jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Isaiah O. Betinol | Saumya Thakur | Jolene P. Reid
Source: ChemRxiv (preprint, 2022-12-16)
Field: Materials Science — Materials Chemistry

An Unsupervised Machine Learning Workflow for Assigning and Predicting Generality in Asymmetric Catalysis The development of chiral catalysts that can provide high enantioselectivities across a wide assortment of substrates or reaction range is a priority for many catalyst design efforts. While several approaches are available to aid in the identification of general catalyst systems there is currently no simple procedure for directly measuring how general a given catalyst could be. Herein, we present a catalyst-agnostic workflow centered on unsupervised machine learning that enables the rapid assessment and quantification of catalyst generality. The workflow uses curated literature data sets and reaction descriptors to visualize and cluster chemical space coverage. This reaction network can then be applied to derive a catalyst generality metric through designer equations and interfaced with other regression techniques for general catalyst prediction. As validating case studies, we have successfully applied this method to identify-through-quantification the most general catalyst chemotype for an organocatalytic asymmetric Mannich reaction and predicted the most general chiral phosphoric acid catalyst for the addition of nucleophile to imines. The mechanistic basis for catalyst generality can then be gleaned from the calculated values by deconstructing the contributions of chemical space and enantiomeric excess to the overall result. We conclude that broadly applicable catalysts may be more adaptative to changes in reactant structure because enantioinduction does not rely on a single set of noncovalent interactions. In contrast, some systems work by engaging in robust noncovalent contacts that do not change significantly in nature when the structure of the reaction component is altered. Ultimately, our findings represent a framework for interrogating and predicting catalyst generality, and this strategy should be relevant to other catalytic systems widely applied in asymmetric synthesis. Generality ; Workflow ; Catalysis ; Computer science ; Identification (biology) ; Chemistry ; Machine learning ; Artificial intelligence ; Organic chemistry ; Database Machine Learning in Materials Science ; Surface Chemistry and Catalysis ; Computational Drug Discovery Methods
Authors: Longbing Qu | Peiyao Wang | Benyamin Motevalli | Qinghua Liang | Kangyan Wang | Wenjie Jiang | Jefferson Zhe Liu | Dan Li
Source: Research Square (preprint, 2022-05-18)
Field: Materials Science — Electronic, Optical and Magnetic Materials

New engineering science insights into the electrodes pairing of electrochemical energy storage devices assisted by machine learning Pairing ; Electrochemical energy storage ; Energy storage ; Science and engineering ; Electrode ; Computer science ; Materials science ; Electrochemistry ; Nanotechnology ; Engineering ; Chemistry ; Physics ; Engineering ethics ; Supercapacitor Supercapacitor Materials and Fabrication ; Conducting polymers and applications ; Advanced Battery Technologies Research
Authors: Elena Fernández Martínez
Source: Austra & Lian Journal of Basic Sciences (article, 2022-06-30)
Field: Materials Science — Materials Chemistry

The Application of Machine Learning in Basic Scientific Research Machine Learning (ML) has rapidly transformed the landscape of basic scientific research by providing novel tools for pattern recognition, prediction, and data-driven hypothesis generation. This paper explores the integration of ML into diverse scientific disciplines such as physics, chemistry, biology, and environmental sciences. It emphasizes how supervised and unsupervised learning models contribute to accelerating discoveries, optimizing experimental design, and uncovering hidden structures within complex datasets. The paper highlights specific case studies where ML significantly impacted scientific advancement and outlines the current limitations and ethical concerns in adopting such methods. Scientific reasoning ; Supervised learning ; Scientific discovery ; Scientific literature ; Scientific modelling Machine Learning in Materials Science ; Big Data and Digital Economy ; Computational Physics and Python Applications
Authors: Marco Rossignolo | Thomas Reisser | Alastair Marshall | Phila Rembold | Alice Pagano | Philipp J. Vetter | Ressa S. Said | Matthias M. Müller | Felix Motzoi | Tommaso Calarco | Fedor Jelezko | Simone Montangero
Source: arXiv (Cornell University) (preprint, 2022-12-21)
Field: Materials Science — Materials Chemistry

