jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Hunter Sturm | Jonas Teufel | Kaitlin A. Isfeld | Pascal Friederich | Rebecca L. Davis
Source: Angewandte Chemie International Edition (article, 2025-05-19)
Field: Materials Science — Materials Chemistry

Mitigating Molecular Aggregation in Drug Discovery With Predictive Insights From Explainable AI Herein, we present the application of multi-channel graph attention network (MEGAN), our explainable AI (xAI) model, for the identification of small colloidally aggregating molecules (SCAMs). This work offers solutions to the long-standing problem of false positives caused by SCAMs in high-throughput screening for drug discovery and demonstrates the power of xAI in the classification of molecular properties that are not chemically intuitive based on our current understanding. We leverage xAI insights and molecular counterfactuals to design alternatives to problematic compounds in drug screening libraries. Additionally, we experimentally validate the MEGAN prediction classification for one of the counterfactuals and demonstrate the utility of counterfactuals for altering the aggregation properties of a compound through minor structural modifications. The integration of this method in high-throughput screening approaches will help combat and circumvent false positives, providing better lead molecules more rapidly and thus accelerating drug discovery cycles. Leverage (statistics) ; Counterfactual conditional ; Drug discovery ; Identification (biology) ; False positive paradox ; Computer science ; Machine learning ; Artificial intelligence ; Data science ; Chemistry ; Counterfactual thinking ; Psychology ; Biology Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Innovative Microfluidic and Catalytic Techniques Innovation
Authors: Kexiang Guo | Xinyu Fan | Letian Chen | Xu Zhang | Zhen Zhou
Source: Scientia Sinica Chimica (article, 2025-04-08)
Field: Materials Science — Materials Chemistry

Machine learning-based design of electrocatalysts and catalytic mechanism research 本综述探讨了机器学习在电催化剂设计中的应用，尤其是在筛选高效电催化剂和加速催化过程中的作用.面对气候变化和能源需求的双重挑战，清洁能源技术成为可持续发展的核心，电催化作为关键技术发挥着重要作用.然而，传统的“试错法”存在高成本和低效率的问题，机器学习通过精确预测电催化性能、加速催化剂筛选与设计，成为解决这一瓶颈的重要工具.描述符能够揭示催化剂的基本特征与性能之间的关系，进而加速筛选过程.本文探讨了描述符如何在电催化剂设计中桥接基本特征与性能之间的关系，并综述了当前机器学习势在催化机制研究中的应用.此外，还介绍了大型语言模型在电催化剂设计中的创新应用.本文展示了机器学习在复杂反应机制探索中的巨大潜力，并展望了未来的发展趋势和挑战. Geography Machine Learning in Materials Science ; Electrocatalysts for Energy Conversion ; CO2 Reduction Techniques and Catalysts
Authors: Y. S. Chang | Chong Teng | Junwei Lucas Bao
Source: Physical Chemistry Chemical Physics (article, 2025-01-01)
Field: Chemistry — Physical and Theoretical Chemistry

First-principle oligopeptide structural optimization with physical prior mean-driven Gaussian processes: a test of synergistic impacts of the kernel functional and coordinate system First-principle molecular structural determination is critical in many aspects of computational modeling, and yet, the precise determination of a local minimum for a large-sized organic molecule is time-consuming. The recently developed nonparametric model, the physical Gaussian Processes (GPs) with physics-informed prior mean function, has demonstrated its efficiency in exploring the potential-energy surfaces and molecular geometry optimizations. Two essential ingredients in physical GPs, the kernel functional and the coordinate systems, could impact the optimization efficiency, and yet the choice of which on the model performance has not yet been studied. In this work, we constructed a testing dataset consisting of 20 oligopeptides and performed a systematic investigation using various combinations of coordinates (structural descriptors) and kernel functionals to optimize these biologically interesting molecules to local minima at the density-functional tight-binding (DFTB) quantum mechanical level. We conclude that the combination of the kernel functional form and coordinate systems matter significantly in model performance as well as its robustness in locating local minima. For our testing set, the synergy between the periodic kernel and the non-redundant delocalized internal coordinates yields the best overall performance for physical GPs, significantly superior to other choices. Kernel (algebra) ; Gaussian ; Biological system ; Statistical physics ; Gaussian process ; Algorithm ; Computer science ; Mathematics ; Computational chemistry ; Physics ; Chemistry ; Biology ; Combinatorics Various Chemistry Research Topics ; Computational Drug Discovery Methods ; DNA and Nucleic Acid Chemistry
Authors: Georgi I. Nikov | Daniella Pretorius | James W. Murray
Source: Bioinformatics (article, 2025-07-18)
Field: Materials Science — Materials Chemistry

