jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Sergey V. Kraevsky | Anastasia A. Valueva | Maria O. Ershova | Ivan D. Shumov | Irina A. Ivanova | S.L. Kanashenko | I. A. Ryazantsev | Yuri D. Ivanov | Tatyana O. Pleshakova
Source: International Journal of Molecular Sciences (article, 2024-12-30)
Field: Chemistry — Physical and Theoretical Chemistry

Using the Radial Distribution Function to Analyze Atomic Force Microscopy Images of Colloidal Systems Biomacromolecules generally exist and function in aqueous media. Is it possible to estimate the state and properties of molecules in an initial three-dimensional colloidal solution based on the structure properties of biomolecules adsorbed on the two-dimensional surface? Using atomic force microscopy to study nanosized objects requires their immobilization on a surface. Particles undergoing Brownian motion in a solution significantly reduce their velocity near the surface and become completely immobilized upon drying. Using radial distribution function (RDF) methods, it is possible to obtain information about the presence of short-range or long-range order in the arrangement of immobilized colloidal particles. In this work, RDF is applied to immobilized gold nanoparticles (AuNPs) and horseradish peroxidase molecules on mica. It is shown that AuNPs maintain mobility on the mica surface when water is present. Upon immobilization, AuNPs organize into an amorphous structure exhibiting short-range order. Protein molecules are immobilized randomly, and their surface density is well described by the Poisson distribution. Mica ; Biomolecule ; Colloid ; Radial distribution function ; Colloidal gold ; Nanoparticle ; Adsorption ; Molecule ; Silanization ; Chemistry ; Chemical physics ; Aqueous solution ; Range (aeronautics) ; Nanotechnology ; Materials science ; Brownian motion ; Molecular dynamics ; Computational chemistry ; Physical chemistry ; Composite material ; Physics ; Organic chemistry Electrostatics and Colloid Interactions ; Material Dynamics and Properties ; Force Microscopy Techniques and Applications
Authors: Faisal Sedeqi | Srikanth Santhanam | Matthias Riegraf | Marc Riedel | Marc P. Heddrich | Syed Asif Ansar
Source: Journal of The Electrochemical Society (article, 2024-07-01)
Field: Materials Science — Materials Chemistry

Solid Oxide Cell Reactor Model for Transient and Stationary Electrochemical H<sub>2</sub>O and CO<sub>2</sub> Conversion Process Studies The ability of high-temperature solid oxide cell (SOC) electrochemical reactors to efficiently convert atmospheric carbon to high value chemicals for industrial and energy storage applications via <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msub> <mml:mrow> <mml:mi mathvariant="normal">CO</mml:mi> </mml:mrow> <mml:mrow> <mml:mn>2</mml:mn> </mml:mrow> </mml:msub> </mml:math> and co-electrolysis makes them a key technology for active carbon utilisation. However, due to additional operational risks from thermochemical reactions on thermal management, limited experimental capacity, and relative novelty, <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msub> <mml:mrow> <mml:mi mathvariant="normal">CO</mml:mi> </mml:mrow> <mml:mrow> <mml:mn>2</mml:mn> </mml:mrow> </mml:msub> </mml:math> and co-electrolysis lag behind steam electrolysis in large-scale adoption. Here, a 1D+1D SOC model based on fundamental first principles considering three-dimensional heat transfer was improved via a unique method for representing co-electrolysis electrochemistry, solving with low computational effort. Validation against experimental data for two compositions and pressures, showed high levels of accuracy with respect to characteristic cell voltages, temperatures, and outlet compositions. The model also showed <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msub> <mml:mrow> <mml:mi mathvariant="normal">CO</mml:mi> </mml:mrow> <mml:mrow> <mml:mn>2</mml:mn> </mml:mrow> </mml:msub> </mml:math> reduction during co-electrolysis mainly occurred via reverse water gas shift, while <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msub> <mml:mrow> <mml:mi mathvariant="normal">CO</mml:mi> </mml:mrow> <mml:mrow> <mml:mn>2</mml:mn> </mml:mrow> </mml:msub> </mml:math> electrolysis still accounted for up to 35% of the total share. Pressurised co-electrolysis operation promotes exothermic methanation, causing pronounced heating of the reactor, consequently reducing the isothermal current density. Therefore, low to moderate pressurisation is likely most suited for coupling with downstream synthesis processes to avoid the installation of unnecessarily large systems and associated high costs. Electrolysis ; Algorithm ; Electrochemistry ; Materials science ; Computer science ; Analytical Chemistry (journal) ; Chemistry ; Electrode ; Physical chemistry Advancements in Solid Oxide Fuel Cells ; Chemical Looping and Thermochemical Processes ; Catalysis and Oxidation Reactions
Authors: Jean Cauvin-Vila | Virginie Ehrlacher | Greta Marino | Jan‐Frederik Pietschmann
Source: Nonlinear Analysis (article, 2024-01-18)
Field: Materials Science — Materials Chemistry

