jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Moonika S. Widjajana | Shih‐Hao Chiu | Yuan Chi | Mahroo Baharfar | Jiewei Zheng | Mohammad B. Ghasemian | Saroj Bhattacharyya | Jianbo Tang | Md. Arifur Rahim | Kourosh Kalantar‐Zadeh
Source: Journal of Materials Chemistry C (article, 2023-01-01)
Field: Materials Science — Materials Chemistry

A liquid metal-based process for tuning the thermoelectric properties of bismuth indium systems A novel liquid metal-based micro structuring tuning process for improving the thermoelectric properties of metal alloys. Materials science ; Indium ; Thermoelectric effect ; Bismuth ; Metal ; Liquid metal ; Process (computing) ; Structuring ; Thermoelectric materials ; Metallurgy ; Composite material ; Thermal conductivity ; Computer science ; Thermodynamics Advanced Thermoelectric Materials and Devices ; Thermal properties of materials ; nanoparticles nucleation surface interactions
Authors: Jing Zhao | Feng Lu | Ziqing Dong
Source: Tissue Engineering and Regenerative Medicine (review, 2023-11-30)
Field: Materials Science — Biomaterials

Strategies for Constructing Tissue-Engineered Fat for Soft Tissue Regeneration Scaffold ; Tissue engineering ; Adipose tissue ; Soft tissue ; Regeneration (biology) ; Biomedical engineering ; Computer science ; Medicine ; Biology ; Surgery ; Cell biology Electrospun Nanofibers in Biomedical Applications ; Tissue Engineering and Regenerative Medicine ; 3D Printing in Biomedical Research
Authors: Guang Chen
Source: Journal of Computational Chemistry (article, 2023-08-19)
Field: Materials Science — Surfaces, Coatings and Films

polyGraft 1.0: A program for molecular structure and topology generation of polymer‐grafted hybrid nanostructures Polymer-grafted hybrid materials have been ubiquitously employed in various engineering applications. The design of these hybrid materials with superior performances requires a molecularly detailed understanding of the structure and dynamics of the polymer brushes and their interactions with the grafting substrate. Molecular dynamics (MD) simulations are very well suited for the study of these materials which can provide molecular insights into the effects of polymer composition and length, grafting density, substrate composition and curvatures, and nanoconfinement. However, few existing tools are available to generate such systems, which would otherwise reduce the barrier of preparation for such systems to enable high throughput simulations. Here polyGraft, a general, flexible, and easy to use Python program, is introduced for automated generation of molecular structure and topology of polymer grafted hybrid materials for MD simulations purposes, ranging from polymer brushes grafted to hard substrates, to densely grafted bottlebrush polymers. polyGraft is openly accessible on GitHub (https://github.com/nanogchen/polyGraft). Polymer ; Molecular dynamics ; Python (programming language) ; Materials science ; Grafting ; Substrate (aquarium) ; Nanotechnology ; Topology (electrical circuits) ; Hybrid material ; Nanostructure ; Computer science ; Chemistry ; Computational chemistry Polymer Surface Interaction Studies ; Force Microscopy Techniques and Applications ; Advanced Sensor and Energy Harvesting Materials
Authors: Kien P. Malarney | Pamela V. Chang
Source: Israel Journal of Chemistry (article, 2023-02-28)
Field: Chemistry — Spectroscopy

Chemoproteomic Approaches for Unraveling Prokaryotic Biology Bacteria are ubiquitous lifeforms with important roles in the environment, biotechnology, and human health. Many of the functions that bacteria perform are mediated by proteins and enzymes, which catalyze metabolic transformations of small molecules and modifications of proteins. To better understand these biological processes, chemical proteomic approaches, including activity-based protein profiling, have been developed to interrogate protein function and enzymatic activity in physiologically relevant contexts. Here, chemoproteomic strategies and technological advances for studying bacterial physiology, pathogenesis, and metabolism are discussed. The development of chemoproteomic approaches for characterizing protein function and enzymatic activity within bacteria remains an active area of research, and continued innovations are expected to provide breakthroughs in understanding bacterial biology. Computational biology ; Function (biology) ; Bacteria ; Chemical biology ; Proteomics ; Systems biology ; Protein function ; Bacterial protein ; Chemistry ; Microbial metabolism ; Biology ; Biochemistry ; Cell biology ; Gene ; Genetics Advanced Proteomics Techniques and Applications ; Bacterial Genetics and Biotechnology ; RNA and protein synthesis mechanisms
Authors: Nina Bao | Jiajia Song | Xinyuan Zhao | Marwan M. A. Rashed | Kefeng Zhai | Zeng Dong
Source: Molecules (article, 2023-12-05)
Field: Chemistry — Analytical Chemistry

