jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Robert M. Hazen | Peter C. Burns | Henderson James Cleaves | Robert T. Downs | Sergey V. Krivovichev | Michael L. Wong
Source: Journal of The Royal Society Interface (article, 2024-02-01)
Field: Materials Science — Materials Chemistry

Molecular assembly indices of mineral heteropolyanions: some abiotic molecules are as complex as large biomolecules Molecular assembly indices, which measure the number of unique sequential steps theoretically required to construct a three-dimensional molecule from its constituent atomic bonds, have been proposed as potential biosignatures. A central hypothesis of assembly theory is that any molecule with an assembly index ≥15 found in significant local concentrations represents an unambiguous sign of life. We show that abiotic molecule-like heteropolyanions, which assemble in aqueous solution as precursors to some mineral crystals, range in molecular assembly indices from 2 for H<sub>2</sub>CO<sub>3</sub> or Si(OH)<sub>4</sub> groups to as large as 21 for the most complex known molecule-like subunits in the rare minerals ewingite and ilmajokite. Therefore, values of molecular assembly indices ≥15 do not represent unambiguous biosignatures. Molecule ; Biomolecule ; Chemistry ; Abiotic component ; Mineral ; Aqueous solution ; Nanotechnology ; Materials science ; Physical chemistry ; Organic chemistry ; Biology Polyoxometalates: Synthesis and Applications ; Radioactive element chemistry and processing ; Chemical Synthesis and Characterization
Authors: Erika Rodríguez‐Sevilla | Jonathan U Álvarez-Martínez | Rigoberto Castro‐Beltrán | Eden Morales‐Narváez
Source: Advanced Science (article, 2024-04-06)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Flexible 3D Plasmonic Web Enables Remote Surface Enhanced Raman Spectroscopy Nanoplasmonic materials concentrate light in specific regions of dramatic electromagnetic enhancement: hot spots. Such regions can be employed to perform single molecule detection via surface-enhanced Raman spectroscopy. However, this phenomenon is challenging since hot spots are expected to be highly intense/abundant and positioning of molecules within such hot spots is crucial to manage with ultrasensitive SERS. Herein, it is discovered that a 3D plasmonic web embedded within a biohybrid (3D-POWER) exhibits plasmonic transmission, spontaneously absorbs the analyte, and meets these so much needed criteria in ultrasensitive SERS. 3D-POWER is built with nanopaper and self-assembled layers of graphene oxide and gold nanorods. According to in silico experiments, 3D-POWER captures light in a small region and performs plasmonic field transmission in a surrounding volume, thereby activating a plasmonic web throughout the simulated volume. The study also provides experimental evidence supporting the plasmonic field transport ability of 3D power, which operates as a SERS signal carrier (even beyond the apparatus field of view), and the ultrasensitive behavior of this ecofriendly and flexible material facilitating yoctomolar limit of detection. Besides, 3D-POWER is proven useful in food and biofluids analysis. It is foreseen that 3D-POWER can be employed as a valuable platform in (bio)analytical applications. Plasmon ; Surface-enhanced Raman spectroscopy ; Materials science ; Raman spectroscopy ; Nanotechnology ; Nanorod ; Plasmonic nanoparticles ; Graphene ; Optoelectronics ; Optics ; Raman scattering ; Physics Gold and Silver Nanoparticles Synthesis and Applications ; Plasmonic and Surface Plasmon Research ; Orbital Angular Momentum in Optics
Authors: Emmanuel Israel Edache | Adebiyi Adedayo | Hadiza Adamu Dawi | Fabian Audu Ugbe
Source: Discover Chemistry. (article, 2024-10-02)
Field: Chemistry — Organic Chemistry