Stationary solutions and large time asymptotics to a cross-diffusion-Cahn–Hilliard system Convexity ; Degenerate energy levels ; Diffusion ; Statistical physics ; Mathematics ; Applied mathematics ; Energy (signal processing) ; Cahn–Hilliard equation ; Order (exchange) ; Mathematical analysis ; Physics ; Thermodynamics Solidification and crystal growth phenomena ; Advanced Mathematical Modeling in Engineering ; nanoparticles nucleation surface interactions
Authors: Liliya Vugmeyster | Dan Fai Au | Bailey Frazier | Wei Qiang | Dmitry Ostrovsky
Source: Physical Chemistry Chemical Physics (article, 2024-01-01)
Field: Chemistry — Spectroscopy

Rigidifying of the internal dynamics of amyloid-beta fibrils generated in the presence of synaptic plasma vesicles We investigated the changes in internal flexibility of amyloid-β<sub>1-40</sub> (Aβ) fibrils grown in the presence of rat synaptic plasma vesicles. The fibrils are produced using a modified seeded growth protocol, in which the Aβ concentration is progressively increased at the expense of the decreased lipid to protein ratio. The morphologies of each generation are carefully assessed at several fibrils' growth time points using transmission electron microscopy. The side-chain dynamics in the fibrils is investigated using deuterium solid-state NMR measurements, with techniques spanning line shapes analysis and several NMR relaxation rates measurements. The dynamics is probed in the site-specific fashion in the hydrophobic C-terminal domain and the disordered N-terminal domain. An overall strong rigidifying effect is observed in comparison with the wild-type fibrils generated in the absence of the membranes. In particular, the overall large-scale fluctuations of the N-terminal domain are significantly reduced, and the activation energies of rotameric inter-conversion in methyl-bearing side-chains of the core (L17, L34, M35, V36), as well as the ring-flipping motions of F19 are increased, indicating a restricted core environment. Membrane-induced flexibility changes in Aβ aggregates can be important for the re-alignment of protein aggregates within the membrane, which in turn would act as a disruption pathway of the bilayers' integrity. Vesicle ; Biophysics ; Fibril ; Amyloid fibril ; Chemistry ; Amyloid (mycology) ; Synaptic vesicle ; BETA (programming language) ; Amyloid β ; Biochemistry ; Biology ; Membrane ; Pathology Advanced NMR Techniques and Applications ; Alzheimer's disease research and treatments ; NMR spectroscopy and applications
Authors: Shijie Wang | Yinghan Wang | Zhengren TAO | Zhengce An | Shi YE
Source: Chinese Journal of Luminescence (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Distinct Thermal Quenching of Upconversion and Downshifting Luminescence Caused by Dynamic Defects in Ion-conductive Na&lt;sub&gt;3&lt;/sub&gt;Sc&lt;sub&gt;2&lt;/sub&gt;（PO&lt;sub&gt;4&lt;/sub&gt;）&lt;sub&gt;3&lt;/sub&gt;∶Yb&lt;sup&gt;3+&lt;/sup&gt;, Er&lt;sup&gt;3+&lt;/sup&gt; Phosphor 2024年4月8日Key Laboratory of Fiber Laser Materials and Applied Techniques的WANG Shijie、YE Shi团队在《发光学报》发文, 掺Eu 2+ 的离子导体 Na 3Sc 23具有优异的抗热猝灭性能，是一种很有前景的大功率照明用发光材料。结果表明，热致缺陷/离子的动态迁移能促进高温下辐射跃迁和抑制非辐射跃迁，导致了上转换发光具有显著的负热猝灭，下转移发光热猝灭较小。本研究研究可为理解发光材料热猝灭机制提供另一种视角。 Photon upconversion ; Luminescence ; Materials science ; Quenching (fluorescence) ; Ion ; Optoelectronics ; Chemistry ; Physics ; Fluorescence ; Optics Luminescence Properties of Advanced Materials ; Radiation Detection and Scintillator Technologies ; Advanced Chemical Sensor Technologies
Authors: Pham Huu Kien | Giap Thi Thuy Trang
Source: International Journal of Molecular Sciences (article, 2024-05-22)
Field: Materials Science — Ceramics and Composites