SOLeNNoID: a deep learning pipeline for solenoid residue detection in protein structures SOLeNNoID is implemented in Python and available on github at https://github.com/gnik2018/SOLeNNoID. The source code and pre-trained models are accessible under a free-software license. Training data are available on Zenodo at https://zenodo.org/records/14927497. Pipeline (software) ; Residue (chemistry) ; Computer science ; Deep learning ; Artificial intelligence ; Chemistry ; Operating system ; Biochemistry Machine Learning in Materials Science ; Force Microscopy Techniques and Applications
Authors: William J. Watson | Sophie Cooper | Matthew K. Horton | Robin W. Grimes
Source: Scientific Reports (article, 2025-06-06)
Field: Materials Science — Materials Chemistry

Structure stability of (U, Pu) C and (U, Pu) N compositions Atomic scale computer simulations based on density functional theory (DFT) are used to calculate the formation energies and structures associated with phases in the U-N, Pu-N, U-C and Pu-C systems. Stable phases across the compositional spaces, from the metal to the nitrogen gas or graphite end members, are identified using convex hull analysis. Many predicted phases correspond to those known from experimental phase diagrams (e.g. UN, U<sub>2</sub>N<sub>3</sub>; PuN; UC, U<sub>2</sub>C<sub>3</sub>; Pu<sub>2</sub>C<sub>3</sub>). However, many phases only sit on the convex hull upon inclusion of a suitably characterised Hubbard parameter (i.e. DFT + U). A nonstoichiometric composition of UN<sub>2-x</sub> is identified on the U-N convex hull but others, including stoichiometric UN<sub>2</sub>, are close to the line. A stoichiometric structure for Pu<sub>3</sub>C<sub>2</sub> with [Formula: see text] symmetry is identified, alongside which a nonstoichiometric PuC<sub>1-x</sub> phase has a similar energy. Convex hull ; Stoichiometry ; Crystallography ; Phase (matter) ; Materials science ; Physics ; Density functional theory ; Combinatorics ; Regular polygon ; Atomic physics ; Chemistry ; Physical chemistry ; Mathematics ; Geometry ; Quantum mechanics Nuclear Materials and Properties ; Rare-earth and actinide compounds ; Radioactive element chemistry and processing
Authors: Bin Shao | Yuanhang Huo | Qingli Yang | Fangyuan Zhao | Jian Ju
Source: Comprehensive Reviews in Food Science and Food Safety (article, 2025-12-15)
Field: Materials Science — Biomaterials

Beyond Tradition: Optimization Strategy for Mechanical Properties of New Generation Biodegradable Packaging Materials As environmental protection awareness grows, there is a tremendous increase in demand for biodegradable packaging materials. However, their poor mechanical qualities have significantly hindered the broader use of biodegradable packaging materials in everyday applications. As a result, the problem of inadequate mechanical qualities in real-world applications of biodegradable packaging materials must be addressed. This is of great significance for promoting the development of biodegradable packaging materials. This paper focuses on the optimization strategies for the mechanical properties of next-generation biodegradable packaging materials, providing a comprehensive analysis from molecular to macrostructural levels. It also discusses traditional optimization approaches and their limitations. Moreover, an in-depth examination of the relationship between biodegradability and the mechanical performance of degradable materials is presented. The research additionally investigates the migration and safety of bioactive constituents within biodegradable packaging. Enhancing the mechanical properties of these materials not only addresses a critical scientific challenge but also transforms biodegradable materials from biodegradable concepts into practical commodities capable of meeting the demands of the modern packaging industry. This research is important for more than just technological progress; it is also important for our ability to create a future that is circular, low-carbon, and economically viable. It represents a vital driver in advancing green transformation and achieving sustainable development. Biodegradation ; Biodegradable polymer ; Environmentally friendly ; Food packaging Nanocomposite Films for Food Packaging ; biodegradable polymer synthesis and properties ; Advanced Cellulose Research Studies
Authors: Theresa Lutz | Jonas De Breuck | Sahar Salehi | Meike N. Leiske
Source: Advanced Functional Materials (article, 2025-07-28)
Field: Materials Science — Biomaterials

