jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Han Guo | Mingjia Huo | Ruiyi Zhang | Pengtao Xie
Source:  (preprint, 2023-05-26)
Field: Materials Science — Materials Chemistry

ProteinChat: Towards Achieving ChatGPT-Like Functionalities on Protein 3D Structures &lt;p&gt;The study of proteins is critical in various scientific disciplines, but understanding their complex structure-function relationships remains challenging. Recent advancements in large language models (LLMs) have demonstrated their ability to comprehend task-specific knowledge, suggesting the potential for specially trained ChatGPT-like systems to accelerate protein research. In this work, we introduce ProteinGPT, a prototype model aimed at learning and understanding protein 3D structures. ProteinGPT enables users to upload proteins, ask questions, and engage in interactive conversations to gain insights. The ProteinChat system consists of three main components: a composite encoder block, a projection layer, and an LLM. The protein undergoes encoding to form a protein embedding, which is then projected to conform with the LLM. The LLM combines user questions with the embedding to generate informative answers. To train ProteinChat, we curated the RCSB-PDB Protein Description Dataset, comprising 143,508 protein-description pairs from publicly available sources. By leveraging the capabilities of ProteinGPT, researchers can potentially expedite their investigations into protein functionalities and structures, benefiting areas such as drug development and therapeutics, food science and nutrition, and various aspects of our lives. This initial step lays the foundation for further exploration and utilization of the ChatGPT-like system in protein research. The code is available at \url{https://github.com/UCSD-AI4H/proteinchat} and the dataset can be downloaded from \url{https://drive.google.com/file/d/1AeJW5BY5C-d8mKJjAULTax6WA4hzWS0N/view?usp=share_link}.&lt;/p&gt; Upload ; Computer science ; Embedding ; Task (project management) ; Function (biology) ; Block (permutation group theory) ; Code (set theory) ; World Wide Web ; Artificial intelligence ; Programming language ; Engineering ; Biology Machine Learning in Materials Science ; Software Engineering Research ; Machine Learning in Bioinformatics
Authors: Hongda Cheng
Source: Molecules (article, 2023-11-22)
Field: Chemistry — Inorganic Chemistry

One-Pot Preparation of HCPT@IRMOF-3 Nanoparticles for pH-Responsive Anticancer Drug Delivery Metal-organic frameworks (MOFs) are considered to be promising materials for drug delivery. In this work, a Zinc-based MOF nanocomposite IRMOF-3 was introduced as a drug carrier for 10-hydroxycamptothecine (HCPT). Without an extra drug-loading process, a nanoscale drug delivery material HCPT@IRMOF-3 was prepared via one-pot synthesis. The composition and structure of the material were investigated, and the drug release character was measured. Compared with preparing IRMOF-3 first and loading the drug, the one-pot-prepared HCPT@IRMOF-3 exhibited a higher drug-loading capacity. The material presented pH-responsive release. The HCPT release rate at pH 5.0 was significantly higher than that at pH 7.4. The cytotoxicity experiments showed that IRMOF-3 was non-toxic, and HCPT@IRMOF-3 exhibited notable cytotoxicity to Hela and SH-SY5Y cells. One-pot synthesis is a simple and rapid method for the preparation of an MOF drug delivery system, and IRMOF-3 can be potentially used in pH-responsive drug delivery systems. Drug delivery ; Drug ; Metal-organic framework ; Cytotoxicity ; HeLa ; Nanoparticle ; Chemistry ; Nanotechnology ; Combinatorial chemistry ; Materials science ; Chemical engineering ; Organic chemistry ; Pharmacology ; Adsorption ; In vitro ; Biochemistry Metal-Organic Frameworks: Synthesis and Applications ; Nanoplatforms for cancer theranostics ; Boron and Carbon Nanomaterials Research
Authors: Zeinab El Hajj | Lucie Pierau | Jean‐Pierre Malval | Jérôme Marrot | Pierre‐Emmanuel Mazeran | Daoud Naoufal | Minh‐Huong Ha‐Thi | Karine Steenkeste | Anne Dolbecq | Sébastien Floquet | Olivier Oms | Davy‐Louis Versace | Pierre Mialane
Source: Macromolecules (article, 2023-07-26)
Field: Materials Science — Materials Chemistry

