jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Ali Shiraee Kasmaee | Mohammad Khodadad | Mehdi Astaraki | Mohammad Arshi Saloot | Nicholas Sherck | Hamidreza Mahyar | Soheila Samiee
Source: ArXiv.org (preprint, 2025-08-03)
Field: Materials Science — Materials Chemistry

ChEmbed: Enhancing Chemical Literature Search Through Domain-Specific Text Embeddings Retrieval-Augmented Generation (RAG) systems in chemistry heavily depend on accurate and relevant retrieval of chemical literature. However, general-purpose text embedding models frequently fail to adequately represent complex chemical terminologies, resulting in suboptimal retrieval quality. Specialized embedding models tailored to chemical literature retrieval have not yet been developed, leaving a substantial performance gap. To address this challenge, we introduce ChEmbed, a domain-adapted family of text embedding models fine-tuned on a dataset comprising chemistry-specific text from the PubChem, Semantic Scholar, and ChemRxiv corpora. To create effective training data, we employ large language models to synthetically generate queries, resulting in approximately 1.7 million high-quality query-passage pairs. Additionally, we augment the tokenizer by adding 900 chemically specialized tokens to previously unused slots, which significantly reduces the fragmentation of chemical entities, such as IUPAC names. ChEmbed also maintains a 8192-token context length, enabling the efficient retrieval of longer passages compared to many other open-source embedding models, which typically have a context length of 512 or 2048 tokens. Evaluated on our newly introduced ChemRxiv Retrieval benchmark, ChEmbed outperforms state-of-the-art general embedding models, raising nDCG@10 from 0.82 to 0.91 (+9 pp). ChEmbed represents a practical, lightweight, and reproducible embedding solution that effectively improves retrieval for chemical literature search. Embedding ; Context (archaeology) ; Chemical nomenclature ; Chemical space ; Document retrieval ; Fragmentation (computing) Machine Learning in Materials Science ; Biomedical Text Mining and Ontologies ; Computational Drug Discovery Methods
Authors: Yutong Liu | Zhaoyuan Zhang | Xiangsheng Zeng | Yihe Zhang | Leping Yu | Yang, Liu | L. Wang | Xi Yu
Source: arXiv (Cornell University) (preprint, 2025-09-07)
Field: Materials Science — Materials Chemistry

Language-Native Materials Processing Design by Lightly Structured Text Database and Reasoning Large Language Model Materials synthesis procedures are predominantly documented as narrative text in protocols and lab notebooks, rendering them inaccessible to conventional structured data optimization. This language-native nature poses a critical challenge for complex, multistage processes--such as the preparation of boron nitride nanosheet (BNNS)--where outcomes depend on path-dependent choices in exfoliation and functionalization. Here, we recast synthesis planning as a text reasoning task enabled by a lightly structured text database, which preserves the conditional logic and causal contexts essential for expert-like decision-making. Building on a heterogeneous schema that indexes both narrative excerpts and computable entities (e.g., reaction conditions), our system implements a hybrid retrieval engine to combine semantic context with precise parameter filtering. On top of this, the framework operates in two modes, i.e. retrieval-augmented generation (RAG), which grounds recommendations in retrieved evidence modules, and experience-augmented reasoning (EAR), which uses iteratively refined text guides distilled from multi-source narrative data. Instead of suggesting single "optimal" settings, the system produces interpretable guidance aligned with expert reasoning patterns--hypotheses, parameter ranges, and citation-backed standard operating procedures--that support iterative planning and failure diagnosis. We validated this framework on the targeted exfoliation of BNNS, a process highly sensitive to multivariate constraints. The system successfully identified optimal combinations of grinding aids, milling configurations, and separation strategies from a wide range of literature-reported methods, which were experimentally verified to yield high-quality nanosheets, illustrating the potential of language-native reasoning to streamline critical operations in materials processing. Rendering (computer graphics) ; Semantic reasoner ; Knowledge base ; Schema (genetic algorithms) ; Context (archaeology) ; Iterative and incremental development ; Automated reasoning ; Expert system Machine Learning in Materials Science
Authors: C.‐C. Jay Kuo | Siyu Chen | Chenghui Yan | Yu Liu
Source: ArXiv.org (preprint, 2025-03-28)
Field: Materials Science — Materials Chemistry