Smart, Bio‐Inspired Polymers and Bio‐Based Molecules Modified by Zwitterionic Motifs to Design Next‐Generation Materials for Medical Applications Abstract In philosophy, yin and yang symbolize opposing and simultaneously correlated forces. This pre‐defined scenario occurs in nature as well, e.g., for zwitterionic materials. Both charges, either positive or negative, act individually, and it is not surprising that their interaction with, for example, tissue surfaces or cell membranes differs. However, the combination of the individual binding affinities allows for establishing and tuning strong and/or surface‐specific interactions. To emphasize this relationship, this review describes novel, naturally‐derived and bio‐inspired (semi‐)synthetic materials with zwitterionic motifs designed for medical applications. Accordingly, it is not only mentioned how these materials are further modified, functionalized, or synthetically designed to obtain zwitterionic charge profiles for addressing various pathological scenarios. It is equally important to highlight how the physicochemical properties of zwitterions contribute to achieving this goal. For this purpose, the detailed understanding and basic knowledge of mediated binding mechanisms and electrostatic interactions of zwitterionic materials with the physiological, aqueous environment and body/artificial surfaces are discussed in‐depth to clarify the dynamics of zwitterionic moieties. Materials science ; Nanotechnology ; Polymer ; Smart polymer ; Molecule ; Biomimetics ; Combinatorial chemistry ; Organic chemistry Supramolecular Self-Assembly in Materials ; Bone Tissue Engineering Materials ; biodegradable polymer synthesis and properties
Authors: A.A. Mohammed | K. Al-Salihi | Rebaz F. Hamarawf
Source: RSC Advances (article, 2025-01-01)
Field: Materials Science — Materials Chemistry

Synthesis, characterization, and application of low-cost Mg-Al/CO <sub>3</sub> and Ni-Al/CO <sub>3</sub> layered double hydroxides (LDHs) as adsorbents for the removal of aniline blue dye from aqueous solutions: adsorption isotherms, kinetics, and thermodynamic studies Low cost Mg-Al/CO<sub>3</sub> and Ni-Al/CO<sub>3</sub> layered double hydroxides (LDHs) were prepared using a co-precipitation technique to improve their dye adsorption efficiency. Characterization techniques were employed to assess their structure and surface properties, including FT-IR, XRD, SEM, BET surface analysis, and UV-vis spectroscopy. The BET analysis revealed surface areas of 82.63 m<sup>2</sup> g<sup>-1</sup> for Mg-Al/CO<sub>3</sub> and 5.95 m<sup>2</sup> g<sup>-1</sup> for Ni-Al/CO<sub>3</sub>, highlighting their porous nature. The materials' capability to adsorb aniline blue from water was tested under various conditions, such as time, pH, dye concentration, and temperature. The adsorption data were analyzed using both Langmuir and Freundlich isotherm models. The Mg-Al/CO<sub>3</sub> LDH exhibited a notably higher maximum adsorption capacity of 704 mg g<sup>-1</sup>, compared to 181 mg g<sup>-1</sup> for Ni-Al/CO<sub>3</sub> LDH, according to the Langmuir model. The correlation coefficients (<i>R</i> <sup>2</sup>) indicate that the Freundlich model better fits the Mg-Al/CO<sub>3</sub> LDH data (<i>R</i> <sup>2</sup> = 0.9829), while the Langmuir model offers a better fit for Ni-Al/CO<sub>3</sub> LDH (<i>R</i> <sup>2</sup> = 0.9576). While kinetic studies showed that the pseudo-second-order model provided the best fit. The process was spontaneous and endothermic based on thermodynamic analysis, with positive entropy changes suggesting increased randomness at the interface. These results underscore the promise of using Mg-Al/CO<sub>3</sub> and Ni-Al/CO<sub>3</sub> LDHs as economical adsorbents in water purification. Layered double hydroxides ; Adsorption ; Aniline ; Coprecipitation ; Precipitation ; Characterization (materials science) ; Inorganic chemistry ; Chemistry ; Materials science ; Nuclear chemistry ; Nanotechnology ; Organic chemistry Layered Double Hydroxides Synthesis and Applications ; Nanomaterials for catalytic reactions ; Magnesium Oxide Properties and Applications
Authors: Mohammad Alhilal | Suzan Alhilal | Sobhi M. Gomha | Basant Farag | İlhan Sabancılar | Salama A. Ouf
Source: BMC Chemistry (article, 2025-08-31)
Field: Chemistry — Organic Chemistry

