jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Nils van Staalduinen | Christoph Bannwarth
Source: ChemRxiv (preprint, 2024-03-06)
Field: Chemistry — Spectroscopy

MolBar: A Molecular Identifier for Inorganic and Organic Molecules with Full Support of Stereoisomerism Before a new molecular structure is registered to a chemical structure database, a duplicate check is essential to ensure the integrity of the database. The Simplified Molecular Input Line Entry Specification (SMILES) and the International Chemical Identifier (InChI) stand out as widely used molecular identifiers for these checks. Notable limitations arise when dealing with molecules from inorganic chemistry or structures characterized by non-central stereochemistry. When the stereoinformation needs to be assigned to a group of atoms, widely used identifiers cannot describe axial and planar chirality due to the atom-centered description of a molecule. To address this limitation, we introduce a novel chemical identifier called the Molecular Barcode (MolBar). Motivated by the field of theoretical chemistry, a fragment-based approach is used in addition to the conventional atomistic description. In this approach, fragments are conceptualized using a specialized force field and characterized by physically inspired matrices derived solely from atomic positions. The resulting permutation-invariant representation is constructed from the eigenvalue spectra, providing comprehensive information on both bonding and stereochemistry. The robustness of MolBar is demonstrated through duplication and permutation invariance tests on the Molecule3D dataset of 3.9 million molecules. A Python implementation is available as open source at https://git.rwth-aachen.de/bannwarthlab/molbar. Identifier ; Chemistry ; Stereoisomerism ; Molecule ; Computational biology ; Organic molecules ; Combinatorial chemistry ; Computer science ; Biology ; Organic chemistry ; Programming language Analytical Chemistry and Chromatography ; Various Chemistry Research Topics ; Molecular spectroscopy and chirality
Authors: Shilei Zhou | Zhenkai Cen | Dandan Han | Bowen Zhang | Junbo Gong
Source: Crystal Research and Technology (article, 2024-07-07)
Field: Materials Science — Materials Chemistry

Oiling‐Out in Industrial Crystallization of Organic Small Molecules: Mechanisms, Characterization, Regulation, and Applications Abstract Oiling‐out is a common phenomenon in industrial crystallization processes that not only prolongs the total operating time but also leads to undesirable crystal morphology, making it challenging to control crystallization paths. This review provides a comprehensive overview of the oiling‐out phenomenon in organic small molecule crystallization. First, the formation mechanisms of oiling‐out are summarized from both thermodynamic and dynamic perspectives, providing the theoretical foundation for understanding the phenomenon. Then, the universal characterization methods for studying the oiling‐out phenomenon of organic small molecules are introduced in detail, covering both offline and online analytical tools. Moreover, the regulation strategy for oiling‐out, including solvents, impurities, seeding, temperature, and mixing methods are discussed. This paper also focuses on the application of oiling‐out in co‐assembly and crystal shape modulation. Finally, future opportunities and challenges are presented to address the current shortcomings and application bottlenecks in the study of organic small molecule oiling‐out phenomena. This review aims to provide valuable insights and guidance for researchers working on the crystallization of organic small molecules, particularly in the pharmaceutical industry, to better understand, control, and utilize the oiling‐out phenomenon. Characterization (materials science) ; Crystallization ; Molecule ; Organic molecules ; Chemistry ; Chemical engineering ; Nanotechnology ; Materials science ; Organic chemistry ; Engineering Crystallization and Solubility Studies ; Chemical Thermodynamics and Molecular Structure ; nanoparticles nucleation surface interactions
Authors: N Fadel | Baydaa Sulaiman Bahnam
Source: International Research Journal of Innovations in Engineering and Technology (article, 2024-01-01)
Field: Chemistry — Analytical Chemistry

Survey of Dairy Products Using Machine Learning Techniques The quality of dairy is of great importance in the food industry, as dairy is one of the main sources of proteins, calcium, vitamins and minerals that the human body needs. Dairy is found in many products, including milk, cream, and cheese, the most important of which is milk. It represents the basic and important element in people's lives, especially children, because it is an indispensable source for their growth, building their bones, and strengthening their bodies. Milk is a perishable product. Every gram of milk of poor quality or structure can cause tons of milk to spoil, causing significant financial losses and can lead to poisoning. Therefore, the quality and safety standards of this product are essential to ensure the provision of healthy and safe products to consumers. Determining the quality of the milk product is crucial for the purpose of monitoring to reduce potential losses and damages. The aim of this research is to provide a brief survey of the methods used in classifying milk quality using artificial intelligence methods, which include the use of machine learning algorithms through Identifying the most important and accurate methods and displaying the results reached using the known metrics: Accuracy, Precision, Recall, and F1_score. Computer science ; Machine learning ; Artificial intelligence Spectroscopy and Chemometric Analyses ; Food Supply Chain Traceability
Authors: Mustafa Güven Kaysım | Ahmet Metin Kumlay | Kamil Haliloğlu | Aras Türkoğlu | Magdalena Piekutowska | Hayrünnisa Nadaroğlu | Azize Alaylı | Gniewko Niedbała
Source: Agronomy (article, 2024-04-08)
Field: Materials Science — Materials Chemistry

