative tasks. Using the capabilities of LLMs, researchers in these fields can benefit from enhanced text processing, more accurate information extraction, and improved understanding of complex chemical concepts, making it a pivotal tool for accelerating discovery in chemically complex spaces, paving the way for novel tasks such as reaction prediction and molecular design. Natural science ; Chemistry ; Nanotechnology ; Biochemical engineering ; Materials science ; Engineering ; Physics ; Astronomy Machine Learning in Materials Science
Authors: Markus Bujotzek | Evelyn Trautmann | Calum Hand | Ian Hales
Source:  (article, 2025-10-14)
Field: Materials Science — Materials Chemistry

Insights into the Unknown: Federated Data Diversity Analysis on Molecular Data AI methods are increasingly shaping pharmaceutical drug discovery. However, their translation to industrial applications remains limited due to their reliance on public datasets, lacking scale and diversity of proprietary pharmaceutical data. Federated learning (FL) offers a promising approach to integrate private data into privacy-preserving, collaborative model training across data silos. This federated data access complicates important data-centric tasks such as estimating dataset diversity, performing informed data splits, and understanding the structure of the combined chemical space. To address this gap, we investigate how well federated clustering methods can disentangle and represent distributed molecular data. We benchmark three approaches, Federated kMeans (Fed-kMeans), Federated Principal Component Analysis combined with Fed-kMeans (Fed-PCA+FedkMeans), and Federated Locality-Sensitive Hashing (Fed-LSH), against their centralized counterparts on eight diverse molecular datasets. Our evaluation utilizes both, standard mathematical and a chemistry-informed evaluation metrics, SF-ICF, that we introduce in this work. The large-scale benchmarking combined with an in-depth explainability analysis shows the importance of incorporating domain knowledge through chemistry-informed metrics, and on-client explainability analyses for federated diversity analysis on molecular data. Benchmarking ; Cluster analysis ; Federated learning ; Domain (mathematical analysis) ; Benchmark (surveying) ; Component (thermodynamics) ; Pharmaceutical manufacturing ; Big data ; Scale (ratio) Machine Learning in Materials Science ; Privacy-Preserving Technologies in Data ; Computational Drug Discovery Methods
Authors: Hua‐Jie Chen | Lei Wang | Shicong Zhang | Yandi Liu | Shu‐Lin Liu | Zhi‐Gang Wang
Source: ACS Nano (article, 2025-07-21)
Field: Materials Science — Biomaterials

Machine Learning-Enhanced Single-Particle Tracking for Rapid Screening of Tumor Immunomodulatory Drugs The tumor microenvironment plays a critical role in tumor progression and immune response, with the extracellular matrix (ECM) regulating immune cell infiltration. However, the interplay between ECM dynamics and tumor immunity remains poorly understood, and current methods for evaluating immunomodulatory drugs are limited by scalability and cost. Here, we present a robust approach combining single-particle tracking (SPT) of quantum dots (QDs) with machine learning to characterize the extracellular space (ECS) in live tumor tissues and assess drug efficacy. Super-resolution images revealed dynamic changes in ECS geometry and ECM composition during tumor progression, validated by transcriptomics and flow cytometry. By extracting diffusion fingerprints from SPT data, we developed machine learning models to classify tumor stages and quantify immune infiltration with high accuracy. This platform enabled rapid ranking of immunomodulatory drugs based on their effects on ECS properties and immune responses, offering a cost-effective, and scalable method for advancing both drug discovery and personalized cancer immunotherapy. Particle (ecology) ; Tracking (education) ; Nanotechnology ; Materials science ; Computer science ; Medicine ; Psychology ; Biology Nanoparticle-Based Drug Delivery ; Immunotherapy and Immune Responses ; Monoclonal and Polyclonal Antibodies Research
Authors: Sergey Nechausov | Patrick Feßer | Boris A. Bulgakov | Ulrich S. Schubert
Source: Advanced Functional Materials (article, 2025-12-31)
Field: Chemistry — Organic Chemistry