Biological evaluation and molecular docking studies of novel aza-acyclic nucleosides as putative antimicrobial, anticancer, and antioxidant agents This study aimed to synthesize new aza-acyclic nucleosides (aza-acyclovir) and evaluate the efficacy of these synthetic compounds as potential antimicrobial, anticancer, and antioxidant agents. We prepared two novel aza-acyclic nucleosides via two reactions. The first reaction involved trichloroisocyanuric acid and dibenzosulphonyl diethylamine, and the second reaction involved trichloroisocyanuric acid and diethanolamine. We then used one-dimensional nuclear magnetic resonance (NMR) spectroscopy, two-dimensional NMR spectroscopy, infrared spectroscopy, and mass spectrometry to determine the structures of the resulting compounds. In this regard, we first tested the antimicrobial activity of these compounds against various bacteria, including Bacillus cereus, B. subtilis, Staphylococcus epidermidis, Staphylococcus aureus, Escherichia coli, Proteus mirabilis, and Pseudomonas aeruginosa, and against fungal pathogens, including Aspergillus fumigatus, Candida tropicalis, and Alternaria solani. Next, the precise mode for the interaction between synthesized aza-acyclic nucleosides and the target protein 8HQ5 was elucidate using molecular docking analysis. Subsequently, we tested the synthesized compounds for putative anticancer activity at different concentrations (i.e., 12.5, 25, 50, 100, and 200 µg/mL) against A549 cell (Human epithelial lung carcinoma) and human umbilical vein endothelial cell (HUVEC) lines. In addition, compounds antioxidant activity was evaluated using the 2,2-diphenyl-1-picrylhydrazyl-based and cupric reducing antioxidant capacity-based methods at different concentrations (i.e., 31.25, 62.5, 125, 250, and 500 µg/mL). Results revealed that both aza-acyclic nucleosides inhibited both bacterial and fungal strains, although toxicity toward bacterial strains was generally greater than toward fungal strains. We also observed that the molecular docking results were consistent with the results of in vitro antimicrobial assessments. Further, both aza-cyclic nucleosides exhibited cytotoxic effects against both the A549 cell and HUVEC lines. Despite exhibiting lower radical scavenging activity than ascorbic acid (an antioxidant compound used as a standard), Compound 1 from the novel synthetic aza-acyclic nucleosides showed a higher reduction capacity, which was dose-dependent. Overall, we report newly synthesized compounds that show promising antimicrobial, anticancer, and antioxidant effects. Antimicrobial ; Docking (animal) ; Chemistry ; Computational biology ; Antioxidant ; Combinatorial chemistry ; Pharmacology ; Biochemistry ; Biology ; Medicine ; Organic chemistry Synthesis and Characterization of Heterocyclic Compounds ; Synthesis and biological activity ; Click Chemistry and Applications
Authors: Ayşenur Betül Bilgin | Pervin Başaran
Source: Comprehensive Reviews in Food Science and Food Safety (review, 2025-07-01)
Field: Chemistry — Analytical Chemistry

Microwave Sensing and Imaging Technology in Food Applications: A Comprehensive Review Microwave sensing (MWS) and imaging (MWI) technologies have gained significant attention as non-destructive methods for assessing food quality, ensuring safety, and verifying authenticity. This review provides a comprehensive evaluation of MW-based systems in food applications, integrating both theoretical foundations and practical implementations. The fundamental principles of MW technology, including its theoretical background, sensing mechanisms, and imaging techniques, are first discussed. The review then explores the applications of MW sensing and imaging in food analysis, encompassing contamination detection (e.g., foreign bodies, microorganisms, and toxins), moisture content evaluation, adulteration detection, quality control, and compositional assessment. Furthermore, the advantages and limitations of MW systems for food applications are critically analyzed, along with an overview of commercial MW-based technologies, relevant patent developments, and ongoing international research initiatives. Finally, the future potential of MWS and MWI in the food industry is discussed, emphasizing their role in advancing real-time, non-invasive quality monitoring and strengthening food integrity. This review aims to provide valuable insights into the current state and future directions of MW-based food inspection technologies. Food safety ; Computer science ; Implementation ; Food quality ; Emerging technologies ; Biochemical engineering ; Systems engineering ; Risk analysis (engineering) ; Nanotechnology ; Process engineering ; Engineering ; Business ; Materials science ; Medicine ; Artificial intelligence Spectroscopy and Chemometric Analyses ; Biosensors and Analytical Detection ; Advanced Chemical Sensor Technologies
Authors: Yudhajit Bhattacharjee | L. N. Mielke | Mahmoud Al‐Hussein | Shivam Singh | Karen Moore Schaefer | Borja Rodriguez‐Barea | Q. Li | Anik Kumar Ghosh | Artur Erbe | Carmen Herrmann | Yana Vaynzof | Andreas Fery | Hendrik Schlicke
Source: Advanced Functional Materials (article, 2025-10-15)
Field: Materials Science — Materials Chemistry

