jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Zhuo Chen | Shuai Zhang | Sihan Wang | Hongxin Xiang | Jianmin Wang | Wenjie Du | Yang Wang
Source:  (article, 2025-09-01)
Field: Materials Science — Materials Chemistry

DO-CoLM: Dynamic 3D Conformation Relationships Capture with Self-Adaptive Ordering Molecular Relational Modeling in Language Models Molecular Relational Learning (MRL) aims to understand interactions between molecular pairs, playing a critical role in advancing biochemical research. Recently, Large Language Models (LLMs), with their extensive knowledge bases and advanced reasoning capabilities, have emerged as powerful tools for MRL. However, existing LLMs, which primarily rely on SMILES strings and molecular graphs, face two major challenges. They struggle to capture molecular stereochemistry and dynamics, as molecules possess multiple 3D conformations with varying reactivity and dynamic transformation relationships that are essential for accurately predicting molecular interactions but cannot be effectively represented by 1D SMILES or 2D molecular graphs. Additionally, these models do not consider the autoregressive nature of LLMs, overlooking the impact of input order on model performance. To address these issues, we propose DO-CoLM: a Dynamic relationship capture and self-adaptive Ordering 3D molecular Conformation LM for MRL. By introducing modules to dynamically model intra-molecular and inter-molecular conformational relationships and adaptively adjust the molecular modality input order, DO-CoLM achieves superior performance, as demonstrated by experimental results on 12 cross-domain datasets. Molecular model ; Molecular dynamics ; Molecular conformation ; Order (exchange) ; Autoregressive model ; Language model ; Face (sociological concept) ; Process (computing) Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Biomedical Text Mining and Ontologies
Authors: Yufei Luo | Heran Yang | Jian Sun
Source: Pattern Recognition (article, 2025-03-07)
Field: Materials Science — Materials Chemistry

Meta-learning of pseudo force field generation and estimation for enhancing 3D molecular property prediction Force field (fiction) ; Property (philosophy) ; Computer science ; Artificial intelligence ; Field (mathematics) ; Estimation ; Machine learning ; Biological system ; Mathematics ; Engineering ; Biology Machine Learning in Materials Science ; Fuel Cells and Related Materials ; Computational Drug Discovery Methods
Authors: Lanli Chen | Zhihua Xiong | Hongduo Hu | Hong Han | Yuanyuan Cui
Source: Journal of Physics and Chemistry of Solids (article, 2025-06-06)
Field: Materials Science — Materials Chemistry

Tunable ohmic contacts in two-dimensional ZnO monolayer via surface-engineered metallic Pd substrates: A first principles study Ohmic contact ; Monolayer ; Materials science ; Metal ; Palladium ; Nanotechnology ; Optoelectronics ; Composite material ; Chemistry ; Metallurgy ; Layer (electronics) ; Catalysis ZnO doping and properties ; 2D Materials and Applications ; MXene and MAX Phase Materials
Authors: Ngoc-Duong Nguyen | Van-Tai Bui | Trung-Kien Nguyen | Thuc P. Vo
Source: Structures (article, 2025-10-17)
Field: Materials Science — Materials Chemistry

Two-variables shear theory for bio-inspired helicoidal composite and carbon nanotube-reinforced composite beams resting on a general viscoelastic Winkler-Pasternak foundation Viscoelasticity ; Foundation (evidence) ; Vibration ; Composite number ; Ritz method ; Stiffness ; Shear (geology) Structural mechanics and materials ; Advanced Theoretical and Applied Studies in Material Sciences and Geometry ; Structural Analysis and Optimization
Authors: Anthony GX-Chen | Jatin Prakash | Jeff Guo | Rob Fergus | Rajesh Ranganath
Source: ArXiv.org (preprint, 2025-10-23)
Field: Materials Science — Materials Chemistry