The Characteristics of Structural Properties and Diffusion Pathway of Alkali in Sodium Trisilicate: Nanoarchitectonics and Molecular Dynamic Simulation Based on nanoarchitectonics and molecular dynamics simulations, we investigate the structural properties and diffusion pathway of Na atoms in sodium trisilicate over a wide temperature range. The structural and dynamics properties are analyzed through the radial distribution function (RDF), the Voronoi Si- and O-polyhedrons, the cluster function f<sub>CL</sub>(r), and the sets of fastest (SFA) and slowest atoms (SSA). The results indicate that Na atoms are not placed in Si-polyhedrons and bridging oxygen (BO) polyhedrons; instead, Na atoms are mainly placed in non-bridging oxygen (NBO) polyhedrons and free oxygen (FO) polyhedrons. Here BO, NBO, and FO represent O bonded with two, one, and no Si atoms, respectively. The simulation shows that O atoms in sodium trisilicate undergo numerous transformations: NBF0 ↔ NBF1, NBF1 ↔ NBF2, and BO0 ↔ BO1, where NBF is NBO or FO. The dynamics in sodium trisilicate are mainly distributed by the hopping and cooperative motion of Na atoms. We suppose that the diffusion pathway of Na atoms is realized via hopping Na atoms alone in BO-polyhedrons and the cooperative motion of a group of Na atoms in NBO- and FO-polyhedrons. Natural bond orbital ; Chemistry ; Molecular dynamics ; Sodium ; Chemical physics ; Polyhedron ; Crystallography ; Diffusion ; Alkali metal ; Computational chemistry ; Density functional theory ; Thermodynamics ; Physics Glass properties and applications ; Zeolite Catalysis and Synthesis ; Mesoporous Materials and Catalysis
Authors: Ylva K. Hommedal | Ymir Kalmann Frodason | Lasse Vines | K. M. Johansen
Source: physica status solidi (b) (article, 2024-10-09)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Diffusion of Ge Donors in β‐Ga<sub>2</sub>O<sub>3</sub> Diffusion of Ge donors in β‐Ga 2 O 3 is studied using a combination of secondary‐ion mass spectrometry, diffusion simulations, and first‐principles calculations, and compared to previous studies on Sn diffusion. Ge is implanted into (01)‐oriented samples and annealed at temperatures from 900 to 1050 °C for a total of 8 h. From previous first‐principles calculations, Sn is predicted to diffuse via the formation of a mobile complex with V Ga that migrates through a sequence of exchange and rotation jumps. Herein, it is similarly predicted that Ge diffusion is mediated by V Ga . However, the microscopic mechanism differs, as Ge can diffuse more easily through exchange combined with complex dissociation, rather than rotational jumps. This is explained by the difference in Ga‐site preference of Ge compared to Sn, and the three‐split mechanism that enables low migration barriers for V Ga . The dissociation mechanism leads to a considerably faster transport for Ge as compared to Sn. The experimentally obtained Ge diffusion profiles are successfully fitted using a reaction–diffusion model based on the predicted diffusion mechanism, yielding a migration barrier of 2.5 ± 0.2 eV for the complex. The 2.72 eV obtained from first‐principles calculations is in good agreement with this value. Diffusion ; Materials science ; Physics ; Thermodynamics Ga2O3 and related materials ; Advanced Photocatalysis Techniques ; ZnO doping and properties
Authors: Jianhui Wei | Lü Min | Libo Pi | Huan Zhao | Qian Lei
Source: Crystals (article, 2024-12-30)
Field: Materials Science — Materials Chemistry

Numerical Simulation Study on Directional Solidification of DD5 Nickel-Based Single-Crystal Turbine Blades Two models with a wax module tree structure were employed for directional solidification simulation. An experimental alloy of a second-generation nickel-based single-crystal superalloy, DD5, was set for this investigation. The temperature gradient value of the conventional model at 80 mm and 160 mm was less than 3.8 K/mm, and the temperature gradient value of the new model structure at the same height could reach more than 5.0 K/mm. The paste–liquid interface paste zone of the new model structure in the directional solidification process was narrower. The solidification interface was more stable than that of the conventional model. The declination angle between the primary dendrite and the principal stress axis was smaller, and the average crystal orientation was about 6.0°. Under the new model, the integrity of the single crystal of the edge plate was good, and no heterocrystalline defects were formed. At the sharp corner of the end face of the edge plate, the solidified dendrites grew staggered, which hindered the effective contraction of other parts of the edge plate and produced micro-looseness. The whole simulation was in line with the test results. Directional solidification ; Turbine blade ; Materials science ; Nickel ; Metallurgy ; Computer simulation ; Single crystal ; Turbine ; Mechanical engineering ; Mechanics ; Engineering ; Microstructure ; Crystallography ; Physics ; Chemistry Solidification and crystal growth phenomena ; Aluminum Alloy Microstructure Properties ; High Temperature Alloys and Creep
Authors: Jonathan-Siu-Loong Robles-Hernández | Dora I. Medina | Katerin Aguirre-Hurtado | Marlene Bosquez | Roberto Salcedo | Alan Miralrio
Source: Beilstein Journal of Nanotechnology (article, 2024-09-19)
Field: Chemistry — Organic Chemistry