Penrose Tiled Low-Rank Compression and Section-Wise Q&amp;A Fine-Tuning: A General Framework for Domain-Specific Large Language Model Adaptation Large language models (LLMs) hold great promise for specialized scientific domains such as materials science, yet adapting them efficiently and accurately to domain-specific knowledge remains challenging due to limited data and high knowledge density. We propose a two-stage framework that combines structured model compression with a scientific fine-tuning regimen to address this challenge. In the compression stage, we decompose the LLM's weight matrices into local low-rank "rank blocks" and arrange these blocks in a Penrose-like non-periodic tiling pattern. Each block is then compacted via spectral transformations (e.g., discrete cosine or Fourier transforms), and a Kullback-Leibler (KL) divergence-based alignment loss preserves the distributional similarity between the compressed model's representations and those of the original full model. In the adaptation stage, the compressed model is further tuned using a human-like scientific reading protocol: it processes technical materials science documents section by section, engaging in a structured question-and-answer routine for each section. This section-wise Q&amp;A fine-tuning strategy extracts explicit reasoning traces and gradually injects domain knowledge, while minimizing catastrophic forgetting of the model's general language capabilities. By balancing efficient compression with targeted adaptation, our two-stage approach enables precise specialization of LLMs to high-value domains under data-scarce conditions. We present this principled yet exploratory pipeline and outline its potential for advancing materials science knowledge integration, laying the groundwork for comprehensive empirical evaluation in future work. Pipeline (software) ; Block (permutation group theory) ; Adaptation (eye) ; Forgetting ; Table (database) ; Data compression ; Domain (mathematical analysis) ; Compression (physics) ; Encoding (memory) Machine Learning in Materials Science ; Topic Modeling ; Advanced Graph Neural Networks
Authors: Ghule, Swapnil | Korenkov, Konstantin O. | Sharapa, Dmitry I. | Amsharov, Konstantin Y. | Kataev, Evgeny A. | Oshchepkov, Alexander S.
Source: KITopen (article, 2025-01-01)
Field: Chemistry — Organic Chemistry

Naphthalimide‐Buckybowl Tweezer for Selective Recognition of Fullerene C$_{70}$ Supramolecular tweezers-like receptors represent a simple and efficient approach for the molecular recognition of fullerenes. Straightforward synthesis and easy fine-tuning of their geometry are the advantages that allow one to achieve strong binding and specific selectivity. However, the use of buckybowls in constructing tweezers and incorporating fluorescent dyes is still underexplored. To achieve this goal, we have designed mono- and di-substituted receptors by attaching indacenopicene to a naphthalimide dye. The tweezers-like receptor shows the highest selectivity for C$_{70}$ with an affinity of 2150 M$^{−1}$, which is about 50-fold stronger than the recognition of C$_{60}$. DFT and NMR data indicate that the preferred binding mode involves the ellipsoidal C$_{70}$molecule coordinating with buckybowls at its poles. In this arrangement, the naphthalimide core establishes two CH–π interactions with the fullerene. The results indicate that conjugating buckybowls with naphthalimides in a suitable design presents a promising method for selective binding and fine-tuning photoinduced electron transfer in the host–guest complex. Molecular tweezers ; Supramolecular chemistry ; Molecular recognition ; Selectivity ; Fluorescence ; Tweezers ; Fullerene ; Intramolecular force Fullerene Chemistry and Applications ; Supramolecular Chemistry and Complexes ; Synthesis and Properties of Aromatic Compounds
Authors: Priyanka Borah | Lenida Kyndiah | Rona Moni Bora | Sangeeta Chingangbam | Amarta Kumar Pal
Source: ChemistrySelect (article, 2025-01-29)
Field: Chemistry — Organic Chemistry

Cobalt‐Mediated Selective Synthesis of Iodine Functionalized Imidazo‐Fused Heterocycles Using 2‐Aminopyridine, Styrene or Acetophenone Abstract In this study, a cobalt‐mediated approach toward the synthesis of iodinated imidazo‐fused heterocycles employing molecular iodine as an iodine source, and 1,2‐DCB as the sovent at 120 °C has been documented. An assortment of iodinated imidazo[1,2 ‐a ]pyridines were acquired in moderate to good yields (71%–84%) by using 2‐aminopyridines and substituted styrenes as initial materials. This fine‐tuned protocol has also been broadened with acetophenones in moderate to good yields (66%–90%). This protocol provides a straightforward pathway for the synthesis of iodoimidazo[1,2 ‐a ]pyridines. Iodoimidazo[1,2 ‐a ]pyridine was further derivatized to 2,3‐diphenylimidazo[1,2 ‐a ]pyridine, an important biologically active molecule, with phenylboronic acid or simple benzene. Additionally, the gram scale reaction shows the high industrial applicability of the protocol. Acetophenone ; Styrene ; Cobalt ; Iodine ; Chemistry ; 2-Aminopyridine ; 4-Aminopyridine ; Combinatorial chemistry ; Organic chemistry ; Nuclear chemistry ; Catalysis ; Copolymer ; Polymer ; Medicine Synthesis and Biological Evaluation ; Catalytic C–H Functionalization Methods ; Oxidative Organic Chemistry Reactions
Authors: Alex Stafford (9248273) | Vincent W. Chen (21647907) | LoriAnne Groo (22773905) | Abigail T. Juhl (2257198) | Luke A. Baldwin (1525828)
Source: Figshare (article, 2025-12-03)
Field: Materials Science — Polymers and Plastics

