jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Anastasia Yu. Molokova | Reza K. Abasabadi | Elisa Borfecchia | Olivier Mathon | Silvia Bordiga | Fei Wen | Gloria Berlier | Ton V. W. Janssens | Kirill A. Lomachenko
Source: Chemical Science (article, 2023-01-01)
Field: Materials Science — Materials Chemistry

Elucidating the reaction mechanism of SO<sub>2</sub> with Cu-CHA catalysts for NH<sub>3</sub>-SCR by X-ray absorption spectroscopy The application of Cu-CHA catalysts for the selective catalytic reduction of NO<sub><i>x</i></sub> by ammonia (NH<sub>3</sub>-SCR) in exhaust systems of diesel vehicles requires the use of fuel with low sulfur content, because the Cu-CHA catalysts are poisoned by higher concentrations of SO<sub>2</sub>. Understanding the mechanism of the interaction between the Cu-CHA catalyst and SO<sub>2</sub> is crucial for elucidating the SO<sub>2</sub> poisoning and development of efficient catalysts for SCR reactions. Earlier we have shown that SO<sub>2</sub> reacts with the [Cu<sub>2</sub><sup>II</sup>(NH<sub>3</sub>)<sub>4</sub>O<sub>2</sub>]<sup>2+</sup> complex that is formed in the pores of Cu-CHA upon activation of O<sub>2</sub> in the NH<sub>3</sub>-SCR cycle. In order to determine the products of this reaction, we use X-ray absorption spectroscopy (XAS) at the Cu K-edge and S K-edge, and X-ray emission spectroscopy (XES) for Cu-CHA catalysts with 0.8 wt% Cu and 3.2 wt% Cu loadings. We find that the mechanism for SO<sub>2</sub> uptake is similar for catalysts with low and high Cu content. We show that the SO<sub>2</sub> uptake proceeds <i>via</i> an oxidation of SO<sub>2</sub> by the [Cu<sub>2</sub><sup>II</sup>(NH<sub>3</sub>)<sub>4</sub>O<sub>2</sub>]<sup>2+</sup> complex, resulting in the formation of different Cu<sup>I</sup> species, which do not react with SO<sub>2</sub>, and a sulfated Cu<sup>II</sup> complex that is accumulated in the pores of the zeolite. The increase of the SO<sub>2</sub> uptake upon addition of oxygen to the SO<sub>2</sub>-containing feed, evidenced by X-ray adsorbate quantification (XAQ) and temperature-programmed desorption of SO<sub>2</sub>, is explained by the re-oxidation of the Cu<sup>I</sup> species into the [Cu<sub>2</sub><sup>II</sup>(NH<sub>3</sub>)<sub>4</sub>O<sub>2</sub>]<sup>2+</sup> complexes, which makes them available for reaction with SO<sub>2</sub>. Catalysis ; X-ray absorption spectroscopy ; Chemistry ; NOx ; Selective catalytic reduction ; Ammonia ; Inorganic chemistry ; Reaction mechanism ; Redox ; Desorption ; Zeolite ; Sulfur ; Absorption spectroscopy ; Adsorption ; Physical chemistry ; Organic chemistry Catalytic Processes in Materials Science ; Ammonia Synthesis and Nitrogen Reduction ; Gas Sensing Nanomaterials and Sensors
Authors: Ashley K. Alexander | Sherif I. Elshahawi
Source: ChemBioChem (review, 2023-06-20)
Field: Chemistry — Organic Chemistry