AI-assisted models to predict chemotherapy drugs modified with C<sub>60</sub> fullerene derivatives Employing quantitative structure-activity relationship (QSAR)/ quantitative structure-property relationship (QSPR) models, this study explores the application of fullerene derivatives as nanocarriers for breast cancer chemotherapy drugs. Isolated drugs and two drug-fullerene complexes (i.e., drug-pristine C<sub>60</sub> fullerene and drug-carboxyfullerene C<sub>60</sub>-COOH) were investigated with the protein CXCR7 as the molecular docking target. The research involved over 30 drugs and employed Pearson's hard-soft acid-base theory and common QSAR/QSPR descriptors to build predictive models for the docking scores. Energetic descriptors were computed using quantum chemistry at the density functional-based tight binding DFTB3 level. The results indicate that drug-fullerene complexes interact more with CXCR7 than isolated drugs. Specific binding sites were identified, with varying locations for each drug complex. Predictive models, developed using multiple linear regression and IBM Watson artificial intelligence (AI), achieved mean absolute percentage errors below 12%, driven by AI-identified key variables. The predictive models included mainly quantitative descriptors collected from datasets as well as computed ones. In addition, a water-soluble fullerene was used to compare results obtained by DFTB3 with a conventional density functional theory approach. These findings promise to enhance breast cancer chemotherapy by leveraging fullerene-based drug nanocarriers. Quantitative structure–activity relationship ; Molecular descriptor ; Fullerene ; Nanocarriers ; Drug ; Density functional theory ; Computational chemistry ; Anticancer drug ; Pharmaceutical sciences ; Chemistry ; Stereochemistry ; Pharmacology ; Medicine ; Organic chemistry Fullerene Chemistry and Applications ; Computational Drug Discovery Methods ; Boron and Carbon Nanomaterials Research
Authors: Mukesh B. Parmar | Manisha K. Vara | Jignesh H. Pandya
Source: Discover Chemistry. (review, 2024-11-26)
Field: Chemistry — Organic Chemistry

A brief review on imidazole, triazine, and isatin derivatives: synthesis approaches and their applications This review article provides a comprehensive overview of imidazole, triazine, and isatin derivatives, focusing on their synthesis approaches and potential applications in pharmaceutical research. These molecules are characterized by their structural diversity, particularly the presence of nitrogen atoms, which can serve as primary functional groups or form complex heterocyclic systems. The derivatives display varying degrees of substitution and oxidation states, contributing to their potent biological activities. Notably, many of these compounds exhibit antiviral, antiulcer, antibacterial, and anticancer properties, with several commercially available drugs and patents utilizing these scaffolds. This review outlines the synthesis methodologies employed for these compounds and details the structural modifications that enhance their pharmacological potential. The article also lists key commercially available drugs and patents filed in various patent agencies, offering insights into the therapeutic relevance of these molecules. By presenting a detailed comparison of synthesis methods and highlighting the pharmacological applications of these scaffolds, the review serves as a valuable resource for researchers and students aiming to develop biologically active compounds. Isatin ; Imidazole ; Triazine ; Combinatorial chemistry ; Chemistry ; Computer science ; Stereochemistry ; Organic chemistry Synthesis and Characterization of Heterocyclic Compounds ; Synthesis and Biological Evaluation ; Synthesis of heterocyclic compounds
Authors: Yitao Yan | Yinglu Chen | Hanxian Hu | Youwei Jiang | Zhengzhong Kang | Jun Wu
Source: Molecules (article, 2024-05-21)
Field: Chemistry — Organic Chemistry