Novel Functional Materials via 3D Printing by Vat Photopolymerization ABSTRACT The growing demand for advanced functional materials has led to the development of various additive manufacturing techniques (AM), with vat photopolymerization (VP) emerging as a key technology. VP is a versatile light‐based AM technique for producing complex 3D structures from a wide range of functional materials. VP material diversity stems from its compatibility with various monomers, oligomers, solvents, and fillers, enabling for the fabrication of materials with tailored properties. This article systematically examines recent advancements in VP fabrication and analyzes strategies for incorporating functional elements into 3D‐printed material structures. We investigate the spectrum of functionalities achieved in novel materials by categorizing design into four main groups: The use of functional additives, the molecular design of the photopolymerizable system, post‐processing procedures, and functional structural architectures. Specifically, we analyze recent reports on novel functional materials in the field of VP, such as conductive, energy‐storing, optical, high‐performance, stimuli‐responsive, self‐healing, shape‐memory, recyclable, bioengineering, and biomedical materials. The article also discusses characterization methods required for the fabrication of state‐of‐the‐art materials. We conclude by underscoring the immense versatility of VP for fabricating functional and multifunctional materials, and its potential for future advancements in applications such as energy, medicine, robotics, and physical AI. Fabrication ; 3D printing ; Photopolymer ; Characterization (materials science) ; Compatibility (geochemistry) ; Functional diversity ; Functional polymers Photopolymerization techniques and applications ; Additive Manufacturing and 3D Printing Technologies ; Polymer composites and self-healing
Authors: Feng-Wei Guo | Xiangyun Kong | Mengya Li | Junhua Wang | Baohua Zhang | Xiang‐Ping Kong | Frank B. Hu | Wishwajith Kandegama | Feng‐Yu Du | Shuai‐Shuai Li
Source: Journal of Agricultural and Food Chemistry (article, 2025-08-13)
Field: Chemistry — Organic Chemistry

Efficient Synthesis of 1′,4′-Dihydro-2′<i>H</i>-spiro[indoline-3,3′-quinoline] Derivatives for the Identification of New Spirocyclic Herbicidal Leads Spiro scaffolds are ubiquitous in natural products and drugs. Their special three-dimensional structure and biological activities have aroused wide interest. Among various spiro compounds, spiro-fused indoline derivatives represent a particularly interesting subset but have attracted less attention for drug discovery, especially in the field of pesticides. In this study, twenty-nine 1',4'-dihydro-2'<i>H</i>-spiro[indoline-3,3'-quinoline] derivatives were designed and efficiently synthesized via one-pot synthesis methods; their herbicidal activity was also evaluated. Most of the synthesized spiro-fused indoline derivatives exhibited considerable herbicidal activity against the growth of <i>Echinochloa crusgalli</i> seedlings. Notably, compounds <b>8a</b>, <b>8d</b>, and <b>8f</b> exhibited root and stem inhibition rates exceeding 95% and 85% at a dosage of 50 mg/L, respectively. Furthermore, a greenhouse experiment revealed that compound <b>8a</b> demonstrated postemergence herbicidal activities against <i>E. crusgalli</i> with a fresh-weight inhibition rate of 73.8% at a dosage of 400 g ai/ha, demonstrating superior activity compared with glyphosate (58.4%). Importantly, compound <b>8a</b> exhibited good crop selectivity against wheat, maize, and oilseed rape. Therefore, <b>8a</b> is a promising herbicidal candidate that is worthy of further development. Indoline ; Quinoline ; Chemistry ; Indole test ; Bioactive compound ; Stereochemistry ; Combinatorial chemistry ; Organic chemistry ; Biochemistry Synthesis and Biological Evaluation ; Weed Control and Herbicide Applications ; Fungal Plant Pathogen Control
Authors: B. L. Zhou | Qiang Zhou | Zunfeng Liu | Xiang Zhou | Lili Bao
Source: SmartSys (article, 2025-09-01)
Field: Materials Science — Biomaterials