Promiscuous Enzymes for Residue‐Specific Peptide and Protein Late‐Stage Functionalization The late-stage functionalization of peptides and proteins holds significant promise for drug discovery and facilitates bioorthogonal chemistry. This selective functionalization leads to innovative advances in in vitro and in vivo biological research. However, it is a challenging endeavor to selectively target a certain amino acid or position in the presence of other residues containing reactive groups. Biocatalysis has emerged as a powerful tool for selective, efficient, and economical modifications of molecules. Enzymes that have the ability to modify multiple complex substrates or selectively install nonnative handles have wide applications. Herein, we highlight enzymes with broad substrate tolerance that have been demonstrated to modify a specific amino acid residue in simple or complex peptides and/or proteins at late-stage. The different substrates accepted by these enzymes are mentioned together with the reported downstream bioorthogonal reactions that have benefited from the enzymatic selective modifications. Bioorthogonal chemistry ; Biocatalysis ; Chemistry ; Enzyme ; Biochemistry ; Residue (chemistry) ; Peptide ; Amino acid residue ; Combinatorial chemistry ; Amino acid ; Bioconjugation ; Protein engineering ; Peptide sequence ; Click chemistry ; Reaction mechanism ; Catalysis Click Chemistry and Applications ; Biochemical and Structural Characterization ; Peptidase Inhibition and Analysis
Authors: Jonathan W. Zheng | William H. Green
Source: The Journal of Physical Chemistry A (article, 2023-11-27)
Field: Chemistry — Organic Chemistry

Experimental Compilation and Computation of Hydration Free Energies for Ionic Solutes Although charged solutes are common in many chemical systems, traditional solvation models perform poorly in calculating solvation energies of ions. One major obstacle is the scarcity of experimental data for solvated ions. In this study, we release an experiment-based aqueous ionic solvation energy data set, IonSolv-Aq, that contains hydration free energies for 118 anions and 155 cations, more than 2 times larger than the set of hydration free energies for singly charged ions contained in the 2012 Minnesota Solvation Database commonly used in benchmarking studies. We discuss sources of systematic uncertainty in the data set and use the data to examine the accuracy of popular implicit solvation models COSMO-RS and SMD for predicting solvation free energies of singly charged ionic solutes in water. Our results indicate that most SMD and COSMO-RS modeling errors for ionic solutes are systematic and correctable with empirical parameters. We discuss two systematic offsets: one across all ions and one that depends on the functional group of the ionization site. After correcting for these offsets, solvation energies of singly charged ions are predicted using COSMO-RS to 3.1 kcal mol<sup>-1</sup> MAE against a challenging test set and 1.7 kcal mol<sup>-1</sup> MAE (about 3% relative error) with a filtered test set. The performance of SMD is similar, with MAE against those same test sets of 2.7 and 1.7 kcal mol<sup>-1</sup>. These results underscore the importance of compiling larger experimental data sets to improve solvation model parametrization and fairly assess performance. Solvation ; Chemistry ; Ionic bonding ; Ion ; Parametrization (atmospheric modeling) ; Computational chemistry ; Chemical physics ; Physics ; Organic chemistry ; Quantum mechanics Free Radicals and Antioxidants ; Spectroscopy and Quantum Chemical Studies ; Computational Drug Discovery Methods
Authors: Kun Lin | Wenbin Zhang | Chengyi Yu | Qiang Sun | Yili Cao | Wenjie Li | Suihe Jiang | Qiang Li | Qiang Zhang | Ke An | Yan Chen | Dunji Yu | Jue Liu | Kenichi Kato | Qinghua Zhang | Lin Gu | Xiaojun Kuang | Yu Tang | Jun Miao | Xianran Xing
Source: Cell Reports Physical Science (article, 2023-01-25)
Field: Materials Science — Materials Chemistry