Physiological and Antioxidative Effects of Strontium Oxide Nanoparticles on Wheat We explored the impact of strontium oxide nanoparticles (SrO-NPs), synthesized through a green method, on seedling growth of bread wheat in hydroponic systems. The wheat plants were exposed to SrO-NPs concentrations ranging from 0.5 mM to 8.0 mM. Various parameters, including shoot length (cm), shoot fresh weight (g), root number, root length (cm), root fresh weight (g), chlorophyll value (SPAD), cell membrane damage (%), hydrogen peroxide (H2O2) value (µmol/g), malondialdehyde (MDA) value (ng/µL), and enzymatic activities like ascorbate peroxidase (APX) activity (EU/g FW), peroxidase (POD) activity (EU/g FW), and superoxide dismutase (SOD) activity (U/g FW), were measured to assess the effects of SrO-NPs on the wheat plants in hydroponic conditions. The results showed that the SrO-NPs in different concentrations were significantly affected considering all traits. The highest values were obtained from the shoot length (20.77 cm; 0.5 mM), shoot fresh weight (0.184 g; 1 mM), root number (5.39; 8 mM), root length (19.69 cm; 0 mM), root fresh weight (0.142 g; 1 mM), SPAD (33.20; 4 mM), cell membrane damage (58.86%; 4 mM), H2O2 (829.95 µmol/g; 6 mM), MDA (0.66 ng/µl; 8 mM), APX (3.83 U/g FW; 6 mM), POD (70.27 U/g FW; 1.50 mM), and SOD (60.77 U/g FW; 8 mM). The data unequivocally supports the effectiveness of SrO-NPs application in promoting shoot and root development, chlorophyll levels, cellular tolerance, and the activation of enzymes in wheat plants. Strontium ; Nanoparticle ; Strontium oxide ; Chemistry ; Food science ; Oxide ; Materials science ; Nanotechnology Nanoparticles: synthesis and applications ; Crop Yield and Soil Fertility
Authors: Guohui Yang | Kaizhi Zhang | Weiqing Xu | Shuping Xu
Source: Frontiers in Neurology (review, 2024-04-08)
Field: Materials Science — Electronic, Optical and Magnetic Materials

A review of clinical use of surface-enhanced Raman scattering-based biosensing for glioma Glioma is the most common malignant tumor of the nervous system in recent centuries, and the incidence rate of glioma is increasing year by year. Its invasive growth and malignant biological behaviors make it one of the most challenging malignant tumors. Maximizing the resection range (EOR) while minimizing the impact on normal brain tissue is crucial for patient prognosis. Changes in metabolites produced by tumor cells and their microenvironments might be important indicators. As a powerful spectroscopic technique, surface-enhanced Raman scattering (SERS) has many advantages, including ultra-high sensitivity, high specificity, and non-invasive features, which allow SERS technology to be widely applied in biomedicine, especially in the differential diagnosis of malignant tumor tissues. This review first introduced the clinical use of responsive SERS probes. Next, the sensing mechanisms of microenvironment-responsive SERS probes were summarized. Finally, the biomedical applications of these responsive SERS probes were listed in four sections, detecting tumor boundaries due to the changes of pH-responsive SERS probes, SERS probes to guide tumor resection, SERS for liquid biopsy to achieve early diagnosis of tumors, and the application of free-label SERS technology to detect fresh glioma specimens. Finally, the challenges and prospects of responsive SERS detections were summarized for clinical use. Glioma ; Raman scattering ; Biomedicine ; Nanotechnology ; Surgical resection ; Liquid biopsy ; Medicine ; Biomedical engineering ; Materials science ; Cancer research ; Radiology ; Raman spectroscopy ; Biology ; Bioinformatics ; Cancer ; Internal medicine ; Optics Gold and Silver Nanoparticles Synthesis and Applications ; Advanced biosensing and bioanalysis techniques ; Nanoplatforms for cancer theranostics
Authors: Nobuya Sato | Akira Takahashi | Shin Kiyohara | Kei Terayama | Ryo Tamura | Fumiyasu Oba
Source: Advanced Intelligent Systems (article, 2024-08-05)
Field: Materials Science — Materials Chemistry