QuOCS: The Quantum Optimal Control Suite Quantum optimal control includes the family of pulse-shaping algorithms that aim to unlock the full potential of a variety of quantum technologies. Our Quantum Optimal Control Suite (QuOCS) unites experimental focus and model-based approaches in a unified framework. The easy usage and installation of QuOCS and the availability of various combinable optimization strategies is designed to improve the performance of many quantum technology platforms, such as color defects in diamond, superconducting qubits, atom- or ion-based quantum computers. It can also be applied to the study of more general phenomena in physics. In this paper, we describe the software and the main toolbox of gradient-free and gradient-based algorithms. We then show how the user can connect it to their experiment. In addition, we provide illustrative examples where our optimization suite solves typical quantum optimal control problems, in both open- and closed-loop settings. Integration into existing experimental control software is already provided for the experiment control software Qudi [J. M. Binder et al., SoftwareX, 6, 85-90, (2017)], and further extensions are investigated and highly encouraged. QuOCS is available from GitHub, under Apache License 2.0, and can be found on the PyPI repository. Toolbox ; Computer science ; Suite ; Qubit ; Software ; Quantum ; Quantum computer ; Optimal control ; Computational science ; Quantum technology ; Focus (optics) ; License ; Theoretical computer science ; Computer engineering ; Mathematical optimization ; Open quantum system ; Physics ; Mathematics ; Programming language ; Operating system ; Quantum mechanics Diamond and Carbon-based Materials Research ; Laser-Matter Interactions and Applications ; Quantum Computing Algorithms and Architecture
Authors: Ajay Sharma | Chris Whittington | Mohammed A. Jabed | S. Gage Hill | Anastasiia Kostenko | Tao Yu | Pengfei Li | Brian M. Hoffman | Adam R. Offenbacher
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-12-07)
Field: Chemistry — Inorganic Chemistry

<sup>13</sup> C ENDOR Spectroscopy-Guided MD Computations Reveals the Structure of the Enzyme-Substrate Complex of an Active, N-linked Glycosylated Lipoxygenase Abstract Lipoxygenases (LOXs) are enzymes responsible for producing important cell signaling mediators and have been extensively studied for their potential clinical relevance as well as to advance our understanding of enzyme catalysis. The common inability to capture and characterize LOX-substrate complexes by Xray co-crystallography requires the development of alternative structural methods. We previously reported the integration of 13 C/ 1 H electron nuclear double resonance (ENDOR) spectroscopy and molecular dynamics (MD) to visualize the complex structure of the paradigmatic LOX from soybean, SLO, with substrate linoleic acid (LA). However, this required substitution of the catalytic mononuclear, nonheme iron by the structurally faithful, yet inactive Mn 2+ ion as a spin-probe. Unlike canonical Fe-LOXs from plants and animals, LOXs from pathogenic fungi contain active mononuclear manganese metallocentres. Here, we report the ground-state active-site structure of the native, fully glycosylated fungal LOX from M. oryzae, Mo LOX complexed with LA obtained through the 13 C/ 1 H ENDOR-guided MD approach. The Mn-oxygen-to-LA donor carbon distance (DAD) for Mo LOX-LA, 3.4 ± 0.3 Å, matches the distance in the single representative X-ray co-structure of an animal 8R-LOX with its natural fatty acid substrate, and slightly elongated from that of the SLO-LA complex, 3.1 ± 0.2 Å, despite its ‘carboxylate-out’ substrate binding orientation versus ‘carboxylate-in’ for SLO. The results provide unique insight into the evolutionary divergence of the ground-state DAD in the LOX family, which influences the activation barrier for hydrogen tunneling, and give a structural basis for guiding development of Mo LOX inhibitors. The work highlights the robustness of ENDOR-guided MD approach to describe LOX-substrate structures that elude conventional X-ray techniques. Active site ; Chemistry ; Substrate (aquarium) ; Carboxylate ; Enzyme ; Stereochemistry ; Lipoxygenase ; Crystallography ; Biochemistry ; Biology Metal-Catalyzed Oxygenation Mechanisms ; Carbohydrate Chemistry and Synthesis ; Microbial Natural Products and Biosynthesis
Authors: David W. Kastner | Aditya Nandy | Rimsha Mehmood | Heather J. Kulik
Source: ChemRxiv (preprint, 2022-09-01)
Field: Chemistry — Inorganic Chemistry