Chemical heterogeneity modulated zero thermal expansion alloy over super-wide temperature range Chemical heterogeneity is usually avoided in solution chemistry, but it may still occur with sometimes dramatic effects on target materials and their properties. Here, we propose chemical heterogeneity as a counterintuitive strategy to design high-performance zero thermal expansion (ZTE) alloys. We apply this approach in a Hf-Ti-Fe alloy with excess Fe in the Hf/Ti sublattice and produce Hf/Ti concentration alternations at the micro level. Such chemical heterogeneity regulates local magnetic interactions in alloy and triggers a dispersed magnetic phase transition that modulates the thermal expansions at the micro level and hence results in a remarkable ZTE behavior over a super-wide temperature window from 10 to 480 K. This mechanism is supported by comprehensive studies on morphological microstructures, crystal and magnetic structures, and theoretical calculations. The strategy of local chemical heterogeneity opens up an avenue to design ZTE and the related functional materials directly via microstructure engineering. Alloy ; Microstructure ; Materials science ; Thermal ; Counterintuitive ; Atmospheric temperature range ; Thermal expansion ; Range (aeronautics) ; Chemical physics ; Condensed matter physics ; Thermodynamics ; Metallurgy ; Chemistry ; Composite material ; Physics Thermal Expansion and Ionic Conductivity ; Ferroelectric and Piezoelectric Materials ; Rare-earth and actinide compounds
Authors: Wataru Matsuoka | Yu Harabuchi | Yuuya Nagata | Satoshi Maeda
Source: Organic & Biomolecular Chemistry (article, 2023-01-01)
Field: Chemistry — Organic Chemistry

Highly chemoselective ligands for Suzuki–Miyaura cross-coupling reaction based on virtual ligand-assisted screening Ligand screening is a crucial step in the development of transition metal catalysis, as it involves identifying the optimal ligand for a particular reaction from a large pool of candidate molecules. Conventionally, this process is performed through an experimental trial-and-error, which can be time-consuming and resource-intensive in many cases. One of the ideal strategies for streamlining this process is a transition state theory (TST)-based approach, which aims to design optimal catalysts that results in the best energy profile for the desired reaction. However, the implementation of TST-based ligand screening remains challenging mainly due to the large number of potential ligands that need to be individually evaluated through quantum chemical calculations. In this study, we experimentally demonstrated a practical TST-based ligand screening in accordance with our virtual ligand-assisted (VLA) screening strategy. As a case study, the electronic anc steric features of phosphine ligands that maximize chemoselectivity in the Suzuki-Miyaura cross-coupling (SMC) reaction of <i>p</i>-chlorophenyl triflate were determined through quantum chemical calculations using virtual ligands, and several phosphine ligands were suggested to exhibit high chemoselectivity. Based on this suggestion, we successfully found that tri(1-adamantyl)phosphine and tri(neopentyl)phosphine show high to excellent selectivity for the C-Cl bond activation. This case study suggests that the VLA screening strategy could be a useful tool for ligand screening. Chemoselectivity ; Ligand (biochemistry) ; Phosphine ; Steric effects ; Combinatorial chemistry ; Chemistry ; Trifluoromethanesulfonate ; Virtual screening ; Catalysis ; Computational chemistry ; Stereochemistry ; Organic chemistry ; Molecular dynamics Catalytic Cross-Coupling Reactions ; Radical Photochemical Reactions ; Machine Learning in Materials Science
Authors: Nikolina Kovačev | Omid Doustdar | Sheng Li | A. Tsolakis | J.M. Herreros | Khamis Essa
Source: Chemical Engineering Science (article, 2023-01-18)
Field: Materials Science — Materials Chemistry

