jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Pei-Ting Chung
Source:  (article, 2025-12-26)
Field: Materials Science — Materials Chemistry

Data Mining Methods for Biomechanical Property Prediction of Biomedical Materials Based on Optimized Feature Dimensionality Reduction This study presents a comprehensive framework for predicting biomechanical properties of biomedical materials through optimized feature dimensionality reduction and data mining techniques. The integration of multi-source data fusion strategies with advanced preprocessing pipelines addresses the fundamental challenge of high-dimensional, sparse datasets characteristic of biomaterial research. A comparative analysis of linear and non-linear dimensionality reduction algorithms reveals that genetic algorithm-based feature selection combined with UMAP visualization achieves improved performance, reducing feature space by 68% while maintaining 91.3% prediction accuracy. Ensemble learning methods, particularly XGBoost and Random Forest, demonstrate strong results across dental, orthopedic, and regenerative medicine applications, with R2 values reaching 0.92 for mechanical property prediction. Small sample learning strategies incorporating transfer learning and few-shot implementations address data scarcity limitations, achieving generalization with datasets containing fewer than 200 samples. The proposed framework contributes to accelerating biomaterial development cycles from traditional 10-15 year periods to 2-3 years, providing a practical pathway for data-driven materials discovery aligned with the Materials Genome Initiative objectives. Dimensionality reduction ; Feature selection ; Preprocessor ; Property (philosophy) ; Feature (linguistics) ; Generalization ; Bottleneck ; Data pre-processing ; Reduction (mathematics) ; Curse of dimensionality Machine Learning in Materials Science ; Titanium Alloys Microstructure and Properties ; Artificial Intelligence in Healthcare and Education
Authors: Lianhua Liu | Xiaohua Yuan | Muhammad Idrees Khan | Qing Zhao | Imran Shakir | Xuping Sun | Fengming Luo
Source: Coordination Chemistry Reviews (article, 2025-12-04)
Field: Materials Science — Materials Chemistry

Nanozymes in respiratory medicine: From ultra-sensitive diagnostics to intelligent therapeutics Disease ; Pulmonary disease ; Lung disease ; Respiratory system ; Translational research Advanced Nanomaterials in Catalysis ; Nanoplatforms for cancer theranostics ; Nanocluster Synthesis and Applications
Authors: Charles Zhou | Emily Zhou
Source: Zenodo (CERN European Organization for Nuclear Research) (preprint, 2025-10-01)
Field: Materials Science — Materials Chemistry

MolAudioNet 2.0: Beyond Spectroscopy Through Hybrid Molecular Sonification Abstract Molecular AI has traditionally relied on two primary modalities: structural representations (SMILES strings, molecular graphs) and numerical descriptors (calculated fingerprints, properties). Our previous work introduced a third modality—audio—through rule-based sonification that encodes molecular structures as musical sequences MolAudioNet (Zhou & Zhou, 2026) [1]. Here, we expand this framework to encompass three complementary pillars: (1) rule-based sonification that encodes stereochemical information (R/S configuration, E/Z isomerism) as musical harmony; (2) multi-spectroscopy learning that fuses six complementary techniques (IR, NMR, Raman, MS, UV-Vis, CD, etc.); and (3) hybrid cross-validation that automatically detects inconsistencies between predicted and measured properties with 95% accuracy. On benchmark tasks, the hybrid system achieves 87% accuracy in property prediction (+12% over single modality), 92% Top-5 accuracy in unknown identification (+24% over spectroscopyonly), and 85% F1 score in mixture deconvolution. Training efficiency improves dramatically: spectroscopic audio requires only 18 hours versus 14 days for text-based models. Informationtheoretic analysis reveals 280 effective bits from multimodal fusion versus 150 bits from structure alone (Figure 7). This work establishes molecular sonification as a complete framework spanning designed encodings, experimental measurements, and hybrid validation—opening new directions for AIdriven molecular discovery, automated spectroscopy interpretation, and quality control in pharmaceutical manufacturing. Keywords: Molecular sonification, multimodal learning, spectroscopy AI, stereochemistry encoding, unknown identification, mixture analysis, cross-modal validation Sonification ; Benchmark (surveying) ; Property (philosophy) ; Sensor fusion ; Hybrid system ; Spectroscopy ; Identification (biology) ; Pattern recognition (psychology) Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Advanced Chemical Sensor Technologies
Authors: Hyun Lee | Sohee Yoon | Jin-Woo Park | S.-I. Chae | Sangkwon Park | Jonghyun Ahn | Y. Jay Jung | Yong Sam Chung | Hong‐Chiang Chang | Su‐Jin Park | Minseok Kang | Jina Kim | Ho-Gyeong Kim | Myeong‐Hun Jeong
Source: ArXiv.org (preprint, 2025-08-31)
Field: Materials Science — Materials Chemistry