Mechanistic Insights Into Substrate Positioning Across Non-heme Fe(II)/alpha-ketoglutarate-dependent Halogenases and Hydroxylases Non-heme iron halogenases and hydroxylases activate inert C-H bonds to selectively catalyze the functionalization of a diversity of biological products under physiological conditions. To better understand the differences in substrate positioning key to their divergent reactivities, we compiled available crystallographic and spectroscopic data, which revealed that hydroxylases prefer an acute oxo-Fe-H target angle, while halogenases prefer a more obtuse angle. With molecular dynamics simulations guided by this experimental information, we simulated the representative hydroxylases TauD and VioC and the halogenases BesD and WelO5 with both acute and obtuse harmonic restraints. We identified key native interactions that maintain the angle of approach in the respective enzymes, such as Asp94 in TauD and His127 in BesD. Moreover, our simulations reveal that the protein environment in halogenases prevents the sampling of acute angles observed in hydrogenases and vice versa. To validate these classical observations, we optimized the structure with large-scale quantum mechanical (QM) simulations and confirmed QM-derived substrate-enzyme hydrogen bond strengths were higher in the native configurations. To understand the effect of positioning on reactivity, we confirmed that reaction barriers for the rate-limiting hydrogen atom transfer reaction was slightly lower from an acute angle regardless of the enzyme-substrate complex. Analysis of the halogenase reaction coordinates reveals the formation of hydrogen bonding networks between the Fe(II)-hydroxyl, monodentate succinate, and a member of the second coordination sphere that may inhibit the hydroxyl rebound. Chemistry ; Substrate (aquarium) ; Molecular dynamics ; Stereochemistry ; Heme ; Hydrogen bond ; Cofactor ; Biocatalysis ; Active site ; Enzyme ; Combinatorial chemistry ; Computational chemistry ; Reaction mechanism ; Molecule ; Catalysis ; Biochemistry ; Organic chemistry Metal-Catalyzed Oxygenation Mechanisms ; Porphyrin Metabolism and Disorders ; Hemoglobin structure and function
Authors: Moses K. Langat | Andreas Hemp | Martin Cheek
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-08-28)
Field: Chemistry — Organic Chemistry

Chemotaxonomy supports morphology in the identification of <i>Vepris hemp</i> (Rutaceae) a new species of Critically Endangered deciduous forest shrub from Usambara Mts, Tanzania ABSTRACT Hemp 7152, a sterile herbarium plot voucher of a shrub from a rare type of deciduous forest in the Usambara Mts, Tanzania was tentatively identified using morphology as a new species of Vepris (Rutaceae). To gain further support for its placement its chemistry was investigated. The compounds isolated from Hemp 7152 were four quinoline alkaloids, kokusaginine ( 1 ), N -methylplaty-desminium ion ( 9 ), ribalinium ion ( 10 ), and isoplatydesmine ( 11 ), and seven acridone alkaloids, arborinine ( 2 ) 1,2,3-trimethoxy- N -methylacridone ( 3 ), 1,2,3,5-tetramethoxy- N -methylacridone ( 4 ), 1,3-dimethoxy- N -methylacridone ( 5 ) and toddaliopsis A ( 6 ), evoxanthine ( 7 ) and tecleanthine ( 8 ). In addition, lupeol and ferulic acid were isolated from this plant. The combination of quinoline and acridone alkaloids is restricted to the Rutaceae family, confirming beyond reasonable doubt the placement of this material in the Rutaceae. Within Rutaceae in tropical Africa, only the genus Vepris is unarmed, with trifoliolate leaves. Using an identification key, and herbarium specimen matching, Hemp 7152 was morphologically placed as close to Vepris uguenensis , sharing xerophytic characters unusual in the genus. The species are geographically close, occurring in adjoining mountains in northern Tanzania. However, Vepris uguenensis contains 13 alkaloids which are not present in Hemp 7152, nor in any other species of Vepris that has been studied, supporting species recognition for Hemp 7152 which is formally named as Vepris hemp , morphologically characterised, illustrated and assessed as Critically Endangered using the IUCN 2012 standard. The new species appears restricted to an almost extinct type of deciduous forest, characterised in this paper. Herbarium ; Rutaceae ; Biology ; IUCN Red List ; Critically endangered ; Botany ; Endangered species ; Ecology ; Habitat Chemical synthesis and alkaloids ; Traditional and Medicinal Uses of Annonaceae ; Plant chemical constituents analysis
Authors: Manish Chowdhury | Kiwon Ok | Yanqi Luo | Zhengchun Liu | Si Chen | Thomas V. O’Halloran | Rajkumar Kettimuthu | Aniket Tekawade
Source:  (preprint, 2022-08-09)
Field: Materials Science — Materials Chemistry