Shifting from UV to Visible-Light the Activity of Organic Photoinitiators via the Covalent Grafting of Polyoxometalates Anthracene-, benzophenone-, and anthraquinone-based UV photoinitiators have been, respectively, covalently grafted on the [Mo6O19]2– polyoxometalate (POM) platform, affording highly colored charge transfer organo-imido Lindqvist complexes. It has been evidenced that photosystems combining N-methyldiethanolamine (MDEA) as the electron donor and these hybrid POMs promote free-radical photopolymerization of acrylate monomer derivatives under irradiation in the visible range, while in similar conditions, no polymerization was observed considering as photoinitiators a mixture of the organic and POM precursors. After 800 s, acrylate conversion yields up to 90% under 405 nm LED irradiation and 50% under 470 nm LED irradiation were thus obtained considering the POM-imidoanthraquinone (POM-AQ) compound. This shows that such organo-imido Lindqvist species can represent new easy-to-synthesize, efficient visible-light photoinitiators. Moreover, due to the presence of the POM, coatings prepared using the POM-AQ/MDEA/soybean oil epoxidized acrylate photosystem exhibit excellent mechanical properties, with very good flexibility, resistance to brittle fracture, and adherence to the steel. Finally, POM-AQ was shown to have a remarkable capacity to generate singlet oxygen species under visible light irradiation, and the antibacterial activity against Staphylococcus aureus under solar light of the related POM-derived surface has been demonstrated. Photopolymer ; Acrylate ; Chemistry ; Photochemistry ; Photoinitiator ; Polymer chemistry ; Visible spectrum ; Monomer ; Covalent bond ; Singlet oxygen ; Polymerization ; Acrylate polymer ; Benzophenone ; Materials science ; Organic chemistry ; Polymer ; Oxygen Polyoxometalates: Synthesis and Applications ; Advanced Photocatalysis Techniques ; Carbon dioxide utilization in catalysis
Authors: Suchetha Shetty | Karam B. Idrees | Haomiao Xie | Bassam Alameddine | Omar K. Farha
Source: CrystEngComm (article, 2023-01-01)
Field: Chemistry — Inorganic Chemistry

Synthesis of zirconium-based metal–organic frameworks with iron(<scp>ii</scp>) clathrochelate ligands Zirconium-based metal organic frameworks (MOFs) are of great significance in supramolecular coordination chemistry, mainly as catalysts, due to their chemical stability and structural diversity. Zirconium ; Supramolecular chemistry ; Catalysis ; Metal ; Chemistry ; Metal-organic framework ; Coordination complex ; Combinatorial chemistry ; Polymer chemistry ; Organic chemistry ; Crystal structure Metal-Organic Frameworks: Synthesis and Applications ; Magnetism in coordination complexes ; Metal complexes synthesis and properties
Authors: Hongyi Suo | Zisheng Zhang | Rui Qu | Yanan Gu | Yusheng Qin
Source: Catalysts (article, 2023-03-29)
Field: Chemistry — Organic Chemistry

Tunable Late-Transition-Metal-Catalyzed Polymerization for Controlled Polymer Synthesis As a powerful protocol for the preparation of common polymers, such as polyolefins, polyesters, and polycarbonates, late-transition-metal-catalyzed polymerization can be carried out by controlling the reaction conditions or developing dynamic catalytic systems that use external stimuli to influence the performance of the active sites, resulting in well-defined polymeric materials. In particularly, under the latter conditions, ‘one catalyst’ can provide more than one kind of polymer with a controlled sequence from the monomer mixture, making full use of the prepared catalyst. In this review, tunable modes, including reaction conditions, redox, light or electrochemical properties, Lewis acids, and alkali metal cations, of late-transition-metal-complex (especially iron, cobalt, and nickel)-catalyzed polymerization were collected and thoroughly discussed. Polymerization ; Catalysis ; Polymer ; Transition metal ; Materials science ; Monomer ; Polyester ; Cobalt ; Polymer chemistry ; Chemistry ; Organic chemistry Organometallic Complex Synthesis and Catalysis ; Carbon dioxide utilization in catalysis ; Synthetic Organic Chemistry Methods
Authors: Rafał Zbonikowski | Pumza Mente | Bartłomiej Bończak | Jan Paczesny
Source: Nanomaterials (review, 2023-02-25)
Field: Materials Science — Biomaterials