KL-Regularized Reinforcement Learning is Designed to Mode Collapse It is commonly believed that optimizing the reverse KL divergence results in "mode seeking", while optimizing forward KL results in "mass covering", with the latter being preferred if the goal is to sample from multiple diverse modes. We show -- mathematically and empirically -- that this intuition does not necessarily transfer well to doing reinforcement learning with reverse/forward KL regularization (e.g. as commonly used with language models). Instead, the choice of reverse/forward KL determines the family of optimal target distributions, parameterized by the regularization coefficient. Mode coverage depends primarily on other factors, such as regularization strength, and relative scales between rewards and reference probabilities. Further, we show commonly used settings such as low regularization strength and equal verifiable rewards tend to specify unimodal target distributions, meaning the optimization objective is, by construction, non-diverse. We leverage these insights to construct a simple, scalable, and theoretically justified algorithm. It makes minimal changes to reward magnitudes, yet optimizes for a target distribution which puts high probability over all high-quality sampling modes. In experiments, this simple modification works to post-train both Large Language Models and Chemical Language Models to have higher solution quality and diversity, without any external signals of diversity, and works with both forward and reverse KL when using either naively fails. Reinforcement learning ; Regularization (linguistics) ; Parameterized complexity ; Intuition ; Leverage (statistics) ; Kullback–Leibler divergence Machine Learning in Materials Science ; Topic Modeling ; Reinforcement Learning in Robotics
Authors: Ananya Kar | K.R. Manu | Lopamudra Giri | Rambabu Dandela
Source: Advanced Sustainable Systems (article, 2025-06-11)
Field: Chemistry — Physical and Theoretical Chemistry

Beyond the Covalent Bond‐ The World of Co‐Crystals to Tune the Physicochemical Properties of Materials Abstract Supramolecular entities, known for their exceptional molecular recognition and complexation skills, have emerged as key drivers of developments in a variety of creative research domains. Cocrystal, an important branch of crystalline organic materials, have received a lot of attention due to their simple fabrication methods and wide range of potential applications, particularly in pharmaceutics, electronics, chemical sensing, and photothermal conversion, etc. This review provides an overview of functional cocrystal research, covering design principles, preparation procedures, assembly modes, and a wide range of applications. Finally, additional challenges and opportunities are given. It is hoped that this review will be a useful and relevant resource for researchers captivated by supramolecular crystalline materials and beyond, encouraging the production of more original and new work in related areas. Covalent bond ; Bond ; Materials science ; Nanotechnology ; Chemistry ; Organic chemistry ; Business Crystallography and molecular interactions ; Chemistry and Chemical Engineering ; Ionic liquids properties and applications
Authors: Ngoc Thinh Nguyen | V. A. Nguyen
Source: Digest Journal of Nanomaterials and Biostructures (article, 2025-06-01)
Field: Materials Science — Materials Chemistry

Fabrication of Fe3O4 nanoparticles via an eco-friendly sonochemical route utilizing cleistocalyx operculatus leaf extract: study of properties and application In this study, Fe3O4 nanoparticles were synthesized by microwave-assisted green chemistry method using Cleistocalyx operculatus leaf extract. The reaction process is simple, environmentally friendly and easy to perform. The characterization of Fe3O4 nanoparticles were analized by XRD, FT-IR, SEM, TEM analysis methods. The results showed that Fe3O4 nanoparticles are spherical, less agglomerated, have a spinel cubic structure and a crystal size of about 12.3 nm. Fe3O4 nanoparticles were used as an adsorbent to remove Congo Red dye. The equilibrium adsorption capacity reached 137.9 mg.g-1. From that, it can be concluded that Fe3O4 nanoparticles are promising adsorbent for dye removal in water environment. Environmentally friendly ; Fabrication ; Nanoparticle ; Nanotechnology ; Materials science Nanoparticles: synthesis and applications ; Bone Tissue Engineering Materials ; Iron oxide chemistry and applications
Authors: D. Seo | Seongyeon Kwon | Gil Ha Yoon | Tai Sun Son | Changhyeon Won | Neetu Singh | Dongwook Kim | Yunjung Baek
Source: Nature Communications (article, 2025-04-15)
Field: Materials Science — Materials Chemistry

Expanding the chemical space of flavins with pentacyclic architecture Inspired by the prominent redox and optical properties of natural flavins, synthetic flavins have found broad applications in organic, photochemical, and biochemical research. Tailoring these properties of flavins, however, remains a challenge. In this work, we present three pentacyclic flavins (C-PF, O-PF, and S-PF) that leverage a strategic molecular design to modify the flavin's electronic structure. Notably, the oxygen- and sulfur-linked pentacyclic flavins (O-PF and S-PF) exhibit deep-red and NIR emission, respectively, driven by enhanced π-conjugation, substituent effects, and charge separation upon excitation. These heteroatom-incorporated pentacyclic flavins exhibit unusual quasi-reversible oxidation, expanding both optical and redox limits of synthetic flavins. Comprehensive spectroscopic, structural, and computational analyses reveal how heteroatom incorporation within this five-ring-fused system unlocks redox and optical properties of flavin-derived chromophores. Chemical space ; Space (punctuation) ; Architecture ; Computer science ; Flavin group ; Data science ; Computational biology ; Biology ; Bioinformatics ; Geography ; Drug discovery ; Biochemistry Porphyrin and Phthalocyanine Chemistry ; Molecular Sensors and Ion Detection ; Conducting polymers and applications
Authors: Ze-Qing Chen | Brian Daly | Chaoyi Yao | Hannah S. N. Crory | Yikai Xu | Ziwei Ye | H. Q. Nimal Gunaratne | Ayumi Kimura | Seiichi Uchiyama | Steven E. J. Bell | Eric V. Anslyn | A. Prasanna de Silva
Source: Nature Communications (article, 2025-03-28)
Field: Chemistry — Spectroscopy