XRF-ROI-Finder: Machine learning to guide region-of-interest scanning for X-ray fluorescence microscopy &lt;p&gt;The microscopy research at the Bionanoprobe (currently at beamline 9-ID and later 2-ID after APS-U) of Argonne National Laboratory focuses on applying synchrotron X-ray fluorescence (XRF) techniques to obtain trace elemental mappings of cryogenic biological samples to gain insights about their role in critical biological activities. The elemental mappings and the morphological aspects of the biological samples, in this instance, the bacterium Escherichia coli (E. coli), also serve as label-free biological fingerprints to identify differently treated samples via fuzzy clustering. The key limitations of achieving good identification performance is the extraction of cells from raw XRF measurement via binary conversion, definition of features based on domain knowledge, dwell time and proportion of differently treated cells in the measurement.&lt;/p&gt; Fluorescence microscope ; Beamline ; X-ray fluorescence ; Synchrotron ; Microscopy ; Fluorescence ; Computer science ; Materials science ; Artificial intelligence ; Nanotechnology ; Physics ; Optics Enzyme Structure and Function ; Advanced X-ray Imaging Techniques ; Nuclear Physics and Applications
Authors: Bowen Liu | Fangcheng Lv | Qing Xie | Xiaozhou Fan
Source: Mathematical Problems in Engineering (article, 2022-09-19)
Field: Materials Science — Materials Chemistry

Performance Analysis of Chopped Fiber Composite Meta-Nano-Aramid IP for Transformer Bushings and to Analyze Environmental Impact To study the effect of nano-SiO2 doping content on the properties of chopped fiber composite meta-nano-aramid insulating paper (IP) for transformer bushings, the laboratory-prepared chopped fiber composite meta-nano-aramid IP with different nano-SiO2 doping content is analyzed to assess its impact on the environment. The study has been carried out by considering crystallographic properties and morphology of chopped fiber composite meta-nano-aramid fiber, the influence-mechanism of nano-SiO2 doping content on the mechanical properties, the thermal stability and insulating properties of aramid paper. The experimental results show that the appropriate graft modification of nano-SiO2 enhances the thermal stability and mechanical properties of the meta-aramid (MA) insulating paper. It also shows lesser carbon emissions. When the results are compared with SiO2 without grafted silane coupling agent, SiO2 with a surface graft ratio of 6%, the former method (SiO2 without grafted silane coupling agent) shows a greater increase in the glass transition temperature of the MAIP. At the same time, it shows weakened molecular weight in terms of MSD. The proposed method shows more prominence in terms of the chain kinematic ability, the resistance to deformation, and shearing in terms of mechanical properties. When SiO2 with the graft ratio of 12% is observed, it does not show any improvement, and also the effects on thermal stability and mechanical properties of IP are not significant which is similar to grafting. After hot pressing at 245°C, 30 MPa for 5 min, the breakdown strength, and volume resistivity can reach as high as 37 kV/mm and 1.34 × 1015 Ω·cm respectively. The proposed method shows a significant environmental impact in terms of less emission of CO and CO2. Aramid ; Materials science ; Composite material ; Thermal stability ; Composite number ; Ultimate tensile strength ; Nano- ; Doping ; Fiber ; Chemical engineering High voltage insulation and dielectric phenomena ; Power Transformer Diagnostics and Insulation ; Vacuum and Plasma Arcs
Authors: P. N. Mozharovskaia | A. V. Ivoilova | A.V. Ivanova | A. N. Kozitsina | V. L. Rusinov | П. Н. Можаровская | А. В Ивойлова | А. С. Иванова | А. Н. Козицина | В. Л. Русинов
Source: Electronic scientific archive of UrFU (Ural Federal University) (article, 2022-01-01)
Field: Chemistry — Organic Chemistry

Electrochemical Study of 2-Methylthio-6-Nitro-7-Hydroxy-4H-1,2,4-Triazolo-4,7-Dihydro[5,1-C]-1,2,4-Triazinide Monohydrate Sodium Salt The redox conversion of a potential antiviral drug was studied by voltammetry methods. It has been established that the cathode signal is due to the occurrence of an irreversible process of electroreduction of the nitro group. The number of electrons involved in the reduction reaction is 3. Electrochemistry ; Redox ; Cyclic voltammetry ; Cathode ; Voltammetry ; Salt (chemistry) ; Reaction mechanism ; Chemical reduction Synthesis and Reactions of Organic Compounds ; Electrochemical Analysis and Applications ; Chemical Reaction Mechanisms
Authors: A.M.Huseynli | G.I.Bayramov
Source: Azerbaijan journal of Chemical News (article, 2022-12-06)
Field: Chemistry — Analytical Chemistry