Mechanochemical-Assisted Extraction and Biological Activity Research of Phenolic Compounds from Lotus Seedpod (Receptaculum Nelumbinis) To explore the feasibility of the mechanochemical-assisted extraction (MCAE) of phenolic compounds from lotus seedpod (<i>Receptaculum Nelumbinis</i>), a single-factor experiment combined with response-surface methodology (RSM) was used to optimize the extraction process. The results showed the optimal extraction conditions as follows: Li<sub>2</sub>CO<sub>3</sub> as a solid reagent (25%), an extraction time of 80 min, liquid/solid ratio of 42.8 mL/g, and extraction temperature of 80.7 °C; and the maximum value of total phenolic content (TPC) was 106.15 ± 1.44 gallic acid equivalents (GAE)/g dry weight (DW). Additionally, the 2,2-Diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azinobis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and ferric reducing antioxidant power (FRAP) were 279.75 ± 18.71, 618.60 ± 2.70, and 634.14 ± 7.17 µmol TE/g, respectively. Ultra-high pressure liquid chromatography combined with triple-time-of-flight mass spectrophotometry (UPLC-Triple-TOF/MS) analysis identified eight phenolic compounds mainly consisting of polyphenols and flavonoids. Moreover, the phenolic compounds showed potent inhibitory effects on both α-amylase and α-glucosidase, with inhibition rates of over 80%. Furthermore, the results showed different degrees of inhibition activity against <i>Bacillus subtilis</i>, <i>Staphylococcus aureus,</i> and <i>Escherichia coli</i>, among which the inhibitory effect on the growth of <i>B. subtilis</i> was the best. This paper shows that the phenolic compounds have good biological activities, which provides a reference for the further exploitation of LSP. Lotus ; Extraction (chemistry) ; Chemistry ; Traditional medicine ; Chromatography ; Food science ; Botany ; Biology ; Medicine Chromatography in Natural Products ; Phytochemistry and biological activity of medicinal plants ; Traditional Chinese Medicine Analysis
Authors: Doriana M. Buda | Edina Szekeres | Lucian Barbu–Tudoran | Julia Esclapez | Horia Leonard Banciu
Source: BMC Microbiology (article, 2023-12-04)
Field: Materials Science — Materials Chemistry

Genome-wide transcriptional response to silver stress in extremely halophilic archaeon Haloferax alexandrinus DSM 27206 T Our results indicated that copA, encoding the copper ATPase, is essential for the survival of Hfx. alexandrinus cells in silver-containing saline media. The silver-exposed cultures underwent several metabolic adjustments that enabled the activation of enzymes involved in the oxidative stress response and impairment of the cellular movement capacity. To our knowledge, this study represents the first comprehensive analysis of gene expression in halophillic archaea facing increased levels of heavy metals. Biology ; Transcriptome ; Archaea ; Gene ; Gene expression ; Microbiology ; Genetics Nanoparticles: synthesis and applications ; Microbial Fuel Cells and Bioremediation ; Geochemistry and Elemental Analysis
Authors: Usana Mahanitipong | Patcharin Kanhakeaw | Metha Rutnakornpituk
Source: Trends in Sciences (article, 2023-01-05)
Field: Materials Science — Biomaterials

