jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Debjyoti Bhattacharya | Wesley F. Reinhart | Michael A. Hickner | Harrison J. Cassady
Source: OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (article, 2024-05-03)
Field: Materials Science — Materials Chemistry

Dataset for "Large Language Models as molecular design engines" claude-gpt-paper.zip :This dataset contains data and results associated with the paper "Large Language Models as molecular designengines" The paper investigates the use of large language models, specifically Claude 3 Opus, for generating and analyzing chemical structures based on various prompts from A-H (as mentioned in the manuscript), and guided design related to electron-withdrawing groups (EWG), electron-donating groups (EDG). The dataset includes: PM7 MOPAC energy calculations for generated molecules, along with their SMILES representations and molecule IDs. PM7-calculated charges for the generated molecules. Output files from the Claude 3 Opus language model for each prompt category along. Original dataset (subset of ZINC database) used to build common keys and the initial design space. JSON file containing common keys for featurizing unknown SMILES. PCA object to convert molecule embeddings to 3-dimensional embeddings. The data is organized into the following folders: pm7_charge_results: Contains HOMO-LUMO energy differences for plotting. pm7_charge_calculation: Contains PM7 MOPAC energy calculations and charges. out: Contains output files from the Claude 3 Opus language model. fact-dropbox: Contains the original dataset, common keys, and PCA object file. The data can be used to reproduce the results presented in the paper and serve as a foundation for further research in this area. For a detailed description of the folder structure and contents, please refer to the File_descriptions.md file included in the dataset.2. llm-visulizer-dashapp.zipThis is the code for the visualizer app for viewing the molecules generated by the LLM. The README.md file has details about running the app. 3. claude-gpt-paper-codes.zip This contains the notebook GPT_modification_just_plots.ipynb for plotting, and other codes. The README.md file has details about running the main notebook for getting the plots. Computer science ; Natural language processing Machine Learning in Materials Science
Authors: Rajendran Lakshmi Priya | Sundaram Ganesh Babu
Source: Sustainable materials and technologies (article, 2024-12-22)
Field: Chemistry — Organic Chemistry

Porous activated carbon from waste chili pedicle encapsulating Cu2O nanoparticles with fine-tuned morphologies: A custom-designed catalyst for friedel-crafts arylation reactions Catalysis ; Nanoparticle ; Porosity ; Friedel–Crafts reaction ; Materials science ; Activated carbon ; Carbon fibers ; Chemical engineering ; Nanotechnology ; Composite number ; Composite material ; Chemistry ; Organic chemistry ; Adsorption ; Engineering Nanomaterials for catalytic reactions ; Catalytic Cross-Coupling Reactions ; Catalysis for Biomass Conversion
Authors: Jia‐Fu Yin | Wei Liu‐Fu | Junsheng Yang | Yuyan Lai | Binghui Xue | Haiyan Xiao | Qing‐Yun Guo | Yuchu Liu | Panchao Yin
Source: The Journal of Physical Chemistry Letters (article, 2024-04-12)
Field: Materials Science — Materials Chemistry

Exploration of Molecular Nanoparticles as Soft Structural Materials and Their Structure–Property Relationship The search for alternative chemical systems other than polymers with chain topologies for soft structural materials raises general interests in fundamental materials and chemical sciences. It is also appealing from an engineering perspective for the urgent need to resolve the typical trade-offs of polymer systems. Herein, a subnanometer molecular cluster, polyhedral oligomeric silsesquioxanes, is assembled into molecular nanoparticles (MNPs) with star topology. Broadly tunable viscoelasticity can be realized by fine-tuning the MNPs' deformability. Being analogous to polymeric systems, the hierarchical structural relaxation dynamics can be observed, and their relaxation time and temperature dependence are dominated by the linker flexibilities. This not only provides microscopic understanding on MNP's unique viscoelasticity but also offers enormous opportunities for modulating their mechanical properties via linker engineering. Our work proves the possibility of applying structural units with particle topologies for the design of soft structural materials. Viscoelasticity ; Materials science ; Nanotechnology ; Polymer ; Nanoparticle ; Relaxation (psychology) ; Topology (electrical circuits) ; Network topology ; Linker ; Cluster (spacecraft) ; Molecular dynamics ; Stress relaxation ; Molecular engineering ; Computer science ; Chemistry ; Composite material ; Computational chemistry ; Engineering Silicone and Siloxane Chemistry ; Supramolecular Chemistry and Complexes ; Luminescence and Fluorescent Materials
Authors: Oren Elishav | Ofir Blumer | T. Kyle Vanderlick | Barak Hirshberg
Source: The Journal of Chemical Physics (article, 2024-04-22)
Field: Materials Science — Materials Chemistry

