jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Petra Bombicz
Source: Structural Dynamics (article, 2025-09-01)
Field: Chemistry — Physical and Theoretical Chemistry

Are these crystals isostructural? Symmetry requirements, extent of difference, and likeness of supramolecular interactions The intentional design of crystalline materials, the fine-tuning of physical and chemical properties by slight chemical alterations - crystal engineering - requires understanding of solid-state assembly including supramolecular interactions and isostructurality. The balance of spatial requirements and electrostatic effects ultimately determines the molecular arrangement. In isostructural crystals, both the placement of the molecules and the conformation of flexible molecules may adjust to the chemical and supramolecular features. A given packing motif may tolerate small molecular changes, and the structures remain isostructural within a limit despite chemical changes. The investigation of isostructurality leads to a deeper understanding of the close packing principles, the role of molecular conformation, supramolecular interactions and symmetries, in order to be able to perform the directed manipulation of the molecular packing arrangements. The prerequisites of isostructurality are similar composition and conformation of the compounds, with analogous molecular arrangement in the crystals. Isostructurality calculations and statistical analyses are efficient tools for the discovery and numerical description of isostructural crystals which is not necessarily straightforward [1]. The presented series of compounds (Figure 1) opens up three questions on isostructurality. Are the corresponding structures required to have the same stoichiometry, space group, Z’ and the same symmetry elements? There is no agreement on these issues. How large can the extent of difference be between the corresponding crystal structures that we may still consider them as being isostructural? Can we consider crystals whose cell parameters are similar, space groups are the same and arrangements of the molecules are analogous, the only difference is in the system of intermolecular interactions to be isostructural? The definition of isostructurality is not explicit about these issues, it deserves reconsideration regarding symmetry, measure of similarity, and formation of supramolecular interactions [2]. Isostructural ; Supramolecular chemistry ; Molecule ; Crystal engineering ; Crystal structure ; Crystal (programming language) ; Symmetry (geometry) Crystallography and molecular interactions ; Crystallization and Solubility Studies ; Chemical Thermodynamics and Molecular Structure
Authors: John M. Bennett | Andrew Bortz | Zheyuan Wang | Muhammed Fastheem | Rudi Fasan
Source: Angewandte Chemie (article, 2025-08-04)
Field: Chemistry — Organic Chemistry

Chemoenzymatic Skeletal Editing of Natural Product Scaffolds via P450‐Controlled Site‐Selective Ring Expansion at Aliphatic C─H Sites Abstract Methods for introducing subtle modifications at the level of single atoms/bonds (“skeletal editing”) are highly desirable in organic and medicinal chemistry, owing to their potential for fine‐tuning the structure and biological activity of organic molecules. Here, we report a chemoenzymatic strategy for enabling the skeletal editing of organic frameworks via ring expansion at the level of one or more aliphatic (methylene) C─H sites, as achieved through the synergistic combination of P450‐mediated site‐selective oxidation with subsequent Baeyer–Villiger rearrangement or ketone homologation. Combining this approach with engineered P450 catalysts exhibiting divergent regioselectivity enabled the expeditious synthesis of a panel of ring‐expanded analogs of various complex natural product substrates. Importantly, the skeletal modification was found to drastically altered the anticancer activity of some of these compounds. By the direct targeting of aliphatic C─H sites with tunable site‐selectivity, this strategy provides a powerful tool to rapidly access skeletally edited derivatives of natural products and other bioactive molecules for applications in drug discovery and chemical biology. Natural product ; Chemistry ; Ring (chemistry) ; Combinatorial chemistry ; Stereochemistry ; Organic chemistry Catalytic C–H Functionalization Methods ; Synthesis and Catalytic Reactions ; Synthetic Organic Chemistry Methods
Authors: Alakananda Patra | Sandeep Kumar | Md Lutfor Rahman
Source: Chemistry - A European Journal (review, 2025-07-04)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Discotic Liquid Crystalline Phenazine Derivatives Phenazines, otherwise known as dibenzo-annulated pyrazines, are a unique class of tricyclic organic molecules. They are chemically stable and highly aromatic due to their extended conjugation. Along with their biomedicinal significance, phenazines often play a major role in manipulating the optical as well as electrical properties of organic semiconductors. The planar structure in the heterocyclic aromatic phenazines and their natural inclination to form stacked columns due to the π-π interactions between two consecutive molecules have made them quite a suitable moiety for the formation as well as extension of the core part of discotic liquid crystals (DLCs). Their efficient charge-carrying ability makes them well-suited for organic electronic materials. Furthermore, their properties can be fine-tuned with simple chemical changes, rendering them appropriate for many advanced applications. This review focuses on the chemistry of phenazine-based DLCs and their significance in optoelectronic applications. Discotic liquid crystal ; Phenazine ; Moiety ; Molecule ; Materials science ; Organic semiconductor ; Supramolecular chemistry ; Alkyl ; Triphenylene ; Organic molecules ; Chemistry ; Combinatorial chemistry ; Nanotechnology ; Organic chemistry ; Optoelectronics Liquid Crystal Research Advancements ; Synthesis and properties of polymers ; Surfactants and Colloidal Systems
Authors: Luiz Paulo Soares Pereira | Marina de Souza Melchiors | Thayne Y. Vieira | Tamara Agner | Bruno Augusto Mattar Carciofi | Pedro Henrique Hermes de Araújo | Débora de Olíveira | Cláudia Sayer
Source: Polímeros (article, 2025-01-01)
Field: Chemistry — Organic Chemistry