Aligning Reasoning LLMs for Materials Discovery with Physics-aware Rejection Sampling AI-driven materials discovery that couples automated experimentation with algorithmic decision-making requires process aware recipe to property predictors that are accurate, calibrated, and physically admissible. We approach this as a reasoning problem with large reasoning models (LRMs). To instill reasoning capability into language models, we curate reasoning traces from a teacher model to train a student model. However, most training pipelines select reasoning traces using binary correctness or learned preference signals that poorly reflect physical admissibility. We introduce Physics-aware Rejection Sampling (PaRS), a training-time trace selection scheme that favors traces consistent with fundamental physics and numerically close to targets, with lightweight halting to control compute. We instantiate our framework with a large student model fine-tuned on traces synthesized by a larger teacher model, and evaluate under matched token budgets against various rejection sampling baselines. Our method improves accuracy and calibration, reduces physics-violation rates, and lowers sampling cost relative to baselines. These results indicate that modest, domain-aware constraints combined with trace-level selection provide a practical path toward reliable, efficient LRMs for process-aware property prediction and closed-loop materials design. Correctness ; Sampling (signal processing) ; TRACE (psycholinguistics) ; Property (philosophy) ; Selection (genetic algorithm) ; Security token ; Process (computing) ; Scheme (mathematics) ; Binary number Machine Learning in Materials Science ; Advanced Graph Neural Networks ; Scientific Computing and Data Management
Authors: E Dhanalakshmi | P Rajesh | M Anbarasu | P Kandan | A Raaza | M Prabhaharan
Source: Indian Journal of Biochemistry and Biophysics (article, 2025-01-01)
Field: Chemistry — Spectroscopy

GC-MS, DFT, LOL, ELF, NCI-RDG, kinetic energy, reactivity, stability, topological molecular descriptors evaluation on 2-propanone, 1-hydroxy-, Isopropyl alcohol and Glycerin: For NLO application The present article provides spectroscopic technique gas chromatography-mass spectrometry (GC-MS) and density functional theory (DFT) analysis to the examined molecular structure of these three compounds namely 2-Propanone, 1-hydroxy-, Isopropyl alcohol and glycerin synthesis from Hybanthus enneaspermus plant by using green method. The optimized structure of title compounds is obtained by using a hybrid DFT/B3LYP/6-311++G(d, p) approach for stability prediction. Molecular descriptors of natural bond orbital (NBO), highest orbital molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), global reactivity, and Mulliken charge to determine its structural characterization, chemical stability and biological aspects interpreted by the same set. Localized orbital locator (LOL), electron localized function (ELF) has been investigated to understand the localization and delocalization of three molecules. The strong, weak and van dar Waals interactions can identify based on electron densityand were estimated by reduced density gradient (RDG) analysis. The thermodynamic properties of entropy (S), capacity (V) and specific heat have been estimated. The dipole moment (µ) and polarizability (α) have been calculated to predict the nature of 2-propanone, 1-hydroxy- (2PH), isopropyl alcohol (IA) and glycerin (GL) molecules and showed excellent nonlinear optical (NLO) candidates. Moreover, the qualitative structure-activity relationship/qualitative structure-property relationship QSAR/QSPR analysis topological descriptors have a strong correlation with physical properties, which is ideally suitable for drug discovery used to prevent enormous biological activity. Isopropyl alcohol ; Isopropyl ; Kinetic energy ; Reactivity (psychology) ; Alcohol ; Computational chemistry ; Chemistry ; Topology (electrical circuits) ; Combinatorial chemistry ; Medicinal chemistry ; Organic chemistry ; Physics ; Medicine ; Quantum mechanics ; Engineering ; Electrical engineering Analytical Chemistry and Chromatography ; Chemical Thermodynamics and Molecular Structure ; Thermodynamic properties of mixtures
Authors: Pakin Noppawan | Kanokkan Worawut | Suthida Kunnasut | Potchanee Keawkumsan | Baramee Phungpis
Source: Chimica Techno Acta (article, 2025-11-17)
Field: Chemistry — Organic Chemistry