Drug-like screening, molecular docking, molecular dynamics simulations, and binding free energies on the interaction of pyrazole derivatives as inhibitors of lysosomal storage disorders and anticancer activity Abstract Lysosomal membrane proteins (LAMPs) are a primary target for treating tumors because of their essential role in the cancer life cycle. In this study, some computational approaches, including drug-like screening, molecular docking, and molecular dynamics (MD) simulation studies coupled with the binding free energy, have been conducted to explore the putative binding modes of pyrazole derivatives as inhibitors of lysosomal storage disorders. Certain pyrazole derivatives outperformed typical medications in molecular docking experiments against the LAMPs receptor; among other substances, molecules CID 44555488 and 45,487,645 were deemed ideal. Additionally, these ligands (CID 44555488 and 45,487,645) were projected to be orally accessible in humans after successfully passing five separate drug-likeness criteria. In the end, it was anticipated that these ligands, CID 44555488 and 45,487,645, would have minimal human toxicity and good ADMET properties, particularly in terms of GI absorption and the lack of P-gp interaction. Compounds CID 44555488 and 45,487,645 with high predicted binding affinities were subjected to further molecular dynamics simulations based on the molecular docking data, and their potential binding mechanisms were investigated. The study's description of the structure-based drug design approach will be very helpful in the creation of novel inhibitors with excellent selectivity and potency. Pyrazole ; Docking (animal) ; Molecular dynamics ; Drug ; Chemistry ; Anticancer drug ; Molecular binding ; Pharmacology ; Combinatorial chemistry ; Stereochemistry ; Computational chemistry ; Medicine ; Molecule ; Organic chemistry Synthesis and biological activity ; Research on Leishmaniasis Studies ; Synthesis and Reactivity of Heterocycles
Authors: Joseph Dodd‐o | Abhishek Roy | Zain Siddiqui | Roya Jafari | Francesco Coppola | Santhamani Ramasamy | Afsal Kolloli | Dilip Kumar | Soni Kaundal | Boyang Zhao | Ranjeet Kumar | Alicia S. Robang | Jeffrey Li | Abdul‐Rahman Azizogli | Varun Pai | Amanda M. Acevedo‐Jake | Corey Heffernan | Alexandra Lucas | Andrew C. McShan | Anant K. Paravastu | B. V. Venkataram Prasad | Selvakumar Subbian | Petr Král | Vivek Kumar
Source: Nature Communications (article, 2024-02-07)
Field: Materials Science — Biomaterials

Antiviral fibrils of self-assembled peptides with tunable compositions The lasting threat of viral pandemics necessitates the development of tailorable first-response antivirals with specific but adaptive architectures for treatment of novel viral infections. Here, such an antiviral platform has been developed based on a mixture of hetero-peptides self-assembled into functionalized β-sheets capable of specific multivalent binding to viral protein complexes. One domain of each hetero-peptide is designed to specifically bind to certain viral proteins, while another domain self-assembles into fibrils with epitope binding characteristics determined by the types of peptides and their molar fractions. The self-assembled fibrils maintain enhanced binding to viral protein complexes and retain high resilience to viral mutations. This method is experimentally and computationally tested using short peptides that specifically bind to Spike proteins of SARS-CoV-2. This platform is efficacious, inexpensive, and stable with excellent tolerability. Fibril ; Chemistry ; Nanotechnology ; Biophysics ; Materials science ; Biochemistry ; Biology Supramolecular Self-Assembly in Materials ; Monoclonal and Polyclonal Antibodies Research ; Influenza Virus Research Studies
Authors: A. Owens | S. N. Yurchenko | Jonathan Tennyson
Source: Monthly Notices of the Royal Astronomical Society (article, 2024-04-23)
Field: Chemistry — Organic Chemistry

ExoMol line lists – LVIII. High-temperature molecular line list of carbonyl sulphide (OCS) ABSTRACT A new molecular line list covering wavelengths λ &amp;gt; 1 μm (the 0–10 000 cm−1 range) for the main isotopologue of carbonyl sulphide 16O12C32S is presented. The OCS line list, named OYT8, contains almost 2.5 billion transitions between 2.4 million rotation-vibration energy levels with the total angular momentum up to J = 223. It is suitable for high-temperature environments up to T = 2000 K. Line list calculations were performed with the variational nuclear motion code trove in conjunction with a highly accurate, empirically refined potential energy surface and a newly computed ab initio dipole moment surface of OCS. The OYT8 line list is adapted for high-resolution applications by replacing computed energy levels with empirically derived values of OCS where available. Comparisons of the OYT8 line list with other OCS line lists and spectra yields excellent agreement for both strong and weak spectroscopic bands. The increased coverage of the OYT8 line list and the many new spectral features that are available will greatly facilitate the future observation of OCS on exoplanets. Carbonyl sulphide joins a growing number of sulphur-bearing molecules available from the ExoMol database. The OYT8 line list along with the associated temperature- and pressure-dependent molecular opacities can be downloaded from www.exomol.com and the CDS astronomical database. Physics ; Line (geometry) ; Astrophysics ; Geometry Chemical Thermodynamics and Molecular Structure ; Gas Sensing Nanomaterials and Sensors ; Thermal and Kinetic Analysis
Authors: Zhiqiang Li | Haoyu Dong | Jian Wang | Linhua Liu | Jia‐Yue Yang
Source: International Journal of Heat and Mass Transfer (article, 2024-03-07)
Field: Materials Science — Materials Chemistry