Engineering Artificial Spider Silk From Biomimetic Synthesis to Advanced Applications ABSTRACT Polymeric materials research is increasingly directed toward biomimicry, exploring designs derived from nature's long evolutionary processes to enhance material properties and sustainability. Scientists have long recognized that spider silk, as a natural polymer, possesses exceptional physicochemical properties, including high tensile strength, superior toughness, good thermal conductivity, ultracontraction, and unique torsional rotation driving capabilities. These remarkable characteristics have inspired ongoing efforts to develop biomimetic spider silk materials, with the aim of replicating the natural structure of spider silk to create polymers with similar or even superior performance. This article aims to explore the synthesis methods of high‐performance biomimetic polymer materials, such as artificial spider silk, and their advanced applications across various fields. The review will discuss recent advances in the synthesis of novel artificial spider silk materials, focusing on polymer molecular design, the construction of secondary cross‐linked networks, micro‐nano assembly structure, and the development of innovative spinning techniques, as well as the potential of artificial spider silk in biomedical and flexible smart wearable applications. Spider silk ; Biomimetic materials ; Biomimetics ; Spider ; SILK ; Biomimetic synthesis ; Natural polymers Silk-based biomaterials and applications ; Diatoms and Algae Research ; Bone Tissue Engineering Materials
Authors: Mary O. Ologe | Sunday J. Olatunji | Elizabeth Ademola | Kehinde Gabriel Obiyenwa | Vincent O. Adimula | Hadley S. Clayton | Ezekiel G. Adeyeni | Allen T. Gordon | Adedibu C. Tella
Source: Discover Molecules (article, 2025-10-09)
Field: Chemistry — Inorganic Chemistry

Iron(III)-Tricarboxylate Metal-Orgonic Framework (MOF) as drug carrier in the loading of codeine Metal-organic frameworks (MOFs) constructed using Fe (III) ion and benzene-1,3,5-tricarboxylate ligand by a solvent-based method and formulated as [Fe3(btc)2] is herein reported. The synthesized compound was characterized by powder X-ray diffraction (PXRD), Braunuer Emmet Teller (BET) analysis, and Scanning Electron Microscope (SEM). The diffraction pattern of the drug-loaded MOFs showed the appearance of new peaks and a decrease in the intensity of some peaks. The BET pore volume of synthesized [Fe3(btc)2] and [Fe3(btc)2]@COD` were 0.290cc g−1 and 0.059 cc g−1 respectively while the BET surface area of synthesized [Fe3(btc)2] and [Fe3(btc)2]@COD` were 849.63 m2 g−1 and 203.4 m2 g−1 respectively confirming the incorporation of codeine into [Fe3(btc)2], the BET analysis confirmed that the codeine was loaded into the pore cavity of [Fe3(btc)2]. The [Fe3(btc)2] was observed to encapsulate 249 mg of codeine drug per 200 mg of [Fe3(btc)2], with a loading efficiency of 91%. Binding energy calculations (DFT) revealed strong interactions, with HOMO localized on codeine and LUMO on trimesic acid, reducing the HOMO-LUMO gap from 5.3 eV (MOF) to 4.19 eV (MOF-Codeine). Molecular dynamics (100 ns) showed stable codeine binding via hydrogen bonding and π-cation interactions, enhanced by water-mediated effects. Molecular docking confirmed stronger binding affinity for codeine (Glide score: -4.349 kcal/mol) compared to nitrogen (-2.632 kcal/mol), attributed to hydrogen bonding and π-cation interactions. These results highlight [Fe₃(btc)₂] as a promising drug delivery system with high loading capacity and stable host-guest interactions. Trimesic acid ; Hydrogen bond ; Scanning electron microscope ; Powder diffraction ; Codeine ; BET theory ; HOMO/LUMO ; Binding energy Metal-Organic Frameworks: Synthesis and Applications ; Computational Drug Discovery Methods ; X-ray Diffraction in Crystallography
Authors: Giulio Pota | Daniele Florio | Luca Cimmino | Paolo A. Netti | Valeria Panzetta | Daniela Marasco | Sara La Manna
Source: Frontiers in Drug Discovery (article, 2025-09-17)
Field: Materials Science — Biomaterials