Modulating molecular weight and crosslinking in thiol-ene polymerization of renewable monomer limonene Abstract Limonene, a renewable material derived from citrus fruit peels, can be used as monomer in thiol-ene polymerization with dithiols and tetrathiols to form linear or crosslinked polymers, respectively. The effect of using a thermal- or photoinitiator on polymer properties was evaluated, with the photoinitiator significantly increasing the conversion of the internal unsaturation of limonene with 1,4-butanedithiol (&gt;90%), resulting in higher molecular weights (9,000 g/mol). With pentaerythritiol tetrakis(3-mercaptopropionate), the gel content remained below 15% in thermally initiated reactions (28,000 g/mol) but increased to above 90% in photoinitiated ones. Finally, combining both thiols resulted in an intermediate molecular weight (~13,000 g/mol) for thermal initiation, and a gel content of about 85% for the photoinitiated ones. Thus, thiol-ene reactions stand out as an effective approach for the synthesis of polymers from limonene, with molecular weight and gel content being fine-tuned by the type/ amount of initiator, and by the combination of di- and tetrathiol. Photoinitiator ; Monomer ; Polymerization ; Polymer ; Degree of unsaturation ; Bulk polymerization ; Prepolymer Photopolymerization techniques and applications ; Synthesis and properties of polymers ; Carbon dioxide utilization in catalysis
Authors: Hanlin Yu (17776399) | Maksym Seredyuk (1558420) | Kateryna Znovjyak (3182649) | Nikita Liedienov (17776402) | Wei Xu (28953) | Francisco Javier Valverde-Muñoz (1664797) | M. Carmen Muñoz (1558426) | Joachim Kusz (2243047) | Maria Książek (14552111) | Ruixin Li (169225) | Quanjun Li (1743778) | Bingbing Liu (649305) | Gábor Molnár (1558435) | Georgiy Levchenko (2408305) | José Antonio Real (1439689)
Source: Figshare (article, 2025-10-09)
Field: Materials Science — Electronic, Optical and Magnetic Materials

AliphaticChains and External Pressure as Tools forFine-Tuning Spin Transition Temperature and Cooperativity In switchable spin crossover (SCO) molecular materials, control of their critical temperature and cooperativeness is essential for practical applications. This requires systematic fine-tuning of the molecular packing in the crystal. Therefore, here we report on the synthesis and characterization of a series of Fe<sup>II</sup> SCO complexes, {Fe<sup>II</sup>L}(ClO<sub>4</sub>)<sub>2</sub>, derived from a tripodal tren-based imino-methyl-pyridine hexadentate-type ligand L with alkoxy chains of varying lengths (<b>C3</b> to <b>C22</b>). The complexes crystallize in the monoclinic <i>P</i>2<sub>1</sub>/c space group, displaying an identical coordination core. The crystal packing, modulated by the length of the alkoxy chains, is governed by the amphiphilic nature of the complexes, where the hydrophilic pseudo-octahedral cationic heads and ClO<sub>4</sub><sup>–</sup> anions define double-layers separated by the growing hydrophobic layer generated by the alkoxy chains. All compounds undergo thermal- and photoinduced SCO behavior featuring transition temperatures and cooperativeness which depend, for most of them, on the odd–even parity of the chains. The pressure dependence of the SCO for selected members (<b>C3</b>, <b>C8</b>, <b>C15</b>, and <b>C16</b>) has been investigated through magnetic, UV–vis, and IR measurements. Both internal pressure generated by the growth of the aliphatic layer and the applied external pressure effects are compared and discussed in the context of fine-tuning modulation of SCO properties. Spin crossover ; Cooperativity ; Context (archaeology) ; Alkoxy group ; Monoclinic crystal system ; Ligand (biochemistry) ; Substituent ; Cationic polymerization Magnetism in coordination complexes ; Metal-Catalyzed Oxygenation Mechanisms ; Organic Light-Emitting Diodes Research
Authors: Mudliar, Swaroop Laxmi | Mudliar, Sai Shashank
Source:  (article, 2025-01-01)
Field: Materials Science — Materials Chemistry