A review of benzotriazole derivatives: versatile scaffolds for advancing therapeutics in medicinal chemistry Benzotriazole (BtH) is recognized as a versatile heterocyclic scaffold that plays an increasingly vital role in modern drug discovery owing to its broad pharmacological potential and structural flexibility. Although BtH was first synthesized in the 19th century, recent advances in synthetic and medicinal chemistry have revitalized interest in BtH and its derivatives for developing multifunctional therapeutics. This review addresses current challenges and opportunities in BtH chemistry by integrating progress in sustainable synthesis, structure–activity relationship (SAR) analyses, and therapeutic applications. The discussion encompasses green methodologies, such as microwave-assisted, ultrasound-assisted, flow, and electrosynthesis techniques, that improve atom economy, reduce waste, and enhance energy efficiency. It also highlights how structural modifications, including halogenation, heterocyclic fusion, and metal complexation, influence biological activity and target selectivity. BtH derivatives exhibit significant antimicrobial, antiviral, anticancer, antioxidant, and enzyme-inhibitory properties, as well as other potential in neuroprotective and anti-inflammatory therapies. However, limited in vivo evaluation, lack of standardized bioassay protocols, and scalability challenges in sustainable synthesis remain key research gaps. Overall, this review synthesizes contemporary developments from 2020–2026, demonstrating that BtH serves as a privileged pharmacophore capable of engaging diverse biological targets. By consolidating mechanistic insights and eco-efficient synthesis strategies, the work provides a foundation for designing next-generation BtH-based drug candidates and advancing sustainable medicinal chemistry. Drug discovery ; Pharmacophore ; Biocompatible material ; Drug Multicomponent Synthesis of Heterocycles ; Synthesis and biological activity ; Click Chemistry and Applications
Authors: Ewa Napiórkowska | Łukasz Szeleszczuk
Source: Research Square (preprint, 2025-08-18)
Field: Chemistry — Physical and Theoretical Chemistry

Conformational landscape of β-cyclodextrin: A computational resource for host-guest modeling in supramolecular systems Cyclodextrin ; Supramolecular chemistry ; Resource (disambiguation) ; Host (biology) ; Chemistry ; Computer science ; Molecule ; Ecology ; Biology ; Biochemistry ; Organic chemistry Crystallography and molecular interactions ; Crystallization and Solubility Studies ; Analytical Chemistry and Chromatography
Authors: Hanifi Kebiroglu
Source: Research Square (preprint, 2025-07-24)
Field: Chemistry — Physical and Theoretical Chemistry