Fine-Tuning the Degree of Negative Charge and Carboxylate Grafting Density of Polymer-Coated Magnetite Nanoparticle The surface of magnetite nanoparticle (MNP) was modified with poly(acrylic acid)(PAA)-poly(ethylene glycol) methyl methacrylate (PEGMA) (co)polymer to obtain water dispersible MNP with pH sensitive surfaces via atom transfer radical polymerization (ATRP) of tert-butyl acrylate (t-BA), followed by the t-BA group deprotection. Molar compositions of the (co)polymer were systematically varied, namely 100:0, 75:25, 50:50 and 25:75 of P(t-BA)/PEGMA, respectively, such that the grafting density of carboxylate groups on the MNP surface after the deprotection can be fine-tuned. Transmission electron microscopy (TEM) indicated that the MNP were spherical (ca.5-12 nm in diameter) with some nanoclustering observed. The roles of PAA and PEGMA affecting the hydrodynamic size and zeta potential of the nanocomposites observed via photocorrelation spectroscopy (PCS) were discussed. The percentages of the polymeric composition in the nanocomposites in each step of the reaction were determined via thermogravimetric analysis (TGA) and their magnetic properties were studied via vibrating sample magnetometry (VSM). These novel nanocomposites with pH sensitive surface and magnetically guidable properties might be advantageous for further conjugations either by covalent or ionic bonding with bioentities. HIGHLIGHTS Magnetite nanoparticle (MNP) coated poly(acrylic acid)(PAA)-poly(ethylene glycol) methyl methacrylate (PEGMA) (co)polymer were fabricated via ATRP The ratio of t-BA to PEGMA used in the copolymerization was studied The nanocomposites showed pH sensitive surface and magnetically guidable properties GRAPHICAL ABSTRACT Ethylene glycol ; Atom-transfer radical-polymerization ; Materials science ; Polymer chemistry ; Methacrylate ; Carboxylate ; Thermogravimetric analysis ; Nanocomposite ; Copolymer ; Polymer ; Chemical engineering ; Methyl methacrylate ; Nanoparticle ; Acrylic acid ; Polymerization ; Chemistry ; Organic chemistry ; Nanotechnology ; Composite material Nanoparticle-Based Drug Delivery ; Iron oxide chemistry and applications
Authors: Geyan Ye | Xibao Cai | Houtim Lai | Xing Wang | Junhong Huang | Longyue Wang | Wei Liu | Xiangxiang Zeng
Source: arXiv (Cornell University) (preprint, 2023-12-28)
Field: Materials Science — Materials Chemistry

DrugAssist: A Large Language Model for Molecule Optimization Recently, the impressive performance of large language models (LLMs) on a wide range of tasks has attracted an increasing number of attempts to apply LLMs in drug discovery. However, molecule optimization, a critical task in the drug discovery pipeline, is currently an area that has seen little involvement from LLMs. Most of existing approaches focus solely on capturing the underlying patterns in chemical structures provided by the data, without taking advantage of expert feedback. These non-interactive approaches overlook the fact that the drug discovery process is actually one that requires the integration of expert experience and iterative refinement. To address this gap, we propose DrugAssist, an interactive molecule optimization model which performs optimization through human-machine dialogue by leveraging LLM's strong interactivity and generalizability. DrugAssist has achieved leading results in both single and multiple property optimization, simultaneously showcasing immense potential in transferability and iterative optimization. In addition, we publicly release a large instruction-based dataset called MolOpt-Instructions for fine-tuning language models on molecule optimization tasks. We have made our code and data publicly available at https://github.com/blazerye/DrugAssist, which we hope to pave the way for future research in LLMs' application for drug discovery. Computer science ; Generalizability theory ; Pipeline (software) ; Data science ; Process (computing) ; Artificial intelligence ; Machine learning ; Programming language Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Chemical Synthesis and Analysis
Authors: Ananya Sridhar | Cyril Koshy Sunil | Rhitayu Sarkar | Suma Sarojini
Source: Topics in Catalysis (article, 2023-11-14)
Field: Chemistry — Organic Chemistry

Greener Assembly of Nano Catalysts and Sustainable Applications of Magnetically Retrievable and Plasmonic Nano Catalysts Nanomaterial-based catalyst ; Nanotechnology ; Catalysis ; Context (archaeology) ; Plasmon ; Materials science ; Biochemical engineering ; Nanoparticle ; Chemistry ; Engineering Nanomaterials for catalytic reactions ; Advanced Photocatalysis Techniques ; Copper-based nanomaterials and applications
Authors: Hongbing Wang | Zhaofeng Liang | Jinping Hu | Wei Sun | Chaoqin Huang | Lei Xie | Zheng Jiang | Fei Song
Source: The Journal of Physical Chemistry Letters (article, 2023-05-25)
Field: Materials Science — Materials Chemistry