The synergy between substrate architecture of 3D-printed catalytic converters and hydrogen for low-temperature aftertreatment systems This study proposes 3D-printed diamond-based lattice substrates as catalytic converters in the automotive aftertreatment system to improve vehicle cold-start emissions. The study aimed to compare the influence of 3D-printed diamond-based catalyst structures on the light-off behaviour compared to the conventional 400 Cell Per Square Inch (CPSI) honeycomb catalyst design in a real exhaust gas environment. Moreover, the benefits of H2 addition on the performance of advanced lattice structures are examined for the first time to further increase the low-temperature catalytic efficiency. Digital Light Processing (DLP) technology was effectively utilised to manufacture lattice structures with high cell density to allow a comparison between conventional and advanced geometry designs. Further, the 3D-printed substrates were catalyst coated, and their light-off behaviour was studied in a diesel exhaust environment. The results of the light-off showed a significant improvement in the light-off temperatures for CO, THC and NO in the 3D-printed lattice structures. Furthermore, H2 presence additionally enhanced the low-temperature activity of the AM lattice structures. Catalysis ; Materials science ; 3d printed ; Diamond ; Mesoporous material ; Lattice (music) ; Chemical engineering ; Converters ; Nanotechnology ; Optoelectronics ; Chemistry ; Composite material ; Engineering ; Electrical engineering ; Organic chemistry ; Biomedical engineering Catalytic Processes in Materials Science ; Catalysis and Oxidation Reactions ; Advancements in Solid Oxide Fuel Cells
Authors: Sanghun Shin | Minjun Kwon | Sewon Kim | Hongyun So
Source: International Journal of Energy Research (article, 2023-09-06)
Field: Chemistry — Spectroscopy

Prediction of Equivalence Ratio in Combustion Flame Using Chemiluminescence Emission and Deep Neural Network A reliable combustion monitoring system is essential to satisfy global carbon neutrality trends. As the concentrations of emissions and flame stability are associated with the air–fuel ratio, the equivalence ratio should be continuously evaluated. In this study, a deep neural network- (DNN-) based regression model is proposed to predict the equivalence ratio of turbulent diffusion flames. Chemiluminescence signals from the OH <a:math xmlns:a="http://www.w3.org/1998/Math/MathML" id="M1"> <a:msup> <a:mrow/> <a:mrow> <a:mo>∗</a:mo> </a:mrow> </a:msup> </a:math> , CH <c:math xmlns:c="http://www.w3.org/1998/Math/MathML" id="M2"> <c:msup> <c:mrow/> <c:mrow> <c:mo>∗</c:mo> </c:mrow> </c:msup> </c:math> , and C2 <e:math xmlns:e="http://www.w3.org/1998/Math/MathML" id="M3"> <e:msup> <e:mrow/> <e:mrow> <e:mo>∗</e:mo> </e:mrow> </e:msup> </e:math> radicals were acquired as input features. In addition, three different optical sensing views were applied to consider the future general measurement conditions. Furthermore, a loss function comparison for model training and hyperparameter tuning techniques, such as random search and Bayesian optimization, were used to improve the prediction performance. Consequently, the enhanced DNN model showed reductions in the mean absolute error and root mean square error of ~17.84% and ~12.06%, respectively, compared with the initial model. In addition, a mean absolute percentage error and <g:math xmlns:g="http://www.w3.org/1998/Math/MathML" id="M4"> <g:mi>R</g:mi> </g:math> -squared value of ~3.61% and ~0.9311, respectively, were obtained. Thus, a novel sensing method has been proposed for flame monitoring systems to realize future digital transformations in the combustion industry. Hyperparameter ; Mean squared error ; Equivalence (formal languages) ; Combustion ; Artificial neural network ; Mathematics ; Mean absolute error ; Approximation error ; Hyperparameter optimization ; Algorithm ; Applied mathematics ; Analytical Chemistry (journal) ; Statistics ; Computer science ; Discrete mathematics ; Machine learning ; Chemistry ; Chromatography ; Organic chemistry Spectroscopy and Laser Applications ; Combustion and flame dynamics ; Air Quality Monitoring and Forecasting
Authors: Taiki Fujimoto | Hiroaki Gotoh
Source: Molecules (article, 2023-02-02)
Field: Chemistry — Organic Chemistry