Modular Epoxy-Thiol Oligosiloxane Vitrimers An emergent class of next-generation materials, vitrimers, combines the structural integrity and bulk properties of cross-linked thermosets with the reprocessability of thermoplastics. In this work, a robust vitrimer network was designed to enable fine-tuning of mechanical properties while maintaining ease of synthesis to achieve tough, lightweight, transparent, and compliant materials. Oligosiloxane-based epoxy-thiol networks were synthesized with varying substituents incorporated into the polymer side chains (-methyl, -ethyl, -isopropyl, and/or -phenyl) to elucidate key structure–property relationships that correlate to different thermomechanical properties. Thiol-epoxy reactions are a form of “click” chemistry with minimal side reactions and enable precise control over cross-link density, resulting in networks with easily tunable material properties. Through oligosiloxane side chain modification and thiol network composition, a material set with a diverse range of properties from near-supersoft networks (elastic modulus <250 kPa) to highly stretchable elastomers (>180% strain) was achieved. Additionally, we demonstrated that extended reprocessing can be accomplished at 150 °C with excellent retention of mechanical properties. The vitrimer toolbox and structure–property relationships identified herein provide key insights that will inform further design and optimization of tunable vitrimer networks with utility in composites, soft optoelectronics, and robotics. Elastomer ; Thermosetting polymer ; Polymer ; Side chain ; Polyurethane ; Modularity (biology) ; Modular design ; Prepolymer Polymer composites and self-healing ; Polyoxometalates: Synthesis and Applications ; Flame retardant materials and properties
Authors: Marco Taddei
Source: ChemRxiv (preprint, 2025-09-17)
Field: Chemistry — Inorganic Chemistry

Aliovalent Solid Solutions of Metal-Organic Frameworks Metal-organic frameworks (MOFs) are amenable to the formation of solid solutions by isomorphous substitution of the organic linker and/or the metal ion. In the case of metal substitution, the incorporation of aliovalent species, i.e., having a different oxidation state from the original ion, leads to the generation of excess charges in the framework, which must be compensated. Depending on the charge compensation mechanism, new properties can emerge. Despite limited work has been done so far in this area of research, aliovalent substitution has the potential to become an important tool to fine tune the physico-chemical properties in MOFs and should be investigated more systematically. Here, the available literature on aliovalent solid solutions of MOFs is critically analysed under the lens of inorganic solid-state chemistry. Solid solution ; Solid-state ; Linker ; Work (physics) ; Metal-organic framework ; Substitution (logic) Metal-Organic Frameworks: Synthesis and Applications ; X-ray Diffraction in Crystallography
Authors: Alex Stafford | Vincent W. Chen | LoriAnne Groo | Abigail T. Juhl | Luke A. Baldwin
Source: Chemistry of Materials (article, 2025-12-03)
Field: Materials Science — Polymers and Plastics

Modular Epoxy-Thiol Oligosiloxane Vitrimers An emergent class of next-generation materials, vitrimers, combines the structural integrity and bulk properties of cross-linked thermosets with the reprocessability of thermoplastics. In this work, a robust vitrimer network was designed to enable fine-tuning of mechanical properties while maintaining ease of synthesis to achieve tough, lightweight, transparent, and compliant materials. Oligosiloxane-based epoxy-thiol networks were synthesized with varying substituents incorporated into the polymer side chains (-methyl, -ethyl, -isopropyl, and/or -phenyl) to elucidate key structure–property relationships that correlate to different thermomechanical properties. Thiol-epoxy reactions are a form of “click” chemistry with minimal side reactions and enable precise control over cross-link density, resulting in networks with easily tunable material properties. Through oligosiloxane side chain modification and thiol network composition, a material set with a diverse range of properties from near-supersoft networks (elastic modulus <250 kPa) to highly stretchable elastomers (>180% strain) was achieved. Additionally, we demonstrated that extended reprocessing can be accomplished at 150 °C with excellent retention of mechanical properties. The vitrimer toolbox and structure–property relationships identified herein provide key insights that will inform further design and optimization of tunable vitrimer networks with utility in composites, soft optoelectronics, and robotics. Elastomer ; Thermosetting polymer ; Polymer ; Side chain ; Polyurethane ; Smart material ; Modular design ; Modularity (biology) Polymer composites and self-healing ; Polyoxometalates: Synthesis and Applications ; Flame retardant materials and properties
Authors: María Álvarez-Sánchez | Margarita Gómez | Carina Santos | Jean Ngouné | Eleuterio Álvarez | Agustı́n Galindo | Claudio Pettinari
Source: ACS Omega (article, 2025-11-14)
Field: Chemistry — Organic Chemistry