DFT and TDDFT Based Investigation of Electronic Structure and Spectral Properties of a Triazole Thiophene Molecule Time-dependent density functional theory ; Thiophene ; Triazole ; Molecule ; Density functional theory ; Spectral properties ; Computational chemistry ; Chemistry ; Materials science ; Organic chemistry Photochemistry and Electron Transfer Studies ; Photochromic and Fluorescence Chemistry ; Photoreceptor and optogenetics research
Authors: Esam A. Alqurashi
Source: JOURNAL of QASSIM UNIVERSITY FOR SCIENCE (article, 2025-10-21)
Field: Chemistry — Organic Chemistry

Recent Advances in the Synthesis and Applications of Imidazole Derivatives This review highlights recent advancements in the synthesis and applications of imidazole derivatives, emphasizing green chemistry approaches and their multifaceted roles in medicinal field specially molecules exhibit diverse biological applications, such as anticancer, antiviral, antimicrobial, anti-as inflammatory, antidiabetic, α-glucosidase inhibitory, kinase inhibitory effects, and cardiomyogenesis promotion and industrial fields. Eco-friendly synthetic methods, including rice husk ash catalysis, solvent-free conditions, and ultrasound-assisted reactions, are discussed, showcasing high yields and sustainability. Imidazole derivatives exhibit diverse biological activities, such as anticancer, antiviral, antimicrobial, and antidiabetic effects, with promising selectivity and potency. Industrial applications include corrosion inhibitors, OLED materials, and chemical sensors. Challenges in scalability and selectivity, along with future directions leveraging computational tools and nanomaterials, are explored, underscoring imidazole’s potential in addressing global health and environmental challenges. Imidazole ; Scalability ; Human health ; Drug discovery Synthesis and Reactions of Organic Compounds ; Synthesis and Biological Evaluation
Authors: S Kayashrini | P Rajesh | E Dhanalakshmi | M Anbarasu | M Kesavan | M Prabhahara | R Mohamed Hisam | R Sudha
Source: Indian Journal of Biochemistry and Biophysics (article, 2025-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Quantum chemical analysis and anticancer evaluation of 1, 4-benzenedicarboxylic acid bis (2-ethylhexyl) ester: Topological indices, reduced density gradient, molecular electrostatic potential, natural bond orbital Liver cancer remains one of the most lethal malignancies worldwide, highlighting the urgent need for improved treatment strategies. This study employed density functional theory (DFT) quantum calculations and molecular docking studies to evaluate the specificity and anticancer potential of therapeutic compounds derived from Hybanthus enneaspermus. The investigation focused on the interaction of 1, 4-Benzenedicarboxylic Acid, Bis (2-Ethylhexyl) Ester (4B2EH) with specific active methylene reagents and hydrogen nucleophiles. Global reactivity descriptors were utilized to assess the compound's molecular stability and reactivity against liver cancer. Compounds extracted through the Soxhlet technique were further confirmed using spectroscopic methods, including FT-IR, ¹H NMR, ¹³C NMR, GC-MS, and UV-Vis analyses. The electronic properties of 4B2EH were examined using the DFT/B3LYP/6-311++G (d, p) functional, employing time-dependent density functional theory (TD-DFT) for advanced insights. The study utilized Veda 04 software for PED values, alongside Gaussian 09W, Gauss View 6.0, and ChemCraft 1.8 for comprehensive molecular visualization and analysis. The investigation focused on key aspects such as the MEP surface, HOMO-LUMO analysis, and NBO interactions, specifically C4 – C5 (π) → C10 – O11 (π*) and π → π* transitions. Additionally, DOS, RDG, ELF, and LOL analyses were conducted to predict the compound's stability, anticancer potential, and reactive sites for electrophilic and nucleophilic attacks.Furthermore, molecular docking simulations were performed against two distinct protein receptors (PDB ID: 2H80 and 9ETE) to evaluate binding conformations and interaction profiles with key liver cancer targets. The simulations revealed binding energies of -5.08 kcal/mol and -5.83 kcal/mol, indicating favourable interactions and potential therapeutic applications. Additionally, topological indices such as the 58.24 RR index, 5.87 RA index, and 5.89 S index demonstrated strong correlations with key molecular properties. These indices, combined with factors like polarity surface area and docking scores, play a crucial role in identifying potential lead compounds for drug development. The analysis highlights essential chemical attributes, biological activity, and other relevant data obtained through degree-based QSPR analysis. Natural bond orbital ; Density functional theory ; Electrophile ; Molecular orbital ; Molecular dynamics ; Reactivity (psychology) ; Hydrogen bond ; Fragment molecular orbital ; Molecule ; Binding energy Nonlinear Optical Materials Research ; Synthesis and biological activity ; Free Radicals and Antioxidants
Authors: Tran Nguyen Ngoc Huyen | Uyen Nguyen Ngoc Phuong | Tran Nguyen Minh An | Thi Hong Anh Nguyen
Source: Royal Society Open Science (article, 2025-10-01)
Field: Chemistry — Organic Chemistry

