jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Jonny Proppe | Johannes Kircher
Source: ChemRxiv (preprint, 2021-07-05)
Field: Chemistry — Physical and Theoretical Chemistry

Uncertainty Quantification of Reactivity Scales ​According to Mayr, polar organic synthesis can be rationalized by a simple empirical relationship linking bimolecular rate constants to as few as three reactivity parameters. Here, we propose an extension to Mayr’s reactivity method that is rooted in uncertainty quantification and transforms the reactivity parameters into probability distributions. Through uncertainty propagation, these distributions can be transformed into uncertainty estimates for bimolecular rate constants. Chemists can exploit these virtual error bars to enhance synthesis planning and to decrease the ambiguity of conclusions drawn from experimental data. We demonstrate the above at the example of the reference data set released by Mayr and co-workers [J. Am. Chem. Soc. 2001, 123, 9500; J. Am. Chem. Soc. 2012, 134, 13902]. As by-product of the new approach, we obtain revised reactivity parameters for 36 π-nucleophiles and 32 benzhydrylium ions. Reactivity (psychology) ; Ambiguity ; Nucleophile ; Chemistry ; Product (mathematics) ; Set (abstract data type) ; Sensitivity (control systems) ; Polar ; Propagation of uncertainty ; Computational chemistry ; Statistical physics ; Biological system ; Computer science ; Mathematics ; Algorithm ; Physics ; Organic chemistry Various Chemistry Research Topics ; Analytical Chemistry and Chromatography ; Chemical Reaction Mechanisms
Authors: Sergey N. VAKHNEEV | Minggong Sha
Source: International Journal of Circuits Systems and Signal Processing (article, 2021-09-15)
Field: Materials Science — Polymers and Plastics

Preparation and Characterization of Magnetite – Silica Core – Shell Nanoparticles In this study, two types of ligands were introduced onto the surface of magnetite nanoparticles by hydrolysis and condensation of organosilicon reagents: organosilane-tetraethoxysilane (TEOS) and aminoorganosilane - aminopropyltriethoxysilane (APTES). It is shown that coatings based on SiO2 solve a double problem: first, they prevent the aggregation of nanoparticles and the oxidation of magnetite; secondly, they allow the surface to be modified with various specific ligands for biomedical applications due to terminal groups. It was shown, that after the modification of TEOS and APTES (in argon and in air), the Fe3O4 content decreases to 66, 42, and 36%, respectively. The formation of a silicon framework on the magnetite surface due to Fe-O-Si and Si-O-Si bonds was determined by IR spectroscopy. The identification of surface amino groups is complicated due to the superposition of absorption bands of NH2- and OH-groups. This opens new prospective for creation of tailored nanocomposites containing magnetite nanoparticles. These materials can be further used as sorbents for various applications. Magnetite ; Organosilicon ; Materials science ; Nanoparticle ; Surface modification ; Chemical engineering ; Nanocomposite ; Reagent ; Magnetite Nanoparticles ; Silicon ; Hydrolysis ; Nanotechnology ; Polymer chemistry ; Chemistry ; Organic chemistry ; Metallurgy ; Magnetic nanoparticles Polymer Nanocomposites and Properties ; Electromagnetic wave absorption materials ; Heat Transfer and Mathematical Modeling
Authors: Lina Alhmoud | Abdul Raouf Al Dairy | Hossam Faris | Ibrahim Aljarah
Source: Symmetry (article, 2021-06-16)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Prediction of Hysteresis Loop of Barium Hexaferrite Nanoparticles Based on Neuroevolutionary Models Neuroevolutionary models are used to predict magnetic hysteresis for barium hexaferrites (to predict magnetic hysteresis for barium hexaferrites). Magnetic hysteresis for a specific set of samples of barium hexaferrite doped with titanium were measured experimentally at room temperature and reported before. Neural networks are trained using these experimental data in order to generate magnetization and predict magnetic hysteresis for various concentrations of titanum. We present the prediction for various methods of neural calculations and the deviations from actual data results were negligible. Finally, the predictions of magnetic hysteresis are summerized for the titanume concentration between 0.0 and 1.0. Hysteresis ; Barium ; Materials science ; Magnetic hysteresis ; Magnetization ; Magnetic nanoparticles ; Condensed matter physics ; Nanoparticle ; Nuclear magnetic resonance ; Magnetic field ; Physics ; Nanotechnology ; Metallurgy Magnetic Properties and Applications ; Magnetic properties of thin films ; Magnetic Properties and Synthesis of Ferrites
Authors: Emmelyne Cuza | Samia Benmansour | Nathalie Cosquer | Françoise Conan | Carlos J. Gómez‐García | Smaı̈l Triki
Source: Preprints.org (preprint, 2021-04-19)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Solvent-Induced Hysteresis Loop in Anionic Spin Crossover (SCO) Isomorph Complexes Reactions of Fe(II) with the tris-(pyridin-2-yl)ethoxymethane (py3C-OEt) tripodal ligand in presence of the pseudohalide ancillary NCE- (E = S, Se, BH3) ligands led to a series of three mononuclear complexes formulated as [Fe(py3C-OEt)2][Fe(py3C-OEt)(NCE)3]2&amp;middot;2CH3CN, with E = S (1), BH3 (2) and Se (3). Single crystal characterizations (complexes 1-2) and X-ray powder diffraction (complexes 1-3) reveal monomeric isomorph structures formed by the spin crossover (SCO) anionic [Fe(py3C-OEt)(NCE)3] complex, associated with the low spin (LS) cationic [Fe(py3C-OEt)2]2+ complex and two solvent acetonitrile molecules. In the [Fe(py3C-OEt)2]2+ cation, the Fe(II) is coordinated by two py3C-OEt tridentate ligands, while the [Fe(py3C-OEt)(NCE)3] anion displays a hexacoordinated environment involving three N-donor atoms of one py3C-OEt ligand and three nitrogen atoms arising from of the three (NCE) coligands. The magnetic studies show the presence of gradual SCO behavior for the three complexes: a one-step transition around 205 K for 1 and two step-transitions for compounds 2 and 3, centred at 245 K and 380 K for 2, and at 170 K and 298 K for 3. The magnetic behaviors of complexes 1 and 2 remain unchanged when heating up to 500 K, while complex 3 shows significant changes which are caused by the crystallisation solvent loss above room temperature. Spin crossover ; Chemistry ; Acetonitrile ; Cationic polymerization ; Ligand (biochemistry) ; Crystallography ; Solvent ; Crystallization ; Magnetic susceptibility ; Monomer ; Ion ; Molecule ; Polymer chemistry ; Polymer ; Organic chemistry Magnetism in coordination complexes ; Lanthanide and Transition Metal Complexes ; Metal-Catalyzed Oxygenation Mechanisms
Authors: Olena Savych | Anastasia V. Gryniukova | Diana Alieksieieva | Igor Dziuba | Petro Borysko | Dmytro Dudenko | В. С. Броварец | Yurii S. Moroz
Source: Journal of organic and pharmaceutical chemistry (article, 2021-12-23)
Field: Materials Science — Materials Chemistry