Molecular Cross‐Linking of MXenes: Tunable Interfaces and Chemiresistive Sensing Abstract MXenes, a family of 2D transition metal compounds, have emerged as promising materials due to their unique electronic properties and tunable surface chemistry. However, the translation of these nanoscale properties into macroscopic devices is constrained by suitable cross‐linking strategies that enable both processability and controlled inter‐flake charge transport. Herein, this study demonstrates the tunability of interfaces and the inter‐layer spacing between Ti 3 C 2 T x MXene flakes through molecular cross‐linking with homologous diamines. Oleylamine is first used to stabilize MXenes in chloroform, followed by diamine‐mediated cross‐linking to tune precisely the interlayer spacing. Grazing incidence X‐ray scattering (GIXRD/GIWAXS) confirmed the correlation between ligand chain length and inter‐layer spacing, which is further supported by Density Functional Theory (DFT) calculations. Furthermore, the charge transport properties of thin films consisting of diamine‐cross‐linked Ti 3 C 2 T x MXenes are investigated and a strong dependence of the conductivity on the cross‐linker length is observed. The dominating charge transport mechanism is variable range hopping (VRH) in accordance with the structure of the films. Finally, chemiresistive vapor sensing is probed using the MXene composites, and a pronounced sensitivity and selectivity for water is observed, highlighting their potential for use in humidity sensors. Insights into molecular cross‐linking and its impact on charge transport open avenues for next‐generation MXene‐based electronic devices. MXenes ; Charge (physics) ; Variable-range hopping ; Scattering ; Density functional theory ; Nanoscopic scale ; Conductivity ; Molecular dynamics MXene and MAX Phase Materials ; 2D Materials and Applications ; Advanced Memory and Neural Computing
Authors: Xu Han | Y. Sun | Kai Chen | Yuxuan Ren | Kang Liu | Q.X. Ye
Source: Journal of Chemical Theory and Computation (preprint, 2025-12-27)
Field: Materials Science — Materials Chemistry

Constraint Decoupled Latent Diffusion for Protein Backmapping Coarse-grained (CG) molecular dynamics simulations enable efficient exploration of protein conformational ensembles. However, reconstructing atomic details from CG structures (backmapping) remains a challenging problem. Current approaches face an inherent trade-off between maintaining atomistic accuracy and exploring diverse conformations, often necessitating complex constraint handling or extensive refinement steps. To address these challenges, we introduce a novel two-stage framework, named CODLAD (COnstraint Decoupled LAtent Diffusion). This framework first compresses atomic structures into discrete latent representations, explicitly embedding structural constraints, thereby decoupling constraint handling from generation. Subsequently, it performs efficient denoising diffusion in this latent space to produce structurally valid and diverse all-atom conformations. Comprehensive evaluations on diverse protein data sets demonstrate that CODLAD achieves state-of-the-art performance in atomistic accuracy, conformational diversity, and computational efficiency while exhibiting strong generalization across different protein systems. Diffusion ; Latent heat ; Latent class model ; Statistical physics ; Computer science ; Physics ; Thermodynamics ; Machine learning Machine Learning in Materials Science ; Algorithms and Data Compression ; Gene expression and cancer classification
Authors: Nadia A. Youssef | Yasser A. Selim | Lubna Shaheen | Ahmed A. Fadda | Hatem E. Gaffer | Sherihan A. El‐Hadidy
Source: Scientific Reports (article, 2025-06-20)
Field: Chemistry — Organic Chemistry

Design and synthesis of novel pyridopyrimidine moieties linked to coumarin ring of potentially active cytotoxic agents and their docking study Many pyridopyrimidine moieties linked to the coumarin ring were synthesized by the reaction of malononitrile with 7-hydroxy-4-methyl-2-oxo-2 H-chromene-8-carbaldehyde (2) directly in the presence of ammonium acetate and different ketones and studied the effect of other basic catalysis, ratio of reactants and the effect of the solvent. The newly synthesized compounds were evaluated for their cytotoxic activity against four cell lines namely HepG2, WI-38, VERO, and MCF-7. The cytotoxic activity showed that compounds 8, 9, 10, and 7 have the highest activity against the studied cell lines. Focusing on the binding affinity and interactions between the five synthesized derivatives with the highest anticancer activity and specific amino acids of 4HJO residues over the molecular docking analysis. Derivative 10 recorded the highest energy score with good RMSD compared to the rest of the derivatives. Malononitrile ; Coumarin ; Docking (animal) ; Chemistry ; Ammonium acetate ; Cytotoxic T cell ; Stereochemistry ; Ring (chemistry) ; Cytotoxicity ; Combinatorial chemistry ; Solvent ; Catalysis ; Organic chemistry ; Biochemistry ; High-performance liquid chromatography ; In vitro Synthesis and biological activity ; Multicomponent Synthesis of Heterocycles ; Synthesis and Biological Evaluation