Influence of divalent metal ions on gelation of a short heterochiral peptide Peptide self-assembly has emerged as a powerful and versatile strategy for the design of supramolecular biomaterials with tunable structural and functional properties. Through the precise organization of short peptide sequences, it is possible to construct nanostructured materials that mimic biological architecture and respond to specific environmental cues. Among the various design elements that influence peptide assembly, the incorporation of metal ions has gained increasing attention as a means to modulate material properties and endow biofunctionality. In this study, we investigated the distinct effects of four divalent metal cations—calcium (Ca 2+ ), magnesium (Mg 2+ ), zinc (Zn 2+ ), and copper (Cu 2+ )—on the hydrogel-forming capabilities of Ac-(L-Phe)-(L-Ile)-(L-Asn)-(D-Tyr)-(L-Val)-(L-Lys)-CONH 2 (FINyVK), an ultrashort heterochiral hexapeptide derived from the second helix of the C-terminal domain of Nucleophosmin 1 (NPM1), a nucleolar protein implicated in both structural maintenance and disease-related aggregation. This peptide sequence is amyloidogenic and capable of forming hydrogels under appropriate conditions. By employing a comprehensive set of biophysical techniques, including circular dichroism (CD), rheology, electron microscopy, and thermal analysis, we characterized the conformational and morphological properties of hydrogels formed both in the presence and absence of metal ions. Our findings revealed that metal coordination can significantly alter peptide assembly pathways, influencing key features such as fibrillar thickness, network porosity, and the kinetics of gelation. Notably, different cations impart distinct effects: while alkaline earth metals like Ca 2+ and Mg 2+ enhance fibrillar alignment and promote reversible gelation, transition metals such as Zn 2+ and Cu 2+ tend to disrupt ordered structures due to stronger coordination with aromatic residues. These results underscore the utility of metal–peptide interactions as a rational design principle for engineering advanced peptide-based hydrogels. Peptide ; Circular dichroism ; Self-healing hydrogels ; Supramolecular chemistry ; Rubredoxin ; Divalent ; Metal ; Self-assembly Supramolecular Self-Assembly in Materials ; Chemical Synthesis and Analysis ; Advanced biosensing and bioanalysis techniques
Authors: Kamal Khanal | Mohan Bahadur Chhetri | Madan Khanal | A. Acharya | Rajesh Maharjan | Kalpana Gyawali | Madhav Prasad Ghimire | Tika Ram Lamichhane
Source: Trends in Sciences (article, 2025-07-10)
Field: Chemistry — Organic Chemistry

DFT Analysis on Electronic Properties, Reactivity and Adsorption Mechanism of Favipiravir/XTiO4H2 (X = Pt, Zr, Zn) Nanocomplexes and their Biological Evaluations The objective of this study is to explore quantum chemical properties of favipiravir- loaded XTiO4H2 nanostructures (X = Pt, Zr, Zn) using density functional theory and to evaluate their toxicity profiling, drug-likeness and binding efficacy to the target proteins. Favipiravir interacted strongly with XTiO4H2 forming the stable nanocomplexes (NCs) having adsorption energy in the range of −2.49 to −4.70 eV in gas phase. The HOMO-LUMO energy gap of favipiravir was 3.56 eV whereas Fav + PtTiO4H2 (NC1), Fav + ZrTiO4H2 (NC2), and Fav + ZnTiO4H2 (NC3) exhibited lower energy gaps of 1.23, 1.43 and 0.65 eV in gas phase, respectively, showing better reactivity of these NCs. The results of dipole moment, global reactivity descriptor, MEP surface, NBO, QTAIM and NCI of the proposed NCs were more favorable than that of favipiravir. The functionalized TiO2 NCs exhibited better docking scores, among which NC2 showed the strongest inhibition of SARS-CoV-2 main protease and spike protein. NC3 having the predicted LD50 of 3,000 mg/kg in toxicity class V appears to be less toxic than favipiravir having LD50 of 1,717 mg/kg in the class IV. This study confirms the possibility of using transition metal-doped titania nanostructures for targeted drug delivery, antiviral therapy and photocatalytic degradation of the drugs. HIGHLIGHTS Favipiravir with XTiO4H2 (X = Pt, Zr, Zn) nanocomplexes exhibited significant adsorption energies ranging from -1.18 to -4.70 eV. The HOMO-LUMO energy gaps of the nanocomplexes (0.65-1.23 eV) were lower than that of favipiravir (3.56 eV), enhancing electronic reactivity. Quantum chemical parameters like dipole moment, global reactivity descriptors, MEP surface, NBO, QTAIM and NCI analyzed the physicochemical properties of the proposed nanocomplexes. Fav+ZrTiO4H2 showed the strongest binding score with SARS-CoV-2 main protease and spike protein, while Fav+ZnTiO4H2 exhibited the least toxicity (LD50 = 3000 mg/kg, class V) GRAPHICAL ABSTRACT Reactivity (psychology) ; Mechanism (biology) ; Chemistry ; Adsorption ; Computational chemistry ; Combinatorial chemistry ; Physical chemistry ; Medicine ; Philosophy ; Epistemology Multicomponent Synthesis of Heterocycles ; Advanced biosensing and bioanalysis techniques ; Nonlinear Optical Materials Research