Regioselective Syntheses of Bis(indazolyl)methane Isomers: Controlling Kinetics and Thermodynamics via Tunable Non-Innocent Amines The selective synthesis of regioisomers from ambident N-heterocycles remains a challenge in organic chemistry. We report a general and modular method for the regioselective syntheses of bis-(indazolyl)-methane isomers, in which the outcome is controlled by the nature of the base. Specifically, we employed structurally diverse amines as noninnocent bases, whose steric and electronic propertiesparticularly their p<i>K</i> <sub>a</sub>H and ability to act as methylene carriers or activatorsplay a decisive role in directing product distribution. By fine-tuning the amine structure, we achieved selective access to symmetrical and unsymmetrical isomers under mild, one-step conditions, without intermediate isolation. The use of amines over conventional inorganic bases was essential to enable both chemo- and regioselective control, while minimizing overactivation or competing pathways. Experimental findings were supported by DFT calculations that rationalize the observed selectivity through differential activation energies and intermediate stabilities. The methodology accommodates both classical methylenating agents (e.g., CH<sub>2</sub>Br<sub>2</sub>) and in situ generated ammonium-based donors. All compounds were fully characterized, and key products were confirmed by single-crystal X-ray diffraction (SCXRD). This strategy highlights the utility of noninnocent amines as tunable reagents for regioselective transformations of ambident nucleophiles, with broad potential applications in ligand design, supramolecular chemistry, and heterocyclic synthesis. Regioselectivity ; Steric effects ; Structural isomer ; Reagent ; Amine gas treating ; Selectivity ; Methylene ; Supramolecular chemistry Synthesis of Indole Derivatives ; Coordination Chemistry and Organometallics ; Catalytic Alkyne Reactions
Authors: Hao Liu | M. C. Ekosso | Avery Glagovich | Sarah Maurer | Joshua Schrier
Source: ChemRxiv (article, 2025-12-08)
Field: Materials Science — Biomaterials

Molecular foundation models for predicting self-assembly in aqueous mixtures Artificial neural network ; Binary number ; Foundation (evidence) ; Bespoke ; Graph ; Aqueous solution ; Molecular graph ; Pulmonary surfactant Supramolecular Self-Assembly in Materials ; Advanced Polymer Synthesis and Characterization ; Surfactants and Colloidal Systems
Authors: Francis K. Migwi | George S. Nyamato | Stephen O. Ojwach | James Darkwa
Source: Coordination Chemistry Reviews (article, 2025-11-20)
Field: Chemistry — Organic Chemistry

A review of the recent coordination chemistry and catalytic applications of pyrazole and pyrazolyl transition metal complexes Transition metal ; Coordination complex ; Pyrazole ; Catalysis ; Steric effects ; Metal ; Organometallic chemistry ; Homogeneous catalysis Catalytic C–H Functionalization Methods ; Catalytic Cross-Coupling Reactions ; N-Heterocyclic Carbenes in Organic and Inorganic Chemistry
Authors: Cansu Akyel | Ahmet Ormancı | Mustafa Çiftçi
Source: Polymer International (article, 2025-08-19)
Field: Chemistry — Organic Chemistry

Metal‐free <scp>ATRP</scp> and <scp>ROP</scp> for graft copolymers: an orthogonal strategy for sequential and concurrent polymerizations at room temperature Abstract Well‐defined poly[(methyl acrylate)‐ co ‐(hydroxyethyl acrylate)]‐ graft ‐ poly(ε‐caprolactone ) copolymers were synthesized using a completely metal‐free strategy by combining atom transfer radical polymerization (ATRP) and ring‐opening polymerization (ROP) at ambient temperature. These two orthogonal, metal‐free, controlled/living processes, tested in both simultaneous and sequential approaches, were employed to fine‐tune grafting density and efficiency by systematically varying monomer concentration and polymerization time. Spectroscopic and chromatographic characterizations confirmed that both ATRP and ROP proceeded in a controlled fashion, yielding graft copolymers with narrowly distributed molecular weights. © 2025 Society of Chemical Industry. Copolymer ; Polymer chemistry ; Materials science ; Chemistry ; Polymer ; Composite material Advanced Polymer Synthesis and Characterization ; Polymer Surface Interaction Studies ; biodegradable polymer synthesis and properties
Authors: Mingming Li (502877) | Xinyi Liu (186154) | Silvio Decurtins (827737) | Shi-Xia Liu (827738)
Source: Figshare (article, 2025-10-07)
Field: Chemistry — Organic Chemistry