Active learning molecular dynamics-assisted insights into ultralow thermal conductivity of two-dimensional covalent organic frameworks Thermal conductivity ; Phonon ; Materials science ; Molecular dynamics ; Chemical physics ; Covalent organic framework ; Thermodynamics ; Computational chemistry ; Condensed matter physics ; Chemistry ; Physics ; Composite material Covalent Organic Framework Applications ; Thermal properties of materials ; Graphene research and applications
Authors: Adam P. Generale | Andreas E. Robertson | Conlain Kelly | Surya R. Kalidindi
Source: Acta Materialia (article, 2024-04-01)
Field: Materials Science — Materials Chemistry

Inverse stochastic microstructure design Curse of dimensionality ; Uncertainty quantification ; Computer science ; Inference ; Inverse problem ; Gaussian process ; Microstructure ; Inverse ; Modular design ; Mathematical optimization ; Gaussian ; Bayesian inference ; Algorithm ; Applied mathematics ; Theoretical computer science ; Bayesian probability ; Materials science ; Artificial intelligence ; Machine learning ; Mathematics ; Mathematical analysis ; Physics Machine Learning in Materials Science ; Advanced Multi-Objective Optimization Algorithms ; Topology Optimization in Engineering
Authors: Ki Yan Lam | Choy Sin Lee | Rachel Yie Hang Tan
Source: RSC Advances (review, 2024-01-01)
Field: Materials Science — Polymers and Plastics

NIR-induced photothermal-responsive shape memory polyurethane for versatile smart material applications Stimuli responsiveness has been an attractive feature of smart material design, allowing the chemical and physical properties of the materials to change in response to small environmental variations. The versatile shape memory polyurethane (SMPU) has been advanced into thermally-responsive SMPU, enabling its use in neurovascular stents, smart fibers for compression garments, and thermal-responsive components for aircraft and aerospace structures. While thermally-induced SMPU materials exhibit excellent shape recovery and fixity, they encounter limitations such as long response times, energy-intensive heating processes, and potential damage to heat-sensitive components, hindering their wide application. Thus, SMPU has further advanced into a photothermal-responsive material by incorporating photothermal agents into the polymer matrix, offering faster response times, compatibility with heat-sensitive materials, and enhanced mechanical properties, expanding the versatility and applicability of shape memory technology. This review focuses on the classes of NIR-induced photothermal agent used in SMPU systems, their synthesis methods, and photothermal-responsive mechanism under NIR-light, which offers a dual responsiveness to the host SMPU. The advantages and limitations of NIR-induced photothermal SMPU are reviewed, and challenges in their development are discussed. Polyurethane ; Photothermal therapy ; Shape-memory alloy ; Smart material ; Materials science ; Nanotechnology ; Photothermal effect ; Composite material Polymer composites and self-healing ; Polydiacetylene-based materials and applications ; Photochromic and Fluorescence Chemistry
Authors: Hossein Omidian | Renae L. Wilson
Source: Journal of Composites Science (article, 2024-05-29)
Field: Materials Science — Biomaterials

Enhancing Hydrogels with Quantum Dots This manuscript explores the interdisciplinary integration of quantum dot–hydrogel composites and smart materials and their applications across a spectrum of fields, including biomedical engineering, environmental sensing, and energy harvesting. It covers the synthesis of novel materials like fluorescent hydrogel nanocomposites that display enhanced chemical stability, mechanical strength, and thermal resistance, highlighting their utility in environmental monitoring and catalysis. In the biomedical sector, innovations include hydrogel composites for targeted drug delivery and advanced therapies such as photothermal DNA hydrogels for tumor treatment. This review also discusses the application of these materials in imaging, diagnostics, and the development of smart sensors capable of detecting various biological and environmental changes. Its scope further extends to optoelectronics and the design of energy-efficient systems, underscoring the versatile functionalities of hydrogels in modern technological applications. Challenges remain in scaling up these technologies for commercial use and ensuring their long-term stability and safety, necessitating future research focused on sustainable, scalable solutions that can be integrated into existing systems. Self-healing hydrogels ; Quantum dot ; Nanotechnology ; Materials science ; Psychology ; Polymer chemistry Supramolecular Self-Assembly in Materials ; Hydrogels: synthesis, properties, applications ; Advanced Materials and Mechanics
Authors: Kaiyue Sun | Juxing Zeng | Ya Liu | Zhuoheng Zhou | Jikai Chen | Jiawei Chen | Xiangyu Huang | Fan Gao | Xin Wang | Xintong Zhang | Xiaofei Wang | Sebastiaan Eeltink | Bo Zhang
Source: Angewandte Chemie International Edition (article, 2024-10-18)
Field: Materials Science — Materials Chemistry