Scaling-up molecular logic to meso-systems via self-assembly Due to the small size and biocompatibility of molecules, molecular logic-based computation is a gateway to the informational basis of life processes. Logic-based computation operates widely with discrete molecules of up to nanometric sizes. The contribution of molecule-based bulk materials of milli/centimetric size to the field has begun in more recent years. However, artificial molecule-based meso-scale systems which intrinsically perform logic operations are very rare. Here, we show that self-assembled systems consisting of cyclophane octacarboxylates and a cationic surfactant can perform such functions, where a membrane itself behaves as a Reset-Set Flip-Flop which is integrated with 7 more logic elements. Now that molecular logic-based computation operates across a wide range of contiguous size-scales, the way opens for its general use in information processing aspects of biology and synthetic biology. Computation ; Scaling ; Logic gate ; Computer science ; Nanotechnology ; Set (abstract data type) ; Biological system ; Theoretical computer science ; Materials science ; Algorithm ; Mathematics ; Biology Molecular Sensors and Ion Detection ; Supramolecular Chemistry and Complexes ; Supramolecular Self-Assembly in Materials
Authors: Sophie R. Thomas | Tristan Tsai Yuan Tan | Guilherme M. D. M. Rúbio | Jia Min Chin | Michael R. Reithofer
Source: ChemRxiv (preprint, 2025-05-23)
Field: Chemistry — Organic Chemistry

Bidentate Acyclic Diamino Carbene-Stabilized Gold Nanoparticles from Symmetric and Asymmetric Gold(I) Complexes: Synthesis, Characterization, and Catalytic Activity A series of gold nanoparticles (AuNPs) stabilized by bidentate acyclic diamino carbenes (ADCs) were synthesized via the reduction of dimeric gold(I) complexes. The resulting ADC-AuNPs were characterized by NMR spectroscopy, UV-Vis spectroscopy, transmission electron microscopy (TEM), and thermogravimetric analysis (TGA), revealing monodisperse particles with sizes ranging from 1.7 to 3.3 nm. This synthetic approach was extended to an asymmetric dinuclear ADC-gold(I) complex, affording slightly larger AuNPs (~4 nm) upon reduction. The ADC-AuNPs with shorter linkers exhibited significant catalytic activity for the reduction of 4-nitrophenol, demonstrating a versatile and efficient route to catalytically active gold nanoparticles stabilized by both symmetric and asymmetric ADC ligands. Carbene ; Denticity ; Catalysis ; Colloidal gold ; Characterization (materials science) ; Chemistry ; Nanoparticle ; Polymer chemistry ; Combinatorial chemistry ; Organic chemistry ; Materials science ; Nanotechnology ; Crystal structure Nanomaterials for catalytic reactions ; Catalytic Alkyne Reactions ; N-Heterocyclic Carbenes in Organic and Inorganic Chemistry
Authors: Zishuo Li
Source: Applied and Computational Engineering (review, 2025-02-21)
Field: Chemistry — Inorganic Chemistry

A Review of the Methanol to Olefin Process This study examines the evolution and strategic significance of the Methanol-to-Olefins (MTO) process, an autonomous technological innovation that efficiently produces ethylene and propylene derivatives. The process, which emerged during the 1980s, stems from seminal research in methanol conversion methodologies, particularly building upon the 1977 Methanol-to-Gasoline (MTG) protocol. Serendipitous findings regarding hydrocarbon formations within the MTG gasoline fraction catalyzed substantial advancements in methanol conversion technologies. The analysis underscores the pivotal role of the UOP/Hydro methodology utilizing SAPO-34 catalysis, which has emerged as the industry-standard approach in olefin synthesis. Through comprehensive examination of reaction kinetics and UOP operational frameworks, this investigation illuminates the technological breakthroughs and industrial applications that have established the MTO process as a cornerstone of chemical manufacturing. Moreover, the study conducts a thorough economic analysis of MTO processes, evaluating their market competitiveness against conventional naphtha cracking methodologies. The research also explores the integration of sustainable feedstock alternatives within the MTO framework, highlighting potential pathways for environmentally conscious production strategies aligned with global sustainability initiatives. Olefin fiber ; Process (computing) ; Methanol ; Process engineering ; Chemistry ; Computer science ; Organic chemistry ; Engineering ; Programming language ; Catalysis Zeolite Catalysis and Synthesis ; Catalysis and Hydrodesulfurization Studies ; Catalysis and Oxidation Reactions
Authors: Jianhang Hu | Wanhua Wu | Cheng Yang
Source: Molecules (review, 2025-09-07)
Field: Chemistry — Organic Chemistry