Cascade C–HHalogenation of Tetraazapyrenewith Iodine Halides Iodine halide as an efficient and selective halogenation reagent is presented for the cascade halogenation of an electron-deficient tetraazapyrene (TAP), yielding both chlorinated and heterohalogenated derivatives. This approach enables precise control over the LUMO energy levels of the resulting TAPs by varying the type and extent of halogenation, offering a powerful strategy for fine-tuning their electronic properties. These findings open new avenues for the rational design of TAP-based materials in organic molecular electronics. Halogenation ; Halide ; Cascade ; Reagent ; Iodine ; HOMO/LUMO Synthesis and Properties of Aromatic Compounds ; Organic and Molecular Conductors Research ; Organic Electronics and Photovoltaics
Authors: William Lowery | G. Kane Jennings | David E. Cliffel
Source: ACS Omega (article, 2025-03-07)
Field: Materials Science — Materials Chemistry

Counteranion Effects on the Incorporation of Photosystem I with Poly(3,4-ethylenedioxythiophene) (PEDOT) Conductive polymers provide an effective interface for proteins, particularly in photovoltaic applications. The synthetic toolbox affords a variety of options in which to fine-tune protein-polymer properties toward better engineered materials. While prior work has shown compatibility between Poly(3,4-ethylenedioxythiophene) (PEDOT) and Photosystem I, a detailed study of counteranion effects with interfacing Photosystem I has yet to be performed. This study, which fills a significant gap in the field, involves the synthesis of PEDOT films with a variety of different potassium-based salts. Morphology, capacitance, and impedances all varied across the films when deposited in the presence of the different anions. These properties were evaluated independently before interfacing PSI. After incorporating PSI within these films through entrapment and deposition approaches, the counteranion dependent properties were explored further through the photoactivity of these composite films. Results showed that films produced with the bromide anion provided the highest photocurrent output due to the porous leaf-like structure of the conducting polymer matrix. PEDOT:PSS ; Poly(3,4-ethylenedioxythiophene) ; Photosystem II ; Chemistry ; Materials science ; Nanotechnology ; Photosynthesis ; Biochemistry ; Layer (electronics) Porphyrin and Phthalocyanine Chemistry ; Electrochemical sensors and biosensors ; Photoreceptor and optogenetics research
Authors: Christoph Fornacon‐Wood | Luca Steiner | Chengzhang Xu | Beate Paulus | Alex J. Plajer
Source: Angewandte Chemie (article, 2025-10-20)
Field: Materials Science — Biomaterials

Recoverable Fluorination Accelerates Ring‐Opening Copolymerisation and Enables Post‐Polymerisation‐Modification of Polyesters Abstract Fluorination of polymers is a powerful strategy to enhance chemical or material properties yet integrating these benefits into degradable polymers remains underexplored. Here, we report a new class of fluorinated polyesters synthesized via ring‐opening copolymerisation of pentafluoro styrene oxide with phthalic anhydride. The pendant C 6 F 5 groups accelerate catalysis through fluorine‐specific π‐stacking interactions and improve obtained molecular weights compared to the non‐fluorinated variant giving access to high weight materials ( M n,max. &gt; 100 kg mol −1 ) with thermal and mechanical properties competitive with commodity plastics. These C 6 F 5 groups then act as reactive handles in the material for efficient post‐polymerisation modification (PPM) in solution, allowing fine‐tuning of thermal, mechanical, optical, and solubility properties. PPM can even be performed on material surfaces, films and fibres can be selectively modified without dissolution. Lastly, degradation enables quantitative recovery of fluorine centres as sodium fluoride, offering a sustainable end‐of‐life option for the incorporated fluorine. Our work demonstrates how targeted fluorination of degradable polyesters can simultaneously enhance catalysis and unlock advanced material functionality. Polyester ; Polymer ; Catalysis ; Fluorine ; Styrene ; Solubility ; Oxide ; Degradation (telecommunications) biodegradable polymer synthesis and properties ; Carbon dioxide utilization in catalysis ; Fiber-reinforced polymer composites