DETERMINATION OF ECOTOXIC SUBSTANCES IN WASTEWATER FORMED IN THE PURIFICATION PROCESS OF PETROLEUM OILS WITH HYDROGEN BY SPECTRAL METHODS The article analyzes the determination of the amount of dissolved ecotoxicants in the sample taken from the industrial wastewater obtained during the process of hydrogen treatment of petroleum oils. During the hydrogenation process, different types of wastes are formed, depending on the nature of each compound contained in petroleum distillates. Every gas, liquid, solid waste formed during the process of hydrogen purification of petroleum distillates by the oil refining industry has a negative impact on the environment in various ways. One of the main directions of our scientific research is the ecological assessment of the environmental impact of wastewater formed in the process of hydrogen treatment of petroleum distillates.Based on the results obtained, the environmental impact of the wastewater was assessed. The amount of volatile ecotoxicants in the wastewater sample was determined by spectral methods and is shown in the table. We used gas chromatography-mass spectrometry method for the polycyclic aromatic hydrocarbons; optical emission spectrometry method for metals; spectrometry method for phenols, dyes and fluorine; nephelometry method for turbidity; the gravimetry method for total suspended particles. Based on the results obtained, it is possible to assess the environmental impact of wastewater generated during the technological process at the hydrogen treatment plant. Keywords: petroleum distillates, hydrogen purification, spectral method, ecotoxicants, effluents. Wastewater ; Distillation ; Petroleum ; Chemistry ; Oil refinery ; Effluent ; Mass spectrometry ; Industrial wastewater treatment ; Pulp and paper industry ; Petroleum product ; Environmental science ; Environmental chemistry ; Waste management ; Chromatography ; Organic chemistry ; Environmental engineering Petroleum Processing and Analysis ; Catalysis and Hydrodesulfurization Studies ; Coal Combustion and Slurry Processing
Authors: Valentin Launay
Source: SPIRE - Sciences Po Institutional REpository (preprint, 2022-05-10)
Field: Materials Science — Materials Chemistry

Activation photothermique dans le proche-infrarouge pour l'impression 4D The objective of this PhD work was the elaboration of materials having 4D printing as final application. For this purpose, this thesis was structured around two fundamental axes. First, research was conducted about the influence of near-infrared absorbing dyes on the generated photothermal effect. Thus, various factors such as the dye concentration, the irradiation wavelength, the irradiance of the light source or the monomer used have been studied in order to control the temperature reached by a polymer under different conditions. This first axis served as a basis for the second one, consisting in modifying the properties of a polymer. Indeed, the generated photothermal effect allowed the bonding of polymers. Moreover, self-healing properties could be observed by optical microscopy. Moreover, it was possible to modify the shape of polymers in a reversible way. The photothermal effect was also exploited to sterilize polymers. Indeed, the very high temperatures obtained during short irradiations allowed the total destruction of mesophilic microorganisms. Finally, these properties have been applied to 3D printed objects, allowing to obtain real 4D applications. Photothermal therapy ; Infrared ; Range (aeronautics) ; Materials science ; Nanotechnology ; Optics ; Physics ; Composite material Phase-change materials and chalcogenides ; Advanced Memory and Neural Computing ; Semiconductor Lasers and Optical Devices
Authors: Allu Ganga Raju | G. Himabindu | Yagati Vamsi Kumar
Source: Journal of Materials Science and Surface Engineering (article, 2022-01-01)
Field: Chemistry — Organic Chemistry

NiO-FeS2 Heterostructure Composite: Benign Photocatalyst for Reduction of Nitrophenol to Aminophenol Aromatic nitro compounds have been promising industrial applications including paper production, pigments, pharmaceuticals, dyes, wood, leather, petrochemical, pesticides, insecticides, fungicides, explosives, and preservatives. US EPA (Environmental Protection Agency) declared that 4-nitrophenol (4-NP) has been recognized as a non-biodegradable pollutant and therefore, a very important to develop an effective method to either modify or remove 4-NP before releasing it into the environment. In that concern, we have developed an efficient, heterostructure composite of NiO-FeS2 via hydrothermal. The 4 mg catalyst dose and 10 mg/L concentration of 4-NP are the optimum conditions for complete reduction of 4-NP to 4-AP by prepared NiO-FeS2 composite. Composite number ; Petrochemical ; Photocatalysis ; Nitrophenol ; Catalysis ; Non-blocking I/O ; 4-Nitrophenol ; Chemistry ; Nuclear chemistry ; Materials science ; Chemical engineering ; Pulp and paper industry ; Organic chemistry ; Composite material ; Engineering Nanomaterials for catalytic reactions ; Copper-based nanomaterials and applications ; Advanced Photocatalysis Techniques