Automating Chemistry Tasks Using Large Language Models (LLMs): A Stepwise Framework for Cheminformatics Cheminformatics ; Expert system ; Software ; Automation ; Language model Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Biomedical Text Mining and Ontologies
Authors: Qi Yang | Lihua Na | Liang Fang | Xiaohua Wang | Heng Liu | Chunyu Zhang | Xuequan Zhang
Source: SSRN Electronic Journal (preprint, 2025-01-01)
Field: Chemistry — Organic Chemistry

Synergistic N–P Coordination Enables Low-Melting, High-Crystallinity Syndiotactic 1,2-Polybutadienes Via Iron-Based Catalyst Crystallinity ; Catalysis ; Tacticity ; Materials science ; Chemical engineering ; Polymer chemistry ; Chemistry ; Crystallography ; Polymer ; Organic chemistry ; Composite material ; Polymerization ; Engineering Organometallic Complex Synthesis and Catalysis ; Asymmetric Hydrogenation and Catalysis ; Catalytic Alkyne Reactions
Authors: Gerardo Salinas | Rana Nakar | Getnet Kassahun | Jochen Lang | Matthieu Raoux | Damien Thuau | Mamatimin Abbas | Eric Cloutet | Alexander Kuhn
Source: Physical Chemistry Chemical Physics (article, 2025-12-12)
Field: Chemistry — Organic Chemistry

Smartphone light-driven electrocatalytic polymerization of thiophenes Herein, we take advantage of the photoelectric effect produced on light-emitting diodes to induce a kinetically controlled electrocatalytic polymerization of 3,4-alkoxythiophenes. Wireless polymerization was achieved by fine-tuning the irradiation time, the power density and the molecular structure of the thiophenes. A smartphone based light-driven system is introduced as a simple and low cost polymerization approach to π-conjugated films. Polymerization ; Polymer ; Diode ; Catalysis ; Irradiation ; Photoelectric effect Radical Photochemical Reactions ; Photopolymerization techniques and applications ; Conducting polymers and applications
Authors: Grace Robertson | Adam Jaffe
Source: Dalton Transactions (article, 2025-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Structural and electronic tuning of hybrid metal thiocyanate <i>N</i>-oxides Hybrid metal thiocyanates are highly tailorable materials isolable under mild synthetic conditions. By varying pyridine-<i>N</i>-oxide derivatives within manganese, cobalt, and nickel congeners, we show fine-tuning of structural and electronic features depending on molecular substituent and metal selection, providing a roadmap for application-specific customization and potential property-tuning. Substituent ; Thiocyanate ; Nickel ; Metal ; Electronic structure ; Electronic effect Organic and Molecular Conductors Research ; Magnetism in coordination complexes ; Perovskite Materials and Applications
Authors: Harminder Pal Singh
Source: Communications on Applied Nonlinear Analysis (article, 2025-04-24)
Field: Materials Science — Biomaterials

Nanofibers: Transforming Drug Delivery with Innovation Polymer have garnered significant interest owing to their exceptional properties, including a large surface area, high porosity, small pore size, robust mechanical strength and the ability to incorporate surface functionalities. Among the techniques for producing nanofibers, electro spinning stands out due to its simplicity, versatility, and cost-effectiveness. Electrospun polymer nanofibers particularly significant in biomedical applications, acting as carriers for the controlled delivery of bioactive molecules like cytokines, growth factors, anticancer drugs, enzymes and vitamins. The ability to fine-tune the physical and chemical properties of nanofibers enables precise control over drug release profiles, enhancing therapeutic outcomes while minimizing side effects. Their high porosity and large surface area enhance drug loading capacity and ensure effective diffusion. Applications of polymer nanofibers extend beyond drug delivery to include tissue engineering, wound dressings, filtration membranes and energy storage devices. Their versatility and potential for innovation make polymer nanofibers a cornerstone of advanced material science. The fabrication of nanofibers employs techniques such as, electro spinning, phase separation, template synthesis and self-assembly. Electro spinning, the most prevalent method, uses an electric field to draw polymer solutions into continuous nanofibers. Critical parameters influencing this process include polymer concentration, solution viscosity, applied voltage, flow rate and environmental factors like humidity and temperature. These parameters directly impact fiber morphology, diameter and uniformity. This article provides an overview of nanofibers, highlighting the various fabrication techniques, methods for their characterization, the key parameters influencing the electro spinning process and their diverse applications. Nanofiber ; Drug delivery ; Drug ; Business ; Nanotechnology ; Materials science ; Pharmacology ; Medicine Electrospun Nanofibers in Biomedical Applications
Authors: Stewart P. Lewis
Source: Topics in Catalysis (article, 2025-01-09)
Field: Chemistry — Organic Chemistry