The iterative application of a large chemical space in the drug discovery process Aim. To demonstrate the advantages of large-scale virtual libraries generated using chemical protocols previously validated in primary steps of the drug discovery process.Results and discussion. Two validated parallel chemistry protocols reported earlier were used to create the chemical space. It was then sampled based on diversity metric, and the sample was subjected to the virtual screening on BRD4 target. Hits of virtual screening were synthesized and tested in the thermal shift assay.Experimental part. The chemical space was generated using commercially available building blocks and synthetic protocols suitable for parallel chemistry and previously reported. After narrowing it down, using MedChem filters, the resulting sub-space was clustered based on diversity metrics. Centroids of the clusters were put to the virtual screening against the BRD4 active center. 29 Hits from the docking were synthesized and subjected to the thermal shift assay with BRD4, and 2 compounds showed noticeable dTm.Conclusions. A combination of cheminformatics and molecular docking was applied to find novel potential binders for BRD4 from a large chemical space. The selected set of predicted molecules was synthesized with a 72 % success rate and tested in a thermal shift assay to reveal a 6 % hit rate. The selection can be performed iteratively to fast support of the drug discovery. Chemical space ; Virtual screening ; Cheminformatics ; Drug discovery ; Computer science ; Chemistry ; Data mining ; Combinatorial chemistry ; Nanotechnology ; Materials science ; Computational chemistry Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Innovative Microfluidic and Catalytic Techniques Innovation
Authors: Rachida Souidi | Yasmina Khane | Lahcen Belarbi | Smaïn Bousalem
Source: Research Square (preprint, 2021-01-15)
Field: Materials Science — Biomaterials