On-Surface Synthesis of Pentagon-Incorporated Graphene-Like Nanoribbons with Multiple Precursors Graphene nanoribbons (GNRs) and their derivatives are receiving increasing attention as a result of their unique electronic and magnetic properties, and many novel derivative structures have been fabricated. The carbon pentagon plays a crucial role in determining both geometric structures and electronic properties of carbon-based materials. Here, we demonstrate that carbon-pentagon-incorporated graphene-like nanoribbons (GLNRs), which are an important class of GNR derivatives, are successfully fabricated via the Ullmann coupling and aromatic cyclodehydrogenation reaction on the surface by a suitable choice of multiple tailored molecular precursors. Our approach provides a basis for the impact of adatoms in the reaction and proves the steering function of the aryl-metal interaction in procedures of self-assembly and organometallic state. In addition, this study paves the way for on-surface synthesis of GNRs and their derivatives as well as the fine tuning of electronic properties of carbon nanoarchitectures by manipulating the edge structures and embedding carbon pentagon heterojunctions. Graphene nanoribbons ; Graphene ; Nanotechnology ; Carbon fibers ; Materials science ; Pentagon ; Heterojunction ; Composite number ; Composite material ; Optoelectronics ; Geometry Graphene research and applications ; Surface Chemistry and Catalysis ; Molecular Junctions and Nanostructures
Authors: A.K. Maurya | R. D. Tyagi
Source: Reviews in Inorganic Chemistry (article, 2023-08-23)
Field: Chemistry — Organic Chemistry

Acyclic diaminocarbenes (ADCs) and their catalytic activity in metal catalysed organic transformation reactions Abstract Acyclic diaminocarbenes (ADCs)–Metal complex having strong donor ability and thermal stability led to extensive usability across every area of inorganic and organometallic chemistry. The unique properties of acyclic diaminocarbenes (ADCs) provide certain advantages over other carbene ligands and have the potential to make a great impact in catalysis. Further, the straightforward synthesis of M–ADCs (metal bound acyclic diaminocarbenes) complexes via metal-mediated reaction provides a wide range of well-defined metal carbene catalysts, which might inspire more researchers to devise unsymmetrically substituted, chiral, and novel acyclic carbene compounds. Although the above synthetic route is limited to a few late transition metals, but have great opportunities to expand the scope of this method. The application of M–ADCs complexes as a catalyst for several organic transformation reactions such as various cross-coupling reactions and asymmetric synthesis like hydroarylation, hydroazidation, hydroamination, cyclization and addition reactions which have shown comparable or even higher activities than the analogous M–NHCs based on all the reports presented. Recent findings of donor ability of several ADC ligands would be useful in fine-tuning the electronic properties, and then a catalyst with a certain combination of donicity and steric requirement could open new doors in catalytic reactivity. Thus, the objective of this review is to assess the recent growths that have been made in designing novel and chiral ADCs ligands and synthesizing ADCs–Metal complexes and to highlight catalytic activities of metal acyclic diaminocarbene complexes for cross-coupling reactions. Chemistry ; Carbene ; Catalysis ; Combinatorial chemistry ; Steric effects ; Reactivity (psychology) ; Hydroamination ; Organic synthesis ; Metal ; Enantioselective synthesis ; Coupling reaction ; Organic chemistry N-Heterocyclic Carbenes in Organic and Inorganic Chemistry ; Catalytic Cross-Coupling Reactions ; Synthetic Organic Chemistry Methods
Authors: Ann‐Kathrin Rückert | Julia Ast | Annie Hasib | Daniela Nasteska | Katrina Viloria | Johannes Broichhagen | David J. Hodson
Source: Diabetic Medicine (article, 2023-09-05)
Field: Materials Science — Materials Chemistry