Developments in the Catalytic Cationic Polymerization of Olefins Cationic polymerization ; Polymerization ; Commercialization ; Olefin polymerization ; Chemistry ; Electrophile ; Catalysis ; Polymer ; Polymer science ; Organic chemistry ; Political science ; Law Organometallic Complex Synthesis and Catalysis ; Synthetic Organic Chemistry Methods ; Carbon dioxide utilization in catalysis
Authors: Bowen Mou | Rongliang Lou
Source: ChemRxiv (article, 2025-11-04)
Field: Materials Science — Materials Chemistry

ChemReactLLM: A Multimodal Large Language Model for Catalyst-Driven Organic Reaction Prediction and Optimization Interpretability ; Embedding ; Generalization ; Process (computing) ; Selection (genetic algorithm) ; Block (permutation group theory) ; Yield (engineering) ; Language model Machine Learning in Materials Science ; Asymmetric Hydrogenation and Catalysis ; Catalysis and Oxidation Reactions
Authors: Judah Immanuel | Avik Mahata
Source: Integrating materials and manufacturing innovation (article, 2025-11-14)
Field: Materials Science — Materials Chemistry

Enhancing Materials Data Workflows Through Object-Oriented Design and Large Language Models Workflow ; Robustness (evolution) ; Scalability ; Modular design ; Cosine similarity ; Embedding ; Software ; Process (computing) Machine Learning in Materials Science ; Additive Manufacturing Materials and Processes ; Advanced Materials Characterization Techniques
Authors: Ivana Đorđević | Sonja Grubišić | Dragana Mitić | Dragan M. Popović | Nemanja Trišović
Source: Journal of the Serbian Chemical Society (article, 2025-01-01)
Field: Materials Science — Materials Chemistry

Tuning crystal packing and reactivity through electrostatic and dispersion interactions: The case of phenytoin and its derivatives Hydantoin derivatives represent a versatile class of heterocycles, known for their pharmacological properties. Because drug efficacy often depends on the fine-tuning of weak intermolecular (non-covalent) interactions, analysis of the crystal structure of a drug molecule is important, as it enables deciphering its interaction profile. In this study, the crystal packing of phenytoin and its selected derivatives were examined through dimeric motifs with different recognition modes using force-field calculations and a density functional theory (DFT) approach. The relatively polar ethoxyacetyl group at the N3 position of the hydantoin ring, capable of forming hydrogen bonds, enhances the contribution of electrostatic and polar components to the total interaction energy. In contrast, the long alkyl chain promotes hydrophobic contacts, leading to dispersion forces dominating over electrostatic interactions. The reactivity of phenytoin and its derivatives were further evaluated by examining the influence of these substituents using conceptual density functional theory (CDFT) descriptors. These findings demonstrate that substituents significantly affect crystal packing and the balance of non-covalent interactions, providing valuable insights for optimizing molecular recognition and drug?target interactions in the design of new therapeutic agents. Density functional theory ; Intermolecular force ; Reactivity (psychology) ; London dispersion force ; Alkyl ; Crystal (programming language) ; Hydrogen bond ; Electrostatics ; Dispersion (optics) Crystallization and Solubility Studies ; Crystallography and molecular interactions ; X-ray Diffraction in Crystallography
Authors: Michael M. Lübtow | Marina Sokolski‐Papkov | Rainer Jordan | Robert Luxenhofer | Thomas Lorson | Malik Salman Haider | Alexander V. Kabanov | Daniel Nahm | Erik Wegener | Solomiia Borova
Source: UNC Libraries (article, 2025-10-14)
Field: Materials Science — Polymers and Plastics