Adaptive 2D and Pseudo-2D Systems: Molecular, Polymeric, and Colloidal Building Blocks for Tailored Complexity Two-dimensional and pseudo-2D systems come in various forms. Membranes separating protocells from the environment were necessary for life to occur. Later, compartmentalization allowed for the development of more complex cellular structures. Nowadays, 2D materials (e.g., graphene, molybdenum disulfide) are revolutionizing the smart materials industry. Surface engineering allows for novel functionalities, as only a limited number of bulk materials have the desired surface properties. This is realized via physical treatment (e.g., plasma treatment, rubbing), chemical modifications, thin film deposition (using both chemical and physical methods), doping and formulation of composites, or coating. However, artificial systems are usually static. Nature creates dynamic and responsive structures, which facilitates the formation of complex systems. The challenge of nanotechnology, physical chemistry, and materials science is to develop artificial adaptive systems. Dynamic 2D and pseudo-2D designs are needed for future developments of life-like materials and networked chemical systems in which the sequences of the stimuli would control the consecutive stages of the given process. This is crucial to achieving versatility, improved performance, energy efficiency, and sustainability. Here, we review the advancements in studies on adaptive, responsive, dynamic, and out-of-equilibrium 2D and pseudo-2D systems composed of molecules, polymers, and nano/microparticles. Nanotechnology ; Materials science ; Protocell ; Coating ; Computer science ; Smart material ; Molybdenum disulfide ; Membrane ; Chemistry Supramolecular Self-Assembly in Materials ; Covalent Organic Framework Applications ; Polydiacetylene-based materials and applications
Authors: Ottavia Bellotto | Paola D’Andrea | Silvia Marchesan
Source: Journal of Materials Chemistry B (review, 2023-01-01)
Field: Materials Science — Biomaterials

Nanotubes and water-channels from self-assembling dipeptides Dipeptides are attractive building blocks for biomaterials in light of their inherent biocompatibility, biodegradability, and simplicity of preparation. Since the discovery of diphenylalanine (Phe-Phe) self-assembling ability into nanotubes, research efforts have been devoted towards the identification of other dipeptide sequences capable of forming these interesting nanomorphologies, although design rules towards nanotube formation are still elusive. In this review, we analyze the dipeptide sequences reported thus far for their ability to form nanotubes, which often feature water-filled supramolecular channels as revealed by single-crystal X-ray diffraction, as well as their properties, and their potential biological applications, which span from drug delivery and regenerative medicine, to bioelectronics and bioimaging. Materials science ; Nanotechnology ; Water channel ; Engineering ; Mechanical engineering Supramolecular Self-Assembly in Materials ; Polydiacetylene-based materials and applications ; Biochemical effects in animals
Authors: Carina I. C. Crucho
Source: Compounds (article, 2023-03-16)
Field: Materials Science — Materials Chemistry

Synthesis of Organoalkoxysilanes: Versatile Organic–Inorganic Building Blocks Organic–inorganic building blocks are an important class of hybrid materials due to the synergistic versatility of organic compounds with the robust properties of inorganic materials. Currently, the growing interest in silica hybrid materials to modify the physical and chemical properties of the silica network has led to an increasing interest in organoalkoxysilanes. A general formula of R-[Si-(OR’)3]n, with OR’ as a hydrolysable alkoxy group and R acting as the organic functional group (n ≥ 1), has led to precursors for many molecules. By introducing adequate organic moieties (R), organoalkoxysilanes effectively engage in surface and matrix modification of silica-based materials with smart-responsive units, coupling agents, targeting moieties, bioactive moieties etc., opening promising applications, specifically biomedical ones. Several synthetic procedures have been established to introduce the alkoxysilane moieties, including hydrosilylation, coupling reactions, and addition reactions to isocyanates. Herein, we review synthetic routes to organoalkoxysilanes and the relationship between structural features to design appropriate organoalkoxysilanes for specific applications. Hydrosilylation ; Alkoxy group ; Organic synthesis ; Combinatorial chemistry ; Materials science ; Surface modification ; Organic molecules ; Hybrid material ; Molecule ; Nanotechnology ; Organic chemistry ; Chemistry ; Catalysis ; Alkyl Silicone and Siloxane Chemistry ; Polyoxometalates: Synthesis and Applications ; Mesoporous Materials and Catalysis
Authors: Abdurrahman Bilican | Priyanka Sharma | Nguyen Khang Tran | Claudia Weidenthaler | Wolfgang Schmidt
Source: ACS Omega (article, 2023-11-22)
Field: Chemistry — Spectroscopy