Discovery of a New Class of Lipophilic Pyrimidine-Biphenyl Herbicides Using an Integrated Experimental-Computational Approach Herbicides are useful tools for managing weeds and promoting food production and sustainable agriculture. In this study, we report on the development of a novel class of lipophilic pyrimidine-biphenyl (PMB) herbicides. Firstly, three PMBs, <b>Ia</b>, <b>IIa</b>, and <b>IIIa</b>, were rationally designed via a scaffold hopping strategy and were determined to inhibit acetohydroxyacid synthase (AHAS). Computational simulation was carried out to investigate the molecular basis for the efficiency of PMBs against AHAS. With a rational binding mode, and the highest in vitro as well as in vivo potency, <b>Ia</b> was identified as a preferable hit. Furthermore, these integrated analyses guided the design of eighteen new PMBs, which were synthesized via a one-step Suzuki-Miyaura cross-coupling reaction. These new PMBs, <b>Iba-ic</b>, were more effective in post-emergence control of grass weeds compared with <b>Ia</b>. Interestingly, six of the PMBs displayed 98-100% inhibition in the control of grass weeds at 750 g ai/ha. Remarkably, <b>Ica</b> exhibited ≥ 80% control against grass weeds at 187.5 g ai/ha. Overall, our comprehensive and systematic investigation revealed that a structurally distinct class of lipophilic PMB herbicides, which pair excellent herbicidal activities with new interactions with AHAS, represent a noteworthy development in the pursuit of sustainable weed control solutions. Pyrimidine ; Biphenyl ; Class (philosophy) ; Combinatorial chemistry ; Chemistry ; Computer science ; Biological system ; Biochemical engineering ; Stereochemistry ; Artificial intelligence ; Organic chemistry ; Engineering ; Biology Synthesis and Characterization of Heterocyclic Compounds ; Synthesis and biological activity ; Chemical Reaction Mechanisms
Authors: Mridul Boro | Subham Banik | Rosa M. Gomila | Antonio Frontera | Miquel Barceló‐Oliver | Manjit K. Bhattacharyya
Source: Preprints.org (preprint, 2024-04-16)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Supramolecular Assemblies in Mn(II) and Zn(II) Metal-Organic Compounds Involving Phenanthroline and Benzoate: Experimental and Theoretical Studies Two new Mn(II) and Zn(II) metal-organic compounds of 1,10-phenanthroline and methyl benzoates viz. [Mn(phen)2Cl2]2-ClBzH (1) and [Zn(4-MeBz)2(2-AmPy)2] (2) (where, 4-MeBz = 4-methylbenzoate, 2-AmPy = 2-aminopyridine, phen = 1,10-phenanthroline, 2-ClBzH = 2-chlorobenzoic acid) have been synthesized and characterized using elemental analysis, TGA, spectroscopic (FTIR, electronic) and single crystal X-ray diffraction techniques. Crystal structure analysis of the compounds reveals the presence of various non-covalent interactions which provides stability to the crystal structures. Crystal structure analysis of the compound 1 reveals the formation of supramolecular dimer of 2-ClBzH enclathrated within the hexameric host cavity formed by the neighboring monomeric units. Compound 2 is a mononuclear compound of Zn(II) where flexible binding topologies of 4-CH3Bz is observed with the metal centre. Moreover various non-covalent interactions such as lp(O)-π, lp(Cl)-π, C‒H∙∙∙Cl, π-stacking interactions as well as N‒H∙∙∙O, C‒H∙∙∙O and C‒H∙∙∙π hydrogen bonding interactions are found to be involved in plateauing the molecular self-association of the compounds. The remarkable enclathration of the H-bonded 2-ClBzH dimer into a supramolecular cavity formed by two [Mn(phen)2Cl2] complexes has been further studied theoretically using density functional theory (DFT) calculations, non-covalent interaction (NCI) plot index and quantum theory of atoms in molecules (QTAIM) computational tools. Synergistic effects have been also analysed using molecular electrostatic potential (MEP) surface analysis. Phenanthroline ; Supramolecular chemistry ; Metal ; Chemistry ; Inorganic chemistry ; Materials science ; Organic chemistry ; Molecule Magnetism in coordination complexes ; Metal complexes synthesis and properties
Authors: Yaqi Yao | Hongying Zhuo | Fanan Wang | Guiyue Bi | Jinming Xu | Xiaofeng Yang | Yanqiang Huang
Source: Catalysis Science & Technology (article, 2024-01-01)
Field: Chemistry — Organic Chemistry

Synergism between B–N atomic pair for promoting the catalytic cracking of 1,2-dichloroethane Synthesis and structural schematic diagram of BNC catalyst. Schematic ; Catalysis ; 1,2-Dichloroethane ; Chemistry ; Diagram ; Fluid catalytic cracking ; Atom (system on chip) ; Cracking ; Combinatorial chemistry ; Physics ; Organic chemistry ; Computer science ; Engineering ; Database Organoboron and organosilicon chemistry ; Ammonia Synthesis and Nitrogen Reduction ; Metal-Organic Frameworks: Synthesis and Applications