Feature Selection for the Interpretation of Antioxidant Mechanisms in Plant Phenolics Antioxidants, represented by plant phenolics, protect living tissues by scavenging reactive oxygen species through diverse reaction mechanisms. Research on antioxidants is often individualized, for example, focusing on the evaluation of their activity against a single reactive oxygen species or examining the antioxidant properties of compounds with similar structures. In this study, multivariate analysis was used to comprehensively examine antioxidant properties. Eighteen features were selected to explain the results of the antioxidant capacity tests. These selected features were then evaluated by supervised learning, using the results of the antioxidant capacity assays. Dimension-reduction techniques were also used to represent the compound space with antioxidants as a two-dimensional distribution. A small amount of data obtained from several assays provided us with comprehensive information on the relationships between the structures and activities of antioxidants. Antioxidant ; Reactive oxygen species ; Antioxidant capacity ; Chemistry ; Feature selection ; Computational biology ; Biological system ; Machine learning ; Biochemistry ; Biology ; Computer science Free Radicals and Antioxidants ; Computational Drug Discovery Methods ; Phytochemicals and Antioxidant Activities
Authors: Baozhi Cui | Jun Cui | Daniel J. Barnard | Leonard J. Bond
Source: Journal of Magnetism and Magnetic Materials (article, 2023-02-11)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Internal defect detection and characterization of samarium-cobalt sintered magnets by ultrasonic testing technique Magnet ; Materials science ; Neodymium magnet ; Samarium ; Machinability ; Nondestructive testing ; Scrap ; Nuclear engineering ; Mechanical engineering ; Metallurgy ; Machining Magnetic Properties of Alloys ; Magnetic Properties and Applications ; Superconducting Materials and Applications
Authors: Shizhuang Weng | Junjie Ma | Wentao Tao | Yujian Tan | Meijing Pan | Zixi Zhang | Linsheng Huang | Ling Zheng | Jinling Zhao
Source: Frontiers in Plant Science (article, 2023-02-28)
Field: Chemistry — Analytical Chemistry

Drought stress identification of tomato plant using multi-features of hyperspectral imaging and subsample fusion Drought stress (DS) is one of the most frequently occurring stresses in tomato plants. Detecting tomato plant DS is vital for optimizing irrigation and improving fruit quality. In this study, a DS identification method using the multi-features of hyperspectral imaging (HSI) and subsample fusion was proposed. First, the HSI images were measured under imaging condition with supplemental blue lights, and the reflectance spectra were extracted from the HSI images of young and mature leaves at different DS levels (well-watered, reduced-watered, and deficient-watered treatment). The effective wavelengths (EWs) were screened by the genetic algorithm. Second, the reference image was determined by ReliefF, and the first four reflectance images of EWs that are weakly correlated with the reference image and mutually irrelevant were obtained using Pearson's correlation analysis. The reflectance image set (RIS) was determined by evaluating the superposition effect of reflectance images on identification. The spectra of EWs and the image features extracted from the RIS by LeNet-5 were adopted to construct DS identification models based on support vector machine (SVM), random forest, and dense convolutional network. Third, the subsample fusion integrating the spectra and image features of young and mature leaves was used to improve the identification further. The results showed that supplemental blue lights can effectively remove the high-frequency noise and obtain high-quality HSI images. The positive effect of the combination of spectra of EWs and image features for DS identification proved that RIS contains feature information pointing to DS. Global optimal classification performance was achieved by SVM and subsample fusion, with a classification accuracy of 95.90% and 95.78% for calibration and prediction sets, respectively. Overall, the proposed method can provide an accurate and reliable analysis for tomato plant DS and is hoped to be applied to other crop stresses. Hyperspectral imaging ; Artificial intelligence ; Support vector machine ; Identification (biology) ; Pattern recognition (psychology) ; Computer science ; Random forest ; Feature (linguistics) ; Multispectral image ; Image fusion ; Remote sensing ; Reflectivity ; Mathematics ; Convolutional neural network ; Computer vision ; Image (mathematics) ; Botany ; Biology ; Geology ; Optics ; Physics Spectroscopy and Chemometric Analyses ; Remote Sensing in Agriculture ; Leaf Properties and Growth Measurement
Authors: Jean‐Louis Barrat | Ludovic Berthier
Source: Comptes Rendus Physique (article, 2023-04-20)
Field: Materials Science — Materials Chemistry