Methylene Blue Adsorption from aqueous solution by low cost vine-wood biomass Abstract In this work, the sawdust of vine wood (VW) was treated with sulfuric acid and used to adsorb methylene blue (MB) from aqueous solutions via a batch adsorption process. The characteristics of the adsorbent were determined by various analytical techniques such as Fourier-transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD) and scanning electron microscopy (SEM) and Brunauer−Emmett−Teller (BET) N 2 adsorption−desorption isotherms. The effects of various experimental parameters including sulfuric acid concentration, particle size of the adsorbent, pH of the solution, contact time, initial concentration, adsorbent dosage and temperature on adsorption of MB by activating sawdust were systematically investigated. The experimental results showed that the adsorption efficiency was increased with contact time and adsorbent dosage. The maximum removal efficiency was found after 180 min of solid/liquid contact with adsorbent doses of 1 g/l for sawdust. The isotherm and kinetic experimental data for MB adsorption on VW sawdust were best-fitted by Langmuir models and Pseudo-second-order, respectively. The calculated values of the entropy (ΔS°), enthalpy (ΔH°) and Gibbs energy (ΔG°) indicated that the adsorption process was exothermic in nature. These results suggest that the activated sawdust can be employed as a low-cost and environmentally friendly adsorbent for the treatment of wastewaters containing dyes. Methylene blue ; Vine ; Adsorption ; Aqueous solution ; Biomass (ecology) ; Chemistry ; Pulp and paper industry ; Methylene ; Waste management ; Environmental science ; Horticulture ; Organic chemistry ; Agronomy ; Engineering ; Biology ; Catalysis Advanced Cellulose Research Studies ; Adsorption and biosorption for pollutant removal ; Enzyme-mediated dye degradation
Authors: Bhuvanesh Sridharan | Sarvesh Mehta | Yashaswi Pathak | U. Deva Priyakumar
Source: ChemRxiv (preprint, 2021-12-15)
Field: Chemistry — Physical and Theoretical Chemistry

Spectra to Structure: Deep Reinforcement Learning for Molecular Inverse Problem Spectroscopy is the study of how matter interacts with electromagnetic radiations of specific frequencies that has led to several monumental discoveries in science. The spectra of any particular molecule is highly information-rich, yet the inverse relation from the spectra to the molecular structure is still an unsolved problem. Nuclear Magnetic Resonance (NMR) spectroscopy is one such critical tool in the tool-set for scientists to characterise any chemical sample. In this work, a novel framework is proposed that attempts to solve this inverse problem by navigating the chemical space to find the correct structure that resulted in the target spectra. The proposed framework uses a combination of online Monte- Carlo-Tree-Search (MCTS) and a set of offline trained Graph Convolution Networks to build a molecule iteratively from scratch. Our method is able to predict the correct structure of the molecule ∼80% of the time in its top 3 guesses. We believe that the proposed framework is a significant step in solving the inverse design problem of NMR spectra to molecule. Inverse problem ; Computer science ; Inverse ; Spectral line ; Monte Carlo method ; Set (abstract data type) ; Algorithm ; Physics ; Mathematics ; Quantum mechanics ; Mathematical analysis Various Chemistry Research Topics ; Machine Learning in Materials Science
Authors: Kamalpreet Kaur | Vivek Asati
Source: Research Square (preprint, 2021-07-19)
Field: Chemistry — Organic Chemistry

Design, Synthesis and Molecular Modeling Studies of Thiosemicarbazone &amp;amp; Thiazole Derivatives as Potential Anti-Malarial Agents Semicarbazone ; Thiazole ; Chemistry ; Combinatorial chemistry ; Stereochemistry ; Biochemistry Synthesis and biological activity ; Research on Leishmaniasis Studies ; Synthesis and Characterization of Heterocyclic Compounds
Authors: Jong‐Won Park | Lee-Woon Jang | Erik C. Jensen | Amanda M. Stockton | Jungkyu Kim
Source: Biosensors (article, 2021-10-23)
Field: Chemistry — Analytical Chemistry

Sensing Techniques for Organochlorides through Intermolecular Interaction with Bicyclic Amidines Toxic organochloride molecules are widely used in industry for various purposes. With their high volatility, the direct detection of organochlorides in environmental samples is challenging. Here, a new organochloride detection mechanism using 1,5-diazabicyclo[4.3.0]non-5-ene (DBN) is introduced to simplify a sensing method with higher detection sensitivity. Three types of organochloride compounds-trichloroethylene (TCE), dichloromethane (DCM), and dichlorodiphenyltrichloroethane (DDT)-were targeted to understand DCM conjugation chemistry by using nuclear magnetic resonance (NMR) and liquid chromatography with a mass spectrometer (LC-MS). <sup>13</sup>C-NMR spectra and LC-MS data indicated that DBN can be labeled on these organochloride compounds by chlorine-nitrogen interaction. Furthermore, to demonstrate the organochloride sensing capability, the labeling yield and limit of detection were determined by a colorimetric assay as well as micellar electrokinetic chromatography (MEKC). The interaction with DBN was most appreciable for TCE, among other organochlorides. TCE was detected at picomolar levels, which is two orders of magnitude lower than the maximum contaminant level set by the United States Environmental Protection Agency. MEKC, in conjunction with this DBN-labeling method, enables us to develop a field-deployable sensing platform for detecting toxic organochlorides with high sensitivity. Chemistry ; Chromatography ; Analyte ; Detection limit ; Dichloromethane ; Chlorine ; Trichloroethylene ; Solvent ; Environmental chemistry ; Organic chemistry Analytical chemistry methods development ; Electrochemical Analysis and Applications ; Molecular Sensors and Ion Detection
Authors: Tianbo Qiao
Source: Annales de Chimie Science des Matériaux (article, 2021-04-30)
Field: Materials Science — Polymers and Plastics