Superfast Synthesis of Carbon Xerogels Carbon xerogels (CXs) provide unique opportunities for numerous applications in the areas of adsorption, separation, insulation, catalysis, and electrochemistry, but their use is hampered by time- and energy-intensive synthesis protocols. Synthesis protocols may require several days or more. Here, we report the synthesis of CXs requiring only 5 h using hydrothermal gelation and direct carbonization of the wet polymer. Drying of the polymer gel is of utmost importance for the synthesis of closely related carbon aerogels and is generally considered to be essential for the preparation of CXs. We show that skipping this step has no detrimental effect on the properties of CXs. They are identical to those obtained via conventional routes. With this "superfast" synthesis route, CXs with specific surface areas of about 700 m<sup>2</sup> g<sup>-1</sup> and total pore volumes up to 1.5 cm<sup>3</sup> g<sup>-1</sup> are obtained very time-efficiently and without loss of performance. Carbonization ; Polymer ; Carbon fibers ; Materials science ; Adsorption ; Chemical engineering ; Hydrothermal synthesis ; Nanotechnology ; Specific surface area ; Catalysis ; Hydrothermal carbonization ; Electrochemistry ; Hydrothermal circulation ; Chemistry ; Organic chemistry ; Electrode ; Composite material Aerogels and thermal insulation ; Supercapacitor Materials and Fabrication ; Catalytic Processes in Materials Science
Authors: Ran Chen | Liang Zhao | Yannanqi Li | Jian Li | Pei Chen | Xinbing Chen | Zhongwei An
Source: Materials Advances (article, 2023-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

High birefringence liquid crystals with a wide temperature range and low melting point for augmented reality displays Precise molecular tailoring was applied to obtain high performance liquid crystal materials for the broad temperature adaptability of LCoS devices in AR displays. Melting point ; Augmented reality ; Birefringence ; Materials science ; Atmospheric temperature range ; Range (aeronautics) ; Point (geometry) ; Optics ; Computer science ; Physics ; Composite material ; Thermodynamics ; Human–computer interaction ; Geometry Liquid Crystal Research Advancements ; Advanced Optical Imaging Technologies ; Semiconductor Lasers and Optical Devices
Authors: Nimrod Benshalom | Maor Asher | Rémy Jouclas | Roman Korobko | Guillaume Schweicher | Jie Liu | Yves Geerts | Olle Hellman | Omer Yaffe
Source: The Journal of Physical Chemistry C (article, 2023-08-31)
Field: Materials Science — Materials Chemistry

Phonon–Phonon Interactions in the Polarization Dependence of Raman Scattering We have found that the polarization dependence of Raman scattering in organic crystals at finite temperatures can only be described by a fourth-rank tensor formalism. This generalization of the second-rank Raman tensor stems from the effect of off-diagonal components in the crystal self-energy on the light scattering mechanism. We thus establish a novel manifestation of phonon-phonon interaction in inelastic light scattering, markedly separate from the better-known phonon lifetime. Phonon ; Raman scattering ; Raman spectroscopy ; Phonon scattering ; Scattering ; Diagonal ; Condensed matter physics ; Physics ; Polarization (electrochemistry) ; X-ray Raman scattering ; Formalism (music) ; Inelastic scattering ; Materials science ; Optics ; Chemistry ; Mathematics ; Geometry Solid-state spectroscopy and crystallography ; Spectroscopy and Quantum Chemical Studies ; Organic and Molecular Conductors Research
Authors: Hanaa M. Abuzeid | C. Julien | Likun Zhu | Ahmed M. Hashem
Source: Preprints.org (preprint, 2023-10-18)
Field: Materials Science — Materials Chemistry

Green Synthesis of Metal and Metal Oxide Nanoparticles for Recent Applications Green synthesis offers a superior alternative to traditional methods for producing metal and metal oxide nanoparticles. This approach is not only benign and safe but also cost-effective, scalable, and straightforward, operating under ambient conditions. Notable metals and metal oxide nanoparticles, such as manganese oxides, iron oxides, silver, and gold, have been produced using various bio-reductants derived from plant extracts. These biological agents not only expedite the reduction process but also stabilize the nanoparticles, serving dual roles as reducing and capping agents. This review presents the green synthesis of nanoparticles (NPs) obtained from biogenic wastes and plant extracts. The green-synthesized nanostructured MnO2 are evaluated as a potential photocatalyst for water treatment and as an electrode material in lithium-ion batteries and supercapacitors. The green-derived iron oxide nanoparticles are examined as promising antioxidant, anti-inflammatory, and anti-diabetic agents. Additionally, this review discusses the green synthesis of precious metal nanoparticles, specifically silver (Ag NPs) and gold (Au NPs), highlighting their potential medical applications in areas like antiviral treatments and cancer therapy. Nanoparticle ; Nanotechnology ; Materials science ; Oxide ; Metal ; Reducing agent ; Chemistry ; Metallurgy ; Organic chemistry Nanoparticles: synthesis and applications
Authors: Alessandra Lattanzi
Source: The Chemical Record (review, 2023-04-12)
Field: Chemistry — Organic Chemistry