Computer simulations of the glass transition and glassy materials We provide an overview of the different types of computational techniques developed over the years to study supercooled liquids, glassy materials and the physics of the glass transition. We organise these numerical strategies into four broad families. For each of them, we describe the general ideas without discussing any technical details. We summarise the type of questions which can be addressed by any given approach and outline the main results which have been obtained. Finally we describe two important directions for future computational studies of glassy systems. Supercooling ; Glass transition ; Computer science ; Statistical physics ; Transition (genetics) ; Engineering physics ; Materials science ; Physics ; Thermodynamics ; Chemistry ; Polymer Material Dynamics and Properties ; Theoretical and Computational Physics ; Glass properties and applications
Authors: Quentin Guillet | Libor Vojáček | Djordje Došenović | Fatima Ibrahim | H. Boukari | Jing Li | Fadi Choueikani | Philippe Ohresser | Abdelkarim Ouerghi | Florie Mesple | V. Renard | Jean‐François Jacquot | D. Jalabert | Hanako Okuno | Mairbek Chshiev | Céline Vergnaud | Frédéric Bonell | A. Marty | Matthieu Jamet
Source: Physical Review Materials (article, 2023-05-16)
Field: Materials Science — Materials Chemistry

Epitaxial van der Waals heterostructures of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mi mathvariant="normal">Cr</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:msub><mml:mi mathvariant="normal">Te</mml:mi><mml:mn>3</mml:mn></mml:msub></mml:math> on two-dimensional materials Achieving large-scale growth of two-dimensional (2D) ferromagnetic materials with high Curie temperature ${T}_{\mathrm{C}}$ and perpendicular magnetic anisotropy (PMA) is highly desirable for the development of ultracompact magnetic sensors and magnetic memories. In this context, van der Waals (vdW) ${\mathrm{Cr}}_{2}{\mathrm{Te}}_{3}$ appears to be a promising candidate. Bulk ${\mathrm{Cr}}_{2}{\mathrm{Te}}_{3}$ exhibits strong PMA and a ${T}_{\mathrm{C}}$ of 180 K. Moreover, both PMA and ${T}_{\mathrm{C}}$ might be adjusted in ultrathin films by engineering composition or strain or applying an electric field. In this work, we demonstrate the molecular beam epitaxy (MBE) growth of vdW heterostructures of five-monolayer quasifreestanding ${\mathrm{Cr}}_{2}{\mathrm{Te}}_{3}$ on three classes of 2D materials: graphene (semimetal), ${\mathrm{WSe}}_{2}$ (semiconductor), and ${\mathrm{Bi}}_{2}{\mathrm{Te}}_{3}$ (topological insulator). By combining structural and chemical analysis down to the atomic level with ab initio calculations, we confirm the single-crystalline character of ${\mathrm{Cr}}_{2}{\mathrm{Te}}_{3}$ films on the 2D materials with sharp vdW interfaces. They all exhibit PMA and ${T}_{\mathrm{C}}$ close to the bulk ${\mathrm{Cr}}_{2}{\mathrm{Te}}_{3}$ value of 180 K. Ab initio calculations confirm this PMA and show how its strength depends on strain. Finally, Hall measurements reveal a strong anomalous Hall effect, which changes sign at a given temperature. We theoretically explain this effect by a sign change of the Berry phase close to the Fermi level. This transition temperature depends on the 2D material in proximity, notably as a consequence of charge transfer. MBE-grown ${\mathrm{Cr}}_{2}{\mathrm{Te}}_{3}$/2D material bilayers constitute model systems for the further development of spintronic devices combining PMA, large spin-orbit coupling, and sharp vdW interface. Condensed matter physics ; Materials science ; van der Waals force ; Curie temperature ; Ab initio ; Ab initio quantum chemistry methods ; Crystallography ; Ferromagnetism ; Physics ; Chemistry ; Quantum mechanics 2D Materials and Applications ; Topological Materials and Phenomena ; Graphene research and applications