Application of Conductive Polymer-Based Hydrogel in Multi-robot Balance Control At present, the flexible electronic materials with both good flexibility and conductivity have become a major development trend of electronic materials in the future. Due to their flexibility in construction, controllable mechanical properties and electrical conductivity, the conductive polymer-based hydrogels (CPHs) are expected to become one of the candidate materials in flexible electronics and other fields, and have received extensive attention from researchers. However, the existing CPH systems generally have shortcomings such as low mechanical strength and single function. To this end, the authors attempt to construct a hydrogel using polyaniline (PANI) as the conductive component and polyacrylic acid (PAA) as the flexible component through in-situ polymerization and physical blending. The designed PAA/PANI conductive polymer-based hydrogel enjoys ultra-long stretchability and high strength. It can be used in the flexible strain sensors and pressure sensors to detect the step cycle of the multi-legged robot in real time, and adjust their rhythm during the walking gait, thereby achieving the physical balance. This paper provides a new idea for the application of the CPHs, and especially offers a wealth of theoretical foundation and practical experience for the research on its application to the flexible strain sensors. Flexibility (engineering) ; Polyaniline ; Materials science ; Self-healing hydrogels ; Electrical conductor ; Conductive polymer ; Robot ; Resistor ; Electronics ; Polyacrylic acid ; Nanotechnology ; Flexible electronics ; Computer science ; Electronic component ; Component (thermodynamics) ; Polymer ; Mechanical engineering ; Composite material ; Polymerization ; Electrical engineering ; Voltage ; Engineering ; Polymer chemistry ; Physics ; Artificial intelligence Conducting polymers and applications ; Advanced Sensor and Energy Harvesting Materials ; Muscle activation and electromyography studies
Authors: Ana Vitória Sousa Penha | Karine Oliveira Moura | Gizeuda L. Paz
Source: Revista Virtual de Química (review, 2021-01-01)
Field: Chemistry — Organic Chemistry

Contaminated Water Treatment: A Review on Adsorption of Amido Black 10B Dye The contamination of water by dyes has become one of the most serious problems in our society, due to the toxicity of these substances, as well as the possibility of damage to the environment and human health. So, the removal of these pollutants from wastewater using adsorption has received much attention due to the efficiency and viability of this process. Therefore, this article provides information from the literature on the removal of the amido black 10B dye in various adsorbents. In general, the results show that adsorption is more favorable at acid pH, increasing the initial concentration of the dye decreases the removal percentage, while increasing the dosage of adsorbent leads to an increase in this percentage. In addition, the adsorption equilibrium data are better suited to the Langmuir or Freundlich models and, in most cases, follow pseudo-second-order kinetic model. Adsorption ; Water treatment ; Chemistry ; Contaminated water ; Environmental chemistry ; Environmental science ; Environmental engineering ; Organic chemistry Synthesis of Tetrazole Derivatives ; Water Quality Monitoring and Analysis ; Dye analysis and toxicity
Authors: Alastair Skeffington | Marc Gentzel | André Ohara | Alexander Milentyev | Christoph Heintze | Lorenz Böttcher | Stefan Görlich | Andrej Shevchenko | Nicole Poulsen | Nils Kröger
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2021-09-19)
Field: Materials Science — Biomaterials