Recent Advances in the Synthesis and Applications of Nitrogen-Containing Macrocyclic Arenes Macrocyclic arenes are rich-electron macrocycles bridged by methylene or methyl groups from aromatic rings substituted by hydroxyl or alkoxy groups. It has attracted great interest in host-guest chemistry and supramolecular self-assembly due to its clear cavity, adjustable structure and multifunctional binding ability. In particular, nitrogen-containing macrocyclic arenes including (hetero) aromatic moieties-constructed from building blocks such as pyrrole, carbazole, phenothiazine, and imidazole-have undergone rapid development, yielding a new generation of functional macrocycles, including calix[4]carbazoles, Tröger's base-derived macrocycles, and phenothiazine-based architectures. These nitrogen-functionalized macrocycles feature rich chemical derivatization potential, unique structural and host-guest characteristics, and exceptional photophysical properties. They show great promise in molecular recognition, selective adsorption and separation, and the development of advanced functional materials. This review summarizes recent advances in the design, synthesis, and application of nitrogen-containing macrocyclic arenes, with a particular focus on structure-property relationships and emerging functions. Supramolecular chemistry ; Calixarene ; Methylene ; Derivatization ; Aromaticity ; Alkoxy group Supramolecular Chemistry and Complexes ; Molecular Sensors and Ion Detection ; Synthesis and Properties of Aromatic Compounds
Authors: Rubén Serrano-Nieto | Christian Rentero | Pablo Salcedo‐Abraira | Catalina Biglione | Agustin M. Cornejo Manrique | Thomas Devic | Valentina Sessini | Marta E. G. Mosquera | Patricia Horcajada
Source: Inorganic Chemistry (article, 2025-06-04)
Field: Chemistry — Inorganic Chemistry

Triazine Mg-Based Phosphonate Metal–Organic Framework for ε-Caprolactone Polymerization A novel three-dimensional metal-organic framework (MOF) based on magnesium and the triazine triphosphonate ligand has been successfully synthesized via the solvothermal method and fully characterized. Denoted as IEF-31 (IEF stands for IMDEA energy framework), its crystal structure was unveiled by single-crystal X-ray diffraction, exhibiting free P-OH groups in two coordination modes (-PO<sub>3</sub>H<sub>2</sub> and -PO<sub>3</sub>H) and an open framework with 1D channels (8 × 7 Å). This robust structure shows high thermal and chemical stability (in several catalytic-relevant organic solvents and water, pH = 2 to 10). Further, this study presents the proof of concept for using an Mg-based P-MOF as a catalyst in the ring-opening polymerization of ε-caprolactone (ε-CL) with relevance in the challenging bioplastic formation. Specifically, IEF-31(Mg) achieved notable monomer conversions and polymer molecular weights with low dispersity values (<i>Đ</i> ≈ 1.1), paving the way for further design and optimization of robust, efficient, and sustainable Mg P-MOFs for clean polymerization processes. Chemistry ; Phosphonate ; Caprolactone ; Triazine ; Polymer chemistry ; Polymerization ; Metal ; Organic chemistry ; Polymer Metal-Organic Frameworks: Synthesis and Applications ; Chemical Synthesis and Characterization ; Polyoxometalates: Synthesis and Applications
Authors: Fahmina Zafar | Muhammad Sultan | Amna Nasir | Abolfazl Kiani | Mohsin Saleem Ghouri | S. Ahmad | Muhammad Yousaf | Uzair Ahmad | Muhammad Murad
Source: Scholars Academic Journal of Biosciences (article, 2025-01-28)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Carbon Nanotubes as Multifunctional Tools Advancing Batteries and Catalysis for Sustainable Solutions With a focus on their application in batteries and catalytic processes for sustainable solutions, this review article explores the revolutionary potential of carbon nanotubes (CNTs) as multifunctional materials that are advancing the fields of energy storage and catalysis. Their remarkable mechanical, electrical, and thermal properties have attracted considerable attention due to their potential to revolutionize energy storage devices such as lithium-ion batteries, supercapacitors, and emerging solid-state technologies. The high surface area, conductivity, and structural versatility of CNTs enable them to improve charge capacity, cycling stability, and efficiency in battery systems. Additionally, CNTs exhibit remarkable catalytic properties, particularly in green chemistry, where they act as active catalysts in energy conversion processes such as hydrogen production, CO2, and decrease and conversion of biomass. The review highlights recent developments in CNT-based materials, the synthesis methods that maximize their performance, and their incorporation into energy systems for sustainable development. It also covers the difficulties in scaling up CNT-based technologies and the potential solutions to these problems, paving the way for their use in large-scale industrial settings. In the end, this analysis underscores the inspiring potential of carbon nanotubes (CNTs) in propelling the transition to a more sustainable energy future, highlighting their versatility in energy storage and catalytic applications. Carbon nanotube ; Nanotechnology ; Catalysis ; Materials science ; Carbon fibers ; Chemistry ; Composite number ; Organic chemistry ; Composite material Supercapacitor Materials and Fabrication ; Graphene and Nanomaterials Applications ; Advanced Battery Technologies Research
Authors: Soňa Ondrušová | Daniel Bůžek | Jan Hynek | Tomáš Plecháček | Lenka Kubíčková | Miroslav Veverka | Tomáš Kmječ | Matyáš Rozprým | J. Kohout | Jan Demel | Matouš Kloda
Source: The Journal of Physical Chemistry C (article, 2025-08-20)
Field: Chemistry — Inorganic Chemistry