Fine‐tuned photochromic sulfonylureas for optical control of beta cell Ca<sup>2+</sup> fluxes We previously developed, synthesized and tested light-activated sulfonylureas for optical control of K<sub>ATP</sub> channels and pancreatic beta cell activity in vitro and in vivo. Such technology relies on installation of azobenzene photoswitches onto the sulfonylurea backbone, affording light-dependent isomerization, alteration in ligand affinity for SUR1 and hence K<sub>ATP</sub> channel conductance. Inspired by molecular dynamics simulations and to further improve photoswitching characteristics, we set out to develop a novel push-pull closed ring azobenzene unit, before installing this on the sulfonylurea glimepiride as a small molecule recipient. Three fine-tuned, light-activated sulfonylureas were synthesized, encompassing azetidine, pyrrolidine and piperidine closed rings. Azetidine-, pyrrolidine- and piperidine-based sulfonylureas all increased beta cell Ca<sup>2+</sup> -spiking activity upon continuous blue light illumination, similarly to first generation JB253. Notably, the pyrrolidine-based sulfonylurea showed superior switch OFF performance to JB253. As such, third generation sulfonylureas afford more precise optical control over primary pancreatic beta cells, and showcase the potential of pyrrolidine-azobenzenes as chemical photoswitches across drug classes. Pyrrolidine ; Azetidine ; Sulfonylurea receptor ; Piperidine ; Sulfonylurea ; Azobenzene ; Beta cell ; Photochromism ; Biophysics ; Stereochemistry ; Photochemistry ; Chemistry ; Molecule ; Medicine ; Insulin ; Biochemistry ; Internal medicine ; Organic chemistry ; Islet ; Biology Photochromic and Fluorescence Chemistry ; Photoreceptor and optogenetics research ; Zebrafish Biomedical Research Applications
Authors: Dipankar Ghosh | Libby J. Marshall | Giuseppe Ciccone | Wanli Liu | Adam M. Squires | Annela M. Seddon | Massimo Vassalli | Dave J. Adams
Source: Macromolecular Materials and Engineering (article, 2023-05-12)
Field: Materials Science — Biomaterials

Fine‐Tuning Supramolecular Assemblies by Controlling Micellar Aggregates Abstract Supramolecular assembly can be used to fabricate complex functional materials by organizing simple building blocks. However, it is difficult to control the hierarchical assembly across multiple length scales. The correlation of a supramolecular gel network and a pre‐gelling aggregate will help to understand how a molecular‐level assembly is translated into a higher order. Here, a functional dipeptide 2NapFF is used that can assemble in different micellar structures at high pH by varying the counterion. Replacing the counterions with a divalent calcium salt results in a cross‐linked gel network, or an interesting analog “gel noodles.” The physical properties of the gel noodles can be varied by choosing specific micellar assemblies as the pre‐gel. The mechanical rigidity of the gel networks is compared by nanoindentation and tensile testing, and the pattern to the structures of the micelles observed by small‐angle X‐ray scattering is correlated. The supramolecular assembly can be fine‐tuned by using different micelles as the pre‐gel without affecting the inherent gel‐state properties. Supramolecular chemistry ; Micelle ; Materials science ; Counterion ; Supramolecular assembly ; Small-angle X-ray scattering ; Self-assembly ; Chemical engineering ; Nanotechnology ; Scattering ; Molecule ; Organic chemistry ; Chemistry ; Aqueous solution ; Ion Supramolecular Self-Assembly in Materials ; Polydiacetylene-based materials and applications ; Supramolecular Chemistry and Complexes
Authors: Max Roemer | William Lewis
Source: Langmuir (article, 2023-08-16)
Field: Chemistry — Organic Chemistry

Azide-Assisted Growth of Copper Nanostructures and Their Application as a Carbon Supported Catalyst in Two-Step Three-Component Azide–Alkyne Cycloadditions Copper nanostructures were obtained from the reduction of Cu(I) under mild conditions in ethanol/water using sodium-l-ascorbate and sodium azide while performing an amination reaction. When the halobenzene substrate was reacted in the presence of a bulk carbon black (CB) support, clustered copper sub-micrometer particles (SMPs) and microparticles (MPs) form. The growth conditions of the MPs were optimized, and the supported nanostructures were isolated and characterized by scanning electron microscopy, energy dispersive X-ray spectroscopy, thermogravimetry, and inductively-coupled plasma mass spectrometry. The particles are mobile and supported within the CB matrix and proved to be active catalysts in the azide-alkyne cycloaddition (CuAAC). The catalytic competency of the particles was assessed in a two-step three-component azide-alkyne cycloaddition of benzyl bromide, sodium azide, and phenylacetylene as a model reaction. The reaction conditions were optimized, and the optimized conditions were applied for the synthesis of triazole compounds with varying levels of functionalization. The recyclability of the catalysts was investigated, depletion modes were discussed, and the conditions were fine-tuned to reach good recyclability. This demonstrates the broader applicability of the SMPs/MPs as CuAAC-catalyst and its limitations. Sodium azide ; Cycloaddition ; Azide ; Alkyne ; Chemistry ; Phenylacetylene ; Catalysis ; Click chemistry ; Copper ; Surface modification ; Inorganic chemistry ; Chemical engineering ; Organic chemistry ; Physical chemistry Click Chemistry and Applications ; Nanomaterials for catalytic reactions ; Innovative Microfluidic and Catalytic Techniques Innovation