Synthesis of a novel coumarin via the Mannich reaction: <i>in vitro</i> and <i>in silico</i> evaluation of anti-cancer, antimicrobial and antioxidant activities The novel coumarin derivatives (<b>2a</b>-<b>2j</b>) were synthesized via the Mannich reaction and evaluated for anti-cancer, antimicrobial and antioxidant activities. Compound (<b>2d</b>) exhibited the most potent cytotoxicity against MCF-7 breast cancer cells (IC<sub>50</sub> = 2.54 ± 0.12 µM), surpassing camptothecin. Compound (<b>2b</b>) showed strong activity against HeLa cervical cancer cells (IC<sub>50</sub> = 5.23 ± 0.12 µM), while compound (<b>2a</b>) demonstrated notable effects on HepG2 liver cancer cells (IC<sub>50</sub> = 8.57 ± 0.42 µM). All three compounds displayed low toxicity toward normal LLCPK1 kidney cells, with IC<sub>50</sub> values exceeding 94 µM. Antimicrobial assays revealed that compounds (<b>2a</b>) and (<b>2f</b>) effectively inhibited <i>Bacillus subtilis</i>, with minimum inhibitory concentration values of 25 and 75 µM, respectively. Compound (<b>2i</b>) showed the strongest antioxidant effect (SC<sub>50</sub> = 7.36 ± 0.18 µM), comparable to Trolox (SC<sub>50</sub> = 6.12 ± 0.15 µM). Molecular docking indicated that compound (<b>2d</b>) (pose 232) binds tightly to the 1T8I enzyme (Δ<i>G</i> = -9.92 kcal mol<sup>-1</sup>, K<sub>i</sub> = 0.01 µM), forming key interactions with Arg 488 and Lys 532. Molecular dynamics simulations confirmed the complex's stability in aqueous solution over 90 ns. Coumarin ; Antioxidant ; Trolox ; Antimicrobial ; HeLa ; Cytotoxicity ; Docking (animal) ; Enzyme Synthesis and biological activity ; Synthesis and Biological Evaluation ; Bioactive Compounds and Antitumor Agents
Authors: Bahaa Fadhil Hamzah
Source: Al-Mustaqbal Journal of Pharmaceutical and Medical Sciences (article, 2025-05-05)
Field: Chemistry — Organic Chemistry