Magnetism, Mössbauer Spectroscopy, and Proton Conductivity of Coordination Polymers Based on Phosphonate and Phosphinate Linkers Coordination polymers (CPs) are versatile materials formed by metal ions and organic ligands, offering a broad range of structural and functional possibilities. Phosphonates and phosphinates are particularly attractive ligands for CPs due to their multiple binding sites, varied coordination geometries, and ability to form robust network structures. Phosphonates, considered harder ligands, form strong bonds with hard metals such as Fe<sup>3+</sup>, while phosphinates offer additional versatility due to the varied pendant groups on phosphorus. This study presents a series of six new coordination polymers, ICR-20 and ICR-21, incorporating Fe<sup>2+</sup>, Co<sup>2+</sup>, and Ni<sup>2+</sup> metal centers, using phosphinate (H<sub>2</sub>PBP-(Me)) or phosphinate-phosphonate (H<sub>3</sub>PPP-(Me)) ligands in combination with 4,4'-bipyridine. The materials are isoreticular despite the incorporation of different functional groups, demonstrating the interchangeability of the phosphinate and phosphonate groups in their design. These polymers were characterized structurally and investigated for their magnetic properties. The combination of local insights from Mössbauer spectroscopy and bulk magnetic data provides complex information on crystal field parameters and magnetic interactions in Fe-based polymers. Additionally, their proton conductivity was evaluated, showing promising results. Phosphinate ; Phosphonate ; Magnetism ; Mössbauer spectroscopy ; Materials science ; Polymer ; Proton ; Conductivity ; Spectroscopy ; Crystallography ; Nanotechnology ; Chemistry ; Physical chemistry ; Condensed matter physics ; Organic chemistry ; Physics ; Metallurgy Metal-Organic Frameworks: Synthesis and Applications ; Magnetism in coordination complexes ; Organic and Molecular Conductors Research
Authors: Liqun Guo | Qiang Zhu | Anna G. Slater
Source: Chemical Communications (review, 2025-01-01)
Field: Materials Science — Materials Chemistry

Self-assembly under continuous flow conditions Self-assembly plays a crucial role in the formation of hierarchical supramolecular structures and functional materials. The use of flow chemistry for self-assembly processes has garnered significant attention due to its enhanced ability to control the formation of complex molecular and nanoscale architectures. Compared to conventional batch processes, flow-based systems offer improved regulation of key reaction parameters, such as mixing dynamics, temperature gradients, and residence time, facilitating continuous and scalable synthesis. This review examines recent advances in self-assembly under flow conditions, highlighting advantages in four domains: scalable production, opportunities to control selectivity, improved product crystallinity, and precise regulation of size and morphology in particle formation. Selected case studies from the literature, including our work in this field, will be discussed to demonstrate that flow-based technology is valuable for the fabrication of supramolecular structures and represents a promising approach for advanced materials science. Flow (mathematics) ; Chemistry ; Materials science ; Computer science ; Nanotechnology ; Mechanics ; Physics Pickering emulsions and particle stabilization ; Micro and Nano Robotics ; Innovative Microfluidic and Catalytic Techniques Innovation