Target Material Property‐Dependent Cluster Analysis of Inorganic Compounds The cluster analysis of materials categorizes them according to similarities based on the features of materials, providing insight into the relationship between the materials. Conventional cluster analyses typically use basic features derived from the chemical composition and crystal structure without considering target material properties such as the bandgap and dielectric constant. However, such approaches do not meet demands for grading materials according to properties of interest simultaneously with chemical and structural similarities. Herein, a clustering method grouping similar materials in terms of both the target properties and basic features is proposed. The clustering is compared considering the cohesive energy with that considering the bandgap of metal oxides, showing that their categorizations are clearly different. Further, several clusters classified by the bandgap are analyzed, and coordination environments related to each range of the bandgap are revealed. The clustering for the electronic static dielectric constant identifies a cluster involving several perovskite‐type oxides and balancing with the bandgap near the Pareto front. The method enables analyses with different viewpoints from those of the conventional clustering and feature importance analyses by taking the relationship between the target property and the basic features into account. Cluster analysis ; Band gap ; Cluster (spacecraft) ; Materials science ; Dielectric ; Material properties ; Property (philosophy) ; Computer science ; Biological system ; Data mining ; Artificial intelligence ; Optoelectronics Machine Learning in Materials Science ; Advanced Photocatalysis Techniques ; Electronic and Structural Properties of Oxides
Authors: Hu Li | Kazuki Denpoh
Source: Journal of Vacuum Science & Technology A Vacuum Surfaces and Films (article, 2024-05-30)
Field: Materials Science — Materials Chemistry

Quantitative analysis of plasma-enhanced chemical vapor deposition mechanisms: Quantum chemical and plasma-fluid dynamics investigation on tetraethoxysilane/O2 plasma This study aimed to investigate the influence of reactive oxygen species (i.e., neutral O atom and O2+ ion) on deposition rates and film thickness uniformity in tetraethoxysilane (TEOS) plasma, utilizing a combination of plasma-fluid dynamic and quantum chemical (QC) simulations. The plasma simulations employed an improved model based on a previous study [H. Li et al., Jpn. J. Appl. Phys. 58, SEED06 (2019)], specifically tailored for a TEOS/O2/Ar/He gas mixture. In the QC simulations, both flat and step silicon oxide (SiO2) surfaces were employed to investigate the adsorption behavior of SiO molecules, the predominant silicon-containing species in TEOS plasma. These simulations also enabled the examination of the rates of SiO molecule adsorption on SiO2 surfaces, facilitating a direct comparison with the sticking coefficients utilized in the plasma simulation. The results of QC simulations revealed that SiO molecules exhibited a higher energetic preference for adsorption on step surfaces than on flat surfaces, resulting in the formation of new SiOH surface sites. Meanwhile, the plasma simulations demonstrated a strong correlation between the deposition rate and film thickness uniformity and the generation of oxygen species, specifically O atoms and O2+ ions, as well as their respective fluxes. This relationship takes precedence over the influence of TEOS or its fragments colliding with the surface. Notably, higher plasma source frequencies were found to enhance the production of atomic O, which contributed significantly to achieving higher deposition rates. Plasma ; Adsorption ; Molecule ; Deposition (geology) ; Ion ; Silicon ; Silicon oxide ; Chemical vapor deposition ; Oxygen ; Quantum chemical ; Chemistry ; Chemical physics ; Plasma-enhanced chemical vapor deposition ; Molecular dynamics ; Plasma processing ; Atom (system on chip) ; Oxide ; Analytical Chemistry (journal) ; Chemical engineering ; Physical chemistry ; Computational chemistry ; Silicon nitride ; Organic chemistry Diamond and Carbon-based Materials Research ; Plasma Diagnostics and Applications ; Metal and Thin Film Mechanics
Authors: Simon Hoellard | A. S. KANA'AN | Aziz Ghoufi
Source: MRS Advances (article, 2024-12-01)
Field: Chemistry — Inorganic Chemistry

Water adsorption within PIM-1 polymer and CAU-23 MOF material from osmotic molecular dynamics simulations Abstract In the context of post-combustion carbon dioxide capture, the existence of the Metal-Organic Framework (MOF) transparency effect, which can enhance carbon dioxide uptake under humid conditions, was recently demonstrated. It is, therefore, essential to first determine the water adsorption capacity within the MOF. In this work, the CAU-23 MOF material, which appears to possess the main chemical and structural characteristics necessary for MOF transparency to occur, was considered. In addition, Mixed Matrix Membrane (MMM) is now considered on an industrial scale for shaping purposes. Among polymers, the intrinsically microporous polymer PIM-1 has shown interesting adhesion properties with MOF surfaces. Thus, before investigating what happens within the MMM, we aim to examine the water adsorption within the bulk CAU-23 and PIM-1 materials using the recently developed osmotic molecular dynamics simulations. These preliminary results show that CAU-23 could be a promising material for enhancing the MOF’s transparency and increasing $$\hbox {CO}_2$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mtext>CO</mml:mtext> <mml:mn>2</mml:mn> </mml:msub> </mml:math> uptake. Graphic abstract Materials science ; Adsorption ; Microporous material ; Polymer ; Transparency (behavior) ; Context (archaeology) ; Molecular dynamics ; Chemical engineering ; Carbon dioxide ; Metal-organic framework ; Thermodynamics ; Physical chemistry ; Organic chemistry ; Computer science ; Computational chemistry ; Chemistry ; Composite material ; Physics Metal-Organic Frameworks: Synthesis and Applications ; Membrane Separation and Gas Transport ; Covalent Organic Framework Applications
Authors: A. Robinson | Elisabeth A. Ryan | Qingpu Wang | David Greene | Chinmayee V. Subban
Source: Sustainability (article, 