Poly(2-oxazoline)s based biomaterials: A comprehensive and critical update Chemist ; Work (physics) ; Diversity (politics) Synthesis and properties of polymers ; biodegradable polymer synthesis and properties ; Silicone and Siloxane Chemistry
Authors: Hoang-Tinh Pham | Khanh-Thien Le | Giang T. Nguyen | Hieu Tran‐Van
Source: World Journal of Microbiology and Biotechnology (article, 2025-11-18)
Field: Materials Science — Biomaterials

Preparation of diatom frustules incorporated with protein A-fused C-terminal silica-binding peptide and interpenetrating polymer network for targeted drug delivery Diatom ; Drug delivery ; Carboxymethyl cellulose ; Mesoporous silica ; Peptide ; Polymer ; Conjugate ; Escherichia coli Diatoms and Algae Research ; Algal biology and biofuel production ; Glycosylation and Glycoproteins Research
Authors: Paul E. Calzada | Zahin Ibnat | Tanvir Rahman | Kamal Kandula | Danyu Lu | Sujan Kumar Saha | Farimah Farahmandi | Mark Tehranipoor
Source: ArXiv.org (preprint, 2025-07-09)
Field: Materials Science — Materials Chemistry

VerilogDB: The Largest, Highest-Quality Dataset with a Preprocessing Framework for LLM-based RTL Generation Large Language Models (LLMs) are gaining popularity for hardware design automation, particularly through Register Transfer Level (RTL) code generation. In this work, we examine the current literature on RTL generation using LLMs and identify key requirements for training and fine-tuning datasets. We construct a robust Verilog dataset through an automated three-pronged process involving database (DB) creation and management with PostgreSQL, data collection from code hosting sites like OpenCores and GitHub, and data preprocessing to verify the codes' syntax, run logic synthesis, and extract relevant module metadata. We implement a scalable and efficient DB infrastructure to support analysis and detail our preprocessing pipeline to enforce high-quality data before DB insertion. The resulting dataset comprises 20,392 Verilog samples, 751 MB of Verilog code data, which is the largest high-quality Verilog dataset for LLM fine-tuning to our knowledge. We further evaluate the dataset, address associated challenges, and explore potential applications for future research and development in LLM-based hardware generation. Verilog ; Preprocessor ; Pipeline (software) ; Scalability ; Data pre-processing ; Construct (python library) ; Process (computing) Machine Learning in Materials Science ; Embedded Systems Design Techniques ; Parallel Computing and Optimization Techniques
Authors: Eduarda Conceição Ferreira | Álefi Marques Lopes da Silva | Mercês Coelho da Silva | Marcos Roberto de Abreu Alves
Source: Synthetic Metals (article, 2025-10-05)
Field: Materials Science — Polymers and Plastics

Copolymers derived from 3-hexylthiophene and 3-methoxythiophene as potential active layers for polymeric electrochromic devices Electrochromism ; Copolymer ; Monomer ; Electrochromic devices ; Polymer ; Thermal stability ; Absorption (acoustics) Conducting polymers and applications ; Transition Metal Oxide Nanomaterials ; Organic Electronics and Photovoltaics
Authors: Hikaru Abe (704539) | Kazushige Sasaki (361426) | Chiharu Sakashita (22783684) | Shunsuke Watanabe (3689113) | Hidetoshi Noda (1616629) | Takumi Watanabe (704540) | Masakatsu Shibasaki (704542)
Source: Figshare (article, 2025-12-04)
Field: Chemistry — Organic Chemistry

Catalytic AsymmetricBenzoin Condensation for theSynthesis of Natural Products and Their Analogs Catalytic enantioselective benzoin condensation conditions that are potentially useful for the total synthesis of cycloimidamicins and structure–activity relationship studies of these natural products were developed. A triazole-based NHC catalyst promoted the transformation to afford the cyclization products. To make the reactions applicable to substrates with complex structural features, a Lewis acidic additive, B(OMe)Et<sub>2</sub>, was used, but fine-tuning of the base and solvent conditions was required to attain a good chemical yield and excellent enantioselectivity. These conditions showed a broad substrate scope and were not limited to substrates useful for the synthesis of cycloimidamicins and their related compounds. This study also clearly demonstrates the utility of N-heterocyclic carbene organocatalysts that have not been reported to exhibit perfect enantioselectivity in intramolecular benzoin condensation. Benzoin ; Catalysis ; Enantioselective synthesis ; Yield (engineering) ; Substrate (aquarium) ; Intramolecular force ; Carbene ; Condensation N-Heterocyclic Carbenes in Organic and Inorganic Chemistry ; Cyclopropane Reaction Mechanisms ; Asymmetric Synthesis and Catalysis