Shedding light on biosilica morphogenesis by comparative analysis of the silica-associated proteomes from three diatom species Summary Morphogenesis of the intricate patterns of diatom silica cell walls is a protein-guided process, yet to date only very few such silica morphogenetic proteins have been identified. Therefore, it is unknown whether all diatoms share conserved proteins of a basal silica forming machinery, and whether unique proteins are responsible for the morphogenesis of species specific silica patterns. To answer these questions, we extracted proteins from the silica of three diatom species ( Thalassiosira pseudonana, Thalassiosira oceanica and Cyclotella cryptica ) by complete demineralization of the cell walls. LC-MS/MS analysis of the extracts identified 92 proteins that we name ‘Soluble Silicome Proteins’ (SSPs). Surprisingly, no SSPs are common to all three species, and most SSPs showed very low similarity to one another in sequence alignments. In depth bioinformatics analyses revealed that SSPs can be grouped into distinct classes bases on short unconventional sequence motifs whose functions are yet unknown. The results from in vivo localization of selected SSPs indicates that proteins, which lack sequence homology but share unconventional sequence motifs may exert similar functions in the morphogenesis of the diatom silica cell wall. Diatom ; Thalassiosira pseudonana ; Morphogenesis ; Biology ; Proteome ; Cell wall ; Frustule ; Botany ; Cell biology ; Biochemistry ; Gene ; Ecology ; Nutrient Diatoms and Algae Research ; Protist diversity and phylogeny ; Marine and coastal ecosystems
Authors: Vaska Petakova | Miroslava Nedyalkova | Joanna Stoycheva | Alia Tadjer | Julia Romanova
Source: Symmetry (article, 2021-08-07)
Field: Chemistry — Organic Chemistry

The Interplay between Diradical Character and Stability in Organic Molecules The number of scientific papers on the unique properties and the potential for various applications of compounds with a diradical character is growing constantly. The diradical character enhances and even engenders certain desired optical properties and its modulation is a modern molecular design strategy. Nowadays, molecules with a non-zero diradical character are regarded as promising materials for new-generation and highly efficient solar cells and photonics devices. What is the price, however, of the unique properties of open-shell compounds? Alongside all the benefits, the diradical character is usually associated with low stability and high reactivity—unwanted molecular qualities for practical purposes. Thus, from a fundamental and applied point of view, it is important to investigate the correlation between the diradical character and laboratory stability, which is the goal of the present paper. Here, we report a combined quantum–chemical study (conceptual DFT and spin-projected HF theory) and multivariate analysis of the diradical character of a series of o- and p-quinomethides, for the stability of which experimental data are available. Our results reveal that a compromise between the diradical character and laboratory stability of a molecule is feasible and that the relationship between these two quantities can be understood in the framework of Clar’s sextet theory. Diradical ; Character (mathematics) ; Stability (learning theory) ; Molecule ; Chemical physics ; Nanotechnology ; Chemistry ; Computer science ; Materials science ; Physics ; Quantum mechanics ; Mathematics Synthesis and Properties of Aromatic Compounds ; Advanced Chemical Physics Studies ; Molecular spectroscopy and chirality
Authors: Henry Wladkowski | Julian Duarte | Shashank R. Nandyala | Joshua S. Walker | Subash Kattel | Jeffrey L. Blackburn | Jeffrey Fagan | Jon M. Pikal | William Rice
Source: Journal of Applied Physics (article, 2021-01-15)
Field: Materials Science — Materials Chemistry

Polyvinyl acetate-based polymer host for optical and far-infrared spectroscopy of individualized nanoparticles Preparation techniques for producing films of individualized solution-dispersed nanoparticles (NPs) for optical spectroscopy are often technically challenging and tailored for a specific NP system. In this work, we present a rapid, easy, and economical technique for producing polyvinyl acetate (PVAc)-based NP-polymer films on the order of 100’s of micrometers thick that exhibit high uniformity, low aggregation, excellent optical transparency, and low terahertz absorption. In addition, we find that these films are robust at cryogenic temperatures and have a high laser damage threshold of 0.3 TW cm−2, which make them suitable for pulsed laser measurements. We show that free-standing, flexible, PVAc films can incorporate both one-dimensional single-wall carbon nanotubes (SWCNTs) and zero-dimensional Au NPs. Using absorbance, Raman scattering, and photoluminescence excitation spectroscopy, we observe that SWCNT individualization is maintained, and minimized polymer strain imposed, when the nanotubes are transitioned from the solution to the polymer host. This PVAc-based polymer host presents researchers with a straightforward method for producing free-standing and flexible NP films with low aggregation. Materials science ; Polyvinyl acetate ; Polymer ; Absorbance ; Spectroscopy ; Raman spectroscopy ; Nanoparticle ; Photoluminescence ; Carbon nanotube ; Chemical engineering ; Nanotechnology ; Optoelectronics ; Composite material ; Optics Carbon Nanotubes in Composites ; Nonlinear Optical Materials Studies ; Silicon Nanostructures and Photoluminescence