The effect of ligands on the size distribution of copper nanoclusters: Insights from molecular dynamics simulations Controlling the size distribution in the nucleation of copper particles is crucial for achieving nanocrystals with desired physical and chemical properties. However, their synthesis involves a complex system of solvents, ligands, and copper precursors with intertwining effects on the size of the nanoclusters. We combine molecular dynamics simulations and density functional theory calculations to provide insights into the nucleation mechanism in the presence of a triphenyl phosphite ligand. We identify the crucial role of the strength of the metal-phosphine interaction in inhibiting the cluster's growth. We demonstrate computationally several practical routes to fine-tune the interaction strength by modifying the side groups of the additive. Our work provides molecular insights into the complex nucleation process of protected copper nanocrystals, which can assist in controlling their size distribution and, eventually, their morphology. Nucleation ; Nanoclusters ; Molecular dynamics ; Copper ; Chemical physics ; Cluster (spacecraft) ; Nanocrystal ; Materials science ; Density functional theory ; Nanotechnology ; Growth theory ; Cluster size ; Computational chemistry ; Chemistry ; Metallurgy ; Organic chemistry ; Computer science Nanocluster Synthesis and Applications ; nanoparticles nucleation surface interactions ; Gold and Silver Nanoparticles Synthesis and Applications
Authors: Yeqi Du | Jinbo Hu | Wenbo Wang | Xinyan Liu | Yanlong Liu | Ranlong Duan | Xinchao Bian | Xuesi Chen
Source: Macromolecules (article, 2024-12-09)
Field: Materials Science — Biomaterials

Highly Regioselective Ring-Opening Polymerization of an Asymmetric Diester Controlling the monomer sequence in hydroxy acid copolymers remains a significant challenge, yet it is essential for fine-tuning the properties of copolyesters. This study presents the regioselective ring-opening polymerization (ROP) of l-3-tert-butyl-6-methyl-1,4-dioxane-2,5-dione (l-tBMG), resulting in the synthesis of alternating polylactic acid-co-2-tert-butylglycolic acid copolymers. The process is facilitated by enantiomerically pure Schiff base aluminum catalysts featuring either a binaphthyl framework or a 2,2-dimethylpropylenediamine and 3,5-dichlorosalicylaldehyde framework. These catalysts promote regioselective ring-opening of the asymmetric cyclic diester specifically at the acyl-oxygen bond of the lactic acid moiety. The molecular chain structure of the resulting polymers was elucidated through heteronuclear multiple bond correlation spectroscopy, while chain regularity was assessed using 1H NMR and quantitative 13C NMR (q-13C NMR). According to the 1H NMR and q-13C NMR test results, the molecular chain regularity is about 0.93. Incorporation of 2-tert-butylglycolic acid units led to a glass transition temperature (Tg) of the random copolymer to 65 °C. Notably, the Tg of the isotactic polymer, synthesized via ROP catalyzed by the aforementioned catalysts, was further elevated to 70 °C. Regioselectivity ; Ring (chemistry) ; Polymerization ; Polymer chemistry ; Chemistry ; Ring-opening polymerization ; Polymer science ; Organic chemistry ; Polymer ; Catalysis biodegradable polymer synthesis and properties ; Advanced Polymer Synthesis and Characterization ; Carbon dioxide utilization in catalysis
Authors: Yuxi Liu | Peter W. McDonald | San H. Thang | Chris Ritchie
Source: Macromolecules (article, 2024-03-15)
Field: Chemistry — Organic Chemistry

Flavylium-Containing Stimuli-Responsive RAFT Polymers: Synthesis and Enhanced Stability Flavyliums are abundant naturally occurring, stimuli-responsive cationic chromophores found in anthocyanins that constitute the majority of red and blue pigments found in flora. While synthetic molecular derivatives have been devised to fine-tune these characteristics, the development of polymeric materials in this regard remains scarce. To address this, a flavylium-based methacrylamide derivative (FlavM-A1) was successfully synthesized, but its radical polymerization proved to be ineffective. To overcome this constraint, a convergent synthetic route for a series of flavylium-containing polymers was developed, employing reversible addition–fragmentation chain transfer (RAFT) polymerization followed by postmodification to install the flavylium chromophore. The flavylium-containing polymers described in this work exhibit improved hydrolytic stability in their flavylium moieties compared to the small-molecule FlavM-A1 while both possess interesting stimuli responsiveness and surfactant-like properties. Raft ; Polymer ; Reversible addition−fragmentation chain-transfer polymerization ; Chemistry ; Polymer science ; Polymer chemistry ; Chemical engineering ; Organic chemistry ; Copolymer ; Radical polymerization ; Engineering Advanced Polymer Synthesis and Characterization ; Supramolecular Chemistry and Complexes ; Silicone and Siloxane Chemistry
Authors: Supriya Sharma | Akhilesh Kumar | Rohan D. Erande
Source: ChemistrySelect (article, 2024-01-22)
Field: Chemistry — Organic Chemistry