Synthesis and Characterization of Novel Derivatives of Imides 1,2,4-triazole Polymers via Microwave and Study Biological Activities New derivatives of imides 1,2,4-triazole polymers as pharmaceutical compounds were prepared from the synthesis of amic acid compounds (1A-E) by reacted of benzocaine with different cyclic anhydrides. Then cyclic imide compounds (2A-E), which prepared from converted amic acid compounds by using acetic anhydrate (CH3CO)2O and anhydrous sodium acetate CH3COONa as a water drawer agent. Compounds (2A-E) were react with nucleophilic addition of hydrazine hydrate to ester cyclic imide compound to produce acid hydrazide cyclic imide compounds. Thereafter, cyclization of compounds (4A-E) and (5A-E) were prepared from react of acid hydrazide cyclic imide compounds with poly acryl amide via microwave to give imides 1,2,4-triazole polymers (4A-E) and in other path acid hydrazide cyclic imide react with poly acrylonitrile via microwave to give imides 1,2,4-triazole polymers (5A-E). All prepared compounds were characterization by physical properties such as melting point, softening point and analytic technique like FT-IR, 1H-NMR for some of them, the compounds were tested anticancer and antibacterial applications were studied. Characterization (materials science) ; Triazole ; Microwave ; 1,2,4-Triazole ; Combinatorial chemistry ; Polymer ; Chemistry ; Organic chemistry ; Materials science ; Nanotechnology ; Computer science Synthesis and Characterization of Heterocyclic Compounds ; Synthesis and biological activity ; Microwave-Assisted Synthesis and Applications
Authors: Lukman O. Olasunkanmi | Oladoyin Grace Famutimi | Idris Olawale Raimi | Olumide Owolabi Omoboye | Ibrahim Waziri | Temitope O. Olomola | Bidini A. Taleatu | Abolanle S. Adekunle
Source: Discover Molecules (article, 2025-12-08)
Field: Materials Science — Materials Chemistry

Theoretical design of green corrosion inhibitors using novel benzimidazolyl-pentane-1,2,3,4,5-pentaol derivatives as a case study: DFT calculations, Monte Carlo simulations and ecotoxicity prediction In an effort to improve the practical application of benzimidazoles as corrosion inhibitors, hydrophilic groups were introduced through the attachment of aldoses to the benzimidazole ring. In this study, computational techniques, including DFT calculations and Monte Carlo simulations were used to predict the potentials of new aldo-benzimidazoles (benzimidazolyl-pentane-1,2,3,4,5-pentaol) as corrosion inhibitors for mild steel in aqueous acid media. The results showed that the compounds, which are inherently more hydrophilic than native benzimidazoles promise to exhibit higher corrosion inhibition efficiencies than conventional benzimidazole derivatives. Highly electron-donating (e.g. -OCH3) and electron-withdrawing (e.g. -NO2) substituents increased the corrosion inhibition efficiencies, making g-bzm-methoxy and g-bzm-nitro to have the highest corrosion inhibition efficiencies as predicted from the QSAR model. All the compounds showed appreciable adsorption energies on Fe(1 1 0) surface with bond distances that suggest non-covalent interactions between the N-atom of the benzimidazole ring and Fe. All the compounds showed lower toxicity to fathead minnow than benzimidazole except g-bzm-benzophenone, g-bzm-diCl, and g-bzm-dimethyl. The compounds also exhibited lower toxicity to Daphnia magna and T. pyriformis, suggesting their eco-friendly attributes. The study provides insights into the sustainability of benzimidazolyl-pentane-1,2,3,4,5-pentaol derivatives as corrosion inhibitors and recommends complementary experimental studies on the compounds. Benzimidazole ; Corrosion ; Ecotoxicity ; Corrosion inhibitor ; Monte Carlo method ; Molecular dynamics ; Aqueous solution Corrosion Behavior and Inhibition ; Concrete Corrosion and Durability ; Synthesis of Tetrazole Derivatives
Authors: Aditi Pandey | Vishakha Choudhary | Bhawna Sharma | Achal Mukhija
Source: RSC Pharmaceutics (article, 2025-01-01)
Field: Chemistry — Physical and Theoretical Chemistry

Bio-physical insights into the interaction of biocompatible iron oxide nanoparticles with biomolecules: microcalorimetric and spectroscopic evaluation Drug delivery systems (DDSs), despite extensive research, have yet to achieve optimal therapeutic outcomes. Biocompatible material ; Nanoparticle ; Iron oxide nanoparticles ; Iron oxide ; Coprecipitation ; Biocompatibility thermodynamics and calorimetric analyses ; Nanoparticle-Based Drug Delivery ; Nanoparticles: synthesis and applications