Microfluidic Precision Manufacture of High Performance Liquid Chromatographic Microspheres A key bottleneck in developing chromatographic material is the chemically entangled control of morphology, pore structure, and material chemistry, which holds back precision material manufacture in order to pursue advanced separation performance. In this work, a precision manufacture strategy based on droplet microfluidics was developed, for production of highly efficient chromatographic microspheres with independent control over particle morphology, pore structure and material chemistry. The droplet-synthesized microspheres display extremely narrow particle size distribution (CV<3 %), enabling a 100 % production yield due to complete elimination of sieving steps. More importantly, the size of the droplet-synthesized microspheres is freely adjustable without the need for re-optimizing chemical recipes or reaction conditions. The resulting materials exhibit excellent separation efficiencies, achieving a reduced plate height of h<sub>min</sub>=1.67. This precision manufacture strategy also allows for flexible pore design and continuous pore size adjustment across three orders of magnitudes, providing a novel vehicle for resolution fine-tuning targeting protein separation. Besides traditional silica, organic-inorganic hybrid silica, zirconia, and titania microspheres can also be precisely synthesized on the same platform, supporting various separation applications and operating conditions. Powered by precision manufacture, super-throughput production, and versatile chemistry, the high-performance droplet-synthesized separation material will pave the way towards green and precision chromatographic industry. Microfluidics ; Bottleneck ; Microsphere ; Nanotechnology ; Dispersity ; Materials science ; Particle (ecology) ; Throughput ; Particle size ; Resolution (logic) ; Yield (engineering) ; Process engineering ; Chemical engineering ; Computer science ; Composite material ; Polymer chemistry Mesoporous Materials and Catalysis ; Innovative Microfluidic and Catalytic Techniques Innovation ; Glycosylation and Glycoproteins Research
Authors: Xiaokang Wang | Hongyan Liu | Meng Sun | Haoyang Wang | Xueying Feng | Wenmiao Chen | Xiang Feng | Weidong Fan | Daofeng Sun
Source: ACS Applied Materials & Interfaces (article, 2024-02-01)
Field: Chemistry — Inorganic Chemistry

Thiadiazole-Functionalized Th/Zr-UiO-66 for Efficient C<sub>2</sub>H<sub>2</sub>/CO<sub>2</sub> Separation Adsorptive separation technology provides an effective approach for separating gases with similar physicochemical properties, such as the purification of acetylene (C<sub>2</sub>H<sub>2</sub>) from carbon dioxide (CO<sub>2</sub>). The high designability and tunability of metal-organic framework (MOF) adsorbents make them ideal design platforms for this challenging separation. Herein, we employ an isoreticular functionalization strategy to fine-tune the pore environment of Zr- and Th-based UiO-66 by the immobilization of the benzothiadiazole group via bottom-up synthesis. The functionalized UPC-120 exhibits an enhanced C<sub>2</sub>H<sub>2</sub>/CO<sub>2</sub> separation performance, which is confirmed by adsorption isotherms, dynamic breakthrough curves, and theoretical simulations. The synergy of ligand functionalization and metal ion fine-tuning guided by isoreticular chemistry provides a new perspective for the design and development of adsorbents for challenging gas separation processes. Materials science ; Adsorption ; Surface modification ; Metal-organic framework ; Gas separation ; Acetylene ; Chemical engineering ; Ligand (biochemistry) ; Metal ; Nanotechnology ; Organic chemistry ; Membrane ; Chemistry Metal-Organic Frameworks: Synthesis and Applications ; Covalent Organic Framework Applications ; Membrane Separation and Gas Transport
Authors: Gayane Chilingaryan | Hovhannes Tamoyan | Ani Tevosyan | Nelly Babayan | Karen Hambardzumyan | Zaven Navoyan | Armen Aghajanyan | Hrant Khachatrian | Lusine Khondkaryan
Source: Journal of Chemical Information and Modeling (article, 2024-07-26)
Field: Materials Science — Materials Chemistry