Selective Functionalization of Indole: Synthesis of Bioinspired 2,2′‐thiobisindoles, 3‐substituted Oxindoles, and 1‐(chloromethyl) Indoline‐2‐dione in One‐pot manner Abstract Indolyl thioethers and indolin‐2‐one motifs are extremely common in pharmaceuticals and organic materials, therefore developing a method to create these scaffolds is considered to be a vital endeavour in the chemical sciences. Here we have reported a unified strategy developed by the fine‐tuning of catalyst‐solvent combination [SOCl 2 /AlCl 3 in CHCl 3 and SOCl 2 /DMSO (1 : 1) in CHCl 3 at 25 °C] towards selective functionalization of Indole to synthesize 2,2′‐thiobisindoles and 3‐chloro‐3‐alkyl substituted oxindoles selectively in one‐pot manner with good to satisfactory yield (52‐86 %; 26 Examples). In application, reactions of 3‐subsituted indole and isatin derivatives produced the 1‐(chloromethyl) indoline‐2,3‐diones by just changing the reaction condition (60 °C), which shows the synthetic utility of the developed method. Indoline ; Surface modification ; Indole test ; Biomimetic synthesis ; Chemistry ; Nanotechnology ; Combinatorial chemistry ; Materials science ; Organic chemistry Sulfur-Based Synthesis Techniques ; Chemical Synthesis and Reactions ; Synthesis and Catalytic Reactions
Authors: Mohammed A. Khuddus | Utreshwar Arjun Gavhane | M. Jayakannan
Source: ACS Polymers Au (article, 2024-07-17)
Field: Materials Science — Biomaterials

Structural Engineering of <scp>l</scp>-Aspartic Amphiphilic Polyesters for Enzyme-Responsive Drug Delivery and Bioimaging in Cancer Cells Design and development of amphiphilic polyesters based on bioresources are very important to cater to the ever-growing need for biodegradable polymers in biomedical applications. Here, we report structural engineering of enzyme-responsive amphiphilic polyesters based on l-amino acid bioresources and study their drug delivery aspects in the cancer cell line. For this purpose, an l-aspartic acid-based polyester platform is chosen, and two noncovalent forces such as hydrogen bonding and side-chain hydrophobic interactions are introduced to study their effect on the aqueous self-assembly of nanoparticles. The synthetic strategy involves the development of l-aspartic acid-based dimethyl ester monomers with acetal and stearate side chains and subjecting them to solvent-free melt polycondensation reactions to produce side-chain-functionalized polyesters in the entire composition range. Postpolymerization acid catalyst deprotection of acetal yielded hydroxyl-functionalized polyesters. Amphiphilicity of the polymer is carefully fine-tuned by varying the composition of the stearate and hydroxyl units in the polymer chains to produce self-assembly in water. Various drugs such as camptothecin (CPT), curcumin (CUR), and doxorubicin (DOX) and biomarkers like 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS), rose bengal (RB), and Nile red (NR) are successfully encapsulated in the polymer nanoparticles. Cytotoxicity of biodegradable polymer nanoparticles is tested in normal and breast cancer cell lines. The polymer nanoparticles are found to be highly biocompatible and delivered the anticancer drugs in the intracellular compartments of the cells. Polyester ; Amphiphile ; Chemistry ; Drug delivery ; Polymer ; Stearate ; Nile red ; Nanoparticle ; Organic chemistry ; Biodegradable polymer ; Combinatorial chemistry ; Polymer chemistry ; Materials science ; Nanotechnology ; Copolymer biodegradable polymer synthesis and properties ; Advanced Polymer Synthesis and Characterization ; Biopolymer Synthesis and Applications
Authors: Sanghoon Lee | Kevin Cruse | Samuel P. Gleason | A. Paul Alivisatos | Gerbrand Ceder | Anubhav Jain
Source: ChemRxiv (preprint, 2024-06-12)
Field: Materials Science — Materials Chemistry

Data-driven analysis of text-mined seed-mediated growth AuNP syntheses Gold nanoparticles (AuNPs) are widely used functional nanomaterials that exhibit adjustable properties based on their shapes and sizes. Creating a comprehensive dataset of AuNP syntheses is useful for understanding control over their shape and size. Here, we employed search-based algorithms and fine-tuned the Llama-2 large language model to extract 492 multi-sourced seed-mediated AuNP synthesis recipes from the literature. With this dataset which we share online, we verified that the seed capping agent type such as CTAB or citrate plays a crucial role in determining the morphology of the AuNPs, aligning with established findings in the field. We also observe a weak correlation between the final AuNR aspect ratio and silver concentration, although a large variance reduces the significance of this relationship. Overall, our work demonstrates the value of literature-based datasets for advancing knowledge in the field of nanomaterial synthesis for further exploration and better reproducibility. Nanomaterials ; Nanotechnology ; Colloidal gold ; Nanoparticle ; Variance (accounting) ; Computer science ; Field (mathematics) ; Materials science ; Mathematics Machine Learning in Materials Science
Authors: Agnideep Das | Oscar Charpentier | Cheriehan Hessin | Jules Schleinitz | David Pianca | Nolwenn Le Breton | Sylvie Choua | Laurence Grimaud | Christophe Gourlaouen | Marine Desage‐El Murr
Source: Angewandte Chemie International Edition (article, 2024-04-17)
Field: Chemistry — Organic Chemistry

Site‐Selective Radical Aromatic C−H Functionalization of Alloxazine and Flavin through Ground‐State Single Electron Transfer Flavins and their alloxazine isomers are key chemical scaffolds for bioinspired electron transfer strategies. Their properties can be fine-tuned by functional groups, which must be introduced at an early stage of the synthesis as their aromatic ring is inert towards post-functionalization. We show that the introduction of a remote metal-binding redox site on alloxazine and flavin activates their aromatic ring towards direct C-H functionalization. Mechanistic studies are consistent with a synthetic sequence involving ground-state single electron transfer (SET) with an electrophilic source followed by radical-radical coupling. This unprecedented reactivity opens new opportunities in molecular editing of flavins by direct aromatic post-functionalization and the utility of the method is demonstrated with the site-selective C6 functionalization of alloxazine and flavin with a CF<sub>3</sub> group, Br or Cl, that can be further elaborated into OH and aryl for chemical diversification. Chemistry ; Surface modification ; Electron transfer ; Flavin group ; Ground state ; Photochemistry ; Combinatorial chemistry ; Organic chemistry ; Physics Radical Photochemical Reactions ; Fluorine in Organic Chemistry ; Catalytic C–H Functionalization Methods
Authors: Yu Xin | Cosimo Ligorio | Maria O’Brien | Richard F. Collins | Siyuan Dong | Aline F. Miller | Alberto Saiani | Julie E. Gough
Source: Journal of Materials Chemistry B (article, 2024-01-01)
Field: Materials Science — Biomaterials

Effect of supramolecular peptide hydrogel scaffold charge on HepG2 viability and spheroid formation Supramolecular bioinspired self-assembling peptide hydrogel (SAPH) scaffolds represent a class of fully defined synthetic materials whose chemical and mechanical properties can be finely engineered. In this study, the relationship between SAPHs physicochemical properties and HepG2 cells viability, spheroid formation and function are discussed. We first report that negatively charged SAPHs promote hepatocyte proliferation and spheroids formation <i>in vitro</i> 3D culture while positively charged SAPHs lead to hepatocyte death irrespective of the hydrogel mechanical properties. More specifically HepG2 cultured in 3D in E(FKFE)<sub>2</sub> negatively charged SAPH maintained a differentiated phenotype and assembled into well-defined spheroids with strong cell-cell interactions. Furthermore, HepG2 spheroids responded to acetaminophen exposure with upregulation of key CYP450 enzymes expression clearly showing their potential for drug toxicity testing. These findings demonstrate how fine-tuned functional SAPH scaffolds can be used to identify key scaffolds parameters affecting cells. In this case we demonstrated the potential of negatively charged SAPHs for the 3D culture of HepG2 with potential applications in drug screening. Spheroid ; Scaffold ; Materials science ; Viability assay ; Supramolecular chemistry ; Self-healing hydrogels ; Peptide ; Biophysics ; Nanotechnology ; Chemical engineering ; Biomedical engineering ; Polymer chemistry ; Chemistry ; Crystallography ; Cell ; In vitro ; Biology ; Medicine ; Biochemistry ; Engineering Supramolecular Self-Assembly in Materials ; RNA Interference and Gene Delivery ; Pancreatic function and diabetes
Authors: Amruta Kulkarni | Gijs de Kort | Gerard Werumeus Buning | Richard Ensinck | Sanjay Rastogi
Source: European Polymer Journal (article, 2024-05-05)
Field: Materials Science — Polymers and Plastics

Flexible and rigid block copolymers from recyclable polyesters Copolymer ; Polyester ; Materials science ; Polymer science ; Block (permutation group theory) ; Polymer chemistry ; Chemical engineering ; Polymer ; Composite material ; Engineering ; Mathematics Polymer crystallization and properties ; biodegradable polymer synthesis and properties ; Polymer Nanocomposites and Properties
Authors: Papri Sutar | Iván Maisuls | Zulema Fernández | Cristian A. Strassert | Gustavo Fernández
Source: Chemistry - A European Journal (article, 2024-09-24)
Field: Chemistry — Inorganic Chemistry

Pathway‐dependent Metallosupramolecular Polymerization Regulated by Ligand Geometry Understanding structure/property correlations in self-assembly is a key but challenging requirement for developing functional materials. Herein, we explore the importance of ligand geometry to fine-tune photophysical properties (MMLCT vs. MLCT excited states) and self-assembly pathways in metallosupramolecular polymerization. To this end, we have designed two hydrophobic Pt(II) complexes, 1 and 2, containing a π-extended bidentate bipyridine ligand with different substitution pattern, resulting in different molecular geometries (linear vs. V-shaped). Detailed comparative studies revealed significant differences for both complexes in terms of their photophysical properties and self-assembly pathways in non-polar media. The V-shaped topology of 1 enables facile face-to-face molecular stacking with a certain curvature leading to luminescent spherical assemblies exhibiting MMLCT states and short Pt⋅⋅⋅Pt contacts via a single-step cooperative pathway. On the other hand, the higher preorganized linear topology of complex 2 induces a two-step competitive self-assembly process leading to the formation of one-dimensional supramolecular polymers with slipped packing and MLCT-originated emission. Our findings broaden the monomer scope for supramolecular polymerization and provide design guidelines for the realization of luminescent supramolecular assemblies. Supramolecular chemistry ; Stacking ; Polymerization ; Ligand (biochemistry) ; Monomer ; Self-assembly ; Coordination polymerization ; Luminescence ; Materials science ; Topology (electrical circuits) ; Excited state ; Denticity ; Polymer ; Chemistry ; Crystallography ; Nanotechnology ; Crystal structure ; Radical polymerization ; Physics ; Organic chemistry Metal-Organic Frameworks: Synthesis and Applications ; Luminescence and Fluorescent Materials ; Supramolecular Chemistry and Complexes
Authors: Griffen Desroches | Carl J. Thrasher | Nicholas Diaco | Ibrahim O. Raji | Dominik Konkolewicz | A. John Hart | Robert J. Macfarlane
Source: ACS Materials Letters (article, 2024-08-15)
Field: Materials Science — Polymers and Plastics

Multivalent Polymer-Grafted Nanoparticles as Reinforcing Fillers for 3D Printable Self-Healing Elastomers 3D printable elastomers capable of self-healing are attractive for fabricating complex biomimetic and soft-robotic devices. While polymer network reorganization can be enabled with dynamic bond exchange, this strategy typically faces intrinsic trade-offs between healability, processability, and mechanical performance. Thus, new material design strategies that can overcome these trade-offs are needed. Here, we report the use of multivalent polymer-grafted nanoparticles (PGNPs) as reinforcing fillers for self-healing photoresins. As each nanoparticle is functionalized with thousands of polymer chains engaging in multivalent interactions with the surrounding elastomeric matrix, the bulk modulus of the composite can be increased without impairing the local segmental motion of polymer chains necessary for self-healing. We also examine PGNP structural parameters to establish structure–property relationships that permit fine-tuning of composite mechanical performance. Finally, these enhancements do not impair the materials’ manufacturability, as they can be used as feedstocks for digital light printing to produce complex and high-resolution 3D objects. Elastomer ; Materials science ; Polymer ; Self-healing ; Nanoparticle ; Composite number ; Composite material ; Nanotechnology ; Self-healing material ; 3D printing ; Design for manufacturability ; Mechanical engineering Polymer composites and self-healing ; Advanced Polymer Synthesis and Characterization ; Advanced Sensor and Energy Harvesting Materials