From Three‐ to Six‐Membered Heterocycles Bearing a Quaternary Stereocenter: an Asymmetric Organocatalytic Approach The development of procedures useful to form quaternary stereocenters stands out as a highly challenging task in asymmetric synthesis. With the arrival of organocatalysis, different activation strategies became available to pursue this intriguing target, thus leading to notable advancements of the area. In this account, our achievements, spanning over a decade, on asymmetric methodologies to access novel three-, five-, six-membered heterocycles, including spiro compounds bearing quaternary stereocenters, will be highlighted. The Michael addition reaction has been often exploited to trigger cascade reactions, using organocatalysts mostly derived from Cinchona alkaloids, and operating under non-covalent activation of the reagents. Further manipulations of the enantioenriched heterocycles, attested them as useful compounds to prepare functionalized building blocks. Stereocenter ; Organocatalysis ; Enantioselective synthesis ; Combinatorial chemistry ; Michael reaction ; Reagent ; Computer science ; Chemistry ; Organic chemistry ; Catalysis Asymmetric Synthesis and Catalysis ; Chemical synthesis and alkaloids ; Synthetic Organic Chemistry Methods
Authors: Nishat Tabassum | Shoeb Ahmed | Mohammad Muhtasim Ittisaf | Md. Rakid-Ul-Haque | M. Azam Ali
Source: Cellulose (article, 2023-08-14)
Field: Materials Science — Biomaterials

A green approach for depolymerization of chitosan: applications in hydrogels Abstract Chitooligosaccharides (COS) are depolymerized chains produced from the natural polymer chitosan and has been determined to exhibit improved biological activities, high solubility in neutral to slightly alkaline pH, because of the lower molecular weight (MW). This makes COS more attractive in biomedical applications. However, earlier studies focused on depolymerization techniques that were either cumbersome or expensive. Here, a convenient two-stage, green synthesis approach was developed and optimized, where gamma irradiation and oxidative degradation with H 2 O 2 were used to depolymerize chitosan to produce COS for biomedical applications. The gamma radiation dose level, H 2 O 2 degradation reaction’s temperature, time and H 2 O 2 concentration were varied to obtain the mildest combination of reaction conditions. The most optimum set of conditions (15 kGy, 25 o C, overnight reaction with 2% H 2 O 2 ) yielded COS that was soluble in physiological pH range (7–8.5). The COS had a MW of 12.8 ± 1.6 kDa (which was a 95% reduction in MW), a 62.3% degree of deacetylation, and a crystallinity index of 33%. A photopolymerized hydrogel using this COS cross-linked with polyethylene glycol diacrylate (PEGDA) and carboxymethyl cellulose (CMC) was also developed. The hydrogel exhibited high swelling ratio (6.44–10.24), a porous morphology, a compression modulus of 4.5 ± 2.7 kPa (similar to soft tissues), and more than 95% biocompatibility with mammalian cells. This newly developed COS hydrogel involves a simple and green approach for the production of COS and shows promise as a scaffold for artificial soft tissue. Depolymerization ; Self-healing hydrogels ; Chitosan ; Crystallinity ; Biocompatibility ; Swelling ; Nuclear chemistry ; Polymer chemistry ; Polyethylene glycol ; Polymer ; Degradation (telecommunications) ; Solubility ; Materials science ; Chemistry ; Chemical engineering ; Organic chemistry ; Composite material Electrospun Nanofibers in Biomedical Applications ; Hydrogels: synthesis, properties, applications ; Nanocomposite Films for Food Packaging
Authors: Dongxing Ren | Liangliang Zhang | Hongwei Qian | Tangxin Xiao
Source: Chemistry (article, 2023-02-07)
Field: Materials Science — Materials Chemistry

Anion-Complexation-Induced Emission Based on Aggregation-Induced Emission Fluorophore Aggregation-induced emission (AIE) materials have attracted increasing research interest in recent years due to their excellent fluorescence properties in an aggregated state. Concurrently, anion coordination interactions have played a key role in the development of supramolecular assemblies and sensors. In the past decade, investigations towards fluorescent materials or sensors based on AIE and anion coordination interactions are continuously being reported. In this minireview, we briefly summarize the burgeoning progress of AIE-based materials and sensors driven by anion coordination interactions. We believe that an increasing number of achievements in anion-coordination induced emission materials will appear in the near future and will demonstrate potential applications, including bio-imaging and bio-sensors. Aggregation-induced emission ; Fluorophore ; Fluorescence ; Ion ; Supramolecular chemistry ; Nanotechnology ; Materials science ; Chemistry ; Molecule ; Physics ; Organic chemistry Luminescence and Fluorescent Materials ; Molecular Sensors and Ion Detection ; Supramolecular Chemistry and Complexes