BartSmiles: Generative Masked Language Models for Molecular Representations We discover a robust self-supervised strategy tailored toward molecular representations for generative masked language models through a series of tailored, in-depth ablations. Using this pretraining strategy, we train BARTSmiles, a BART-like model with an order of magnitude more compute than previous self-supervised molecular representations. In-depth evaluations show that BARTSmiles consistently outperforms other self-supervised representations across classification, regression, and generation tasks, setting a new state-of-the-art on eight tasks. We then show that when applied to the molecular domain, the BART objective learns representations that implicitly encode our downstream tasks of interest. For example, by selecting seven neurons from a frozen BARTSmiles, we can obtain a model having performance within two percentage points of the full fine-tuned model on task Clintox. Lastly, we show that standard attribution interpretability methods, when applied to BARTSmiles, highlight certain substructures that chemists use to explain specific properties of molecules. The code and pretrained model are publicly available. Interpretability ; Computer science ; Generative model ; Generative grammar ; Task (project management) ; Artificial intelligence ; Language model ; Code (set theory) ; ENCODE ; Machine learning ; Natural language processing ; Series (stratigraphy) ; Set (abstract data type) Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Protein Structure and Dynamics
Authors: Sílvia Escayola | Jorge Labella | Dariusz W. Szczepanik | Albert Poater | Tomás Torres⊗ | Miquel Solà | Eduard Matito
Source: Inorganic Chemistry (article, 2024-09-19)
Field: Materials Science — Materials Chemistry

From (Sub)Porphyrins to (Sub)Phthalocyanines: Aromaticity Signatures in the UV–Vis Absorption Spectra The development of novel synthetic methods has greatly expanded the toolbox available to chemists for engineering porphyrin and phthalocyanine derivatives with precise electronic and optical properties. In this study, we focus on the UV-vis absorption characteristics of substituted phthalocyanines and their contracted analogs, subphthalocyanines, which feature nonplanar, bowl-shaped geometries. These macrocycles, which are central to numerous applications in materials science and catalysis, possess extensive π-conjugated systems that drive their unique electronic properties. We explore how the change from a metalloid (B) to a metal (Zn) and the resulting coordination environments influence the aromaticity and, consequently, the spectroscopic features of these systems. A combined computational and experimental approach reveals a direct correlation between the aromaticity of the external conjugated pathways and the Q bands in the UV-vis spectra. Our findings highlight key structural modifications that can be leveraged to fine-tune the optical properties of porphyrinoid systems, offering new pathways for the design of advanced materials and catalysts with tailored functionalities. Chemistry ; Aromaticity ; Spectral line ; Absorption spectroscopy ; Phthalocyanine ; Absorption (acoustics) ; Porphyrin ; Photochemistry ; Molecule ; Organic chemistry ; Optics Porphyrin and Phthalocyanine Chemistry ; Photochemistry and Electron Transfer Studies ; Photochromic and Fluorescence Chemistry
Authors: Aliakbar Jafari | Ahmed Al‐Ostaz | Sasan Nouranian
Source: Polymers for Advanced Technologies (article, 2024-11-25)
Field: Materials Science — Biomaterials

Biomedical Potential of Cellulose: Current Trends and Future Directions ABSTRACT The exploration of cellulose, a natural polysaccharide derived from renewable biomass, has seen significant advancements in recent years due to its biocompatibility, biodegradability, and versatility. This review paper comprehensively covers the latest developments in cellulose and its derivatives as functional biomaterials for various biomedical applications. Emphasis is placed on the intrinsic properties of cellulose, such as its mechanical strength, thermal stability, and chemical modifiability, which enable its wide‐ranging use in drug delivery systems, wound dressings, tissue engineering, and biosensors. The article further delves into the modification techniques—such as oxidation, esterification, and etherification—that enhance cellulose's performance, allowing it to be fine‐tuned for specialized medical applications, including the creation of scaffolds for tissue regeneration and smart materials for responsive drug release. Additionally, the hybridization of cellulose with inorganic materials offers potential in developing materials with superior antimicrobial properties and improved mechanical characteristics. This review also addresses the challenges in cellulose processing, particularly concerning optimizing its structure for specific applications, while highlighting future opportunities in the field of personalized medicine and intelligent healthcare devices. By examining both the current innovations and future trends, this review highlights the growing importance of cellulose as a sustainable and versatile resource in the biomedical industry. Cellulose ; Materials science ; Current (fluid) ; Nanotechnology ; Polymer science ; Biochemical engineering ; Engineering ethics ; Data science ; Chemical engineering ; Engineering ; Computer science ; Electrical engineering Advanced Cellulose Research Studies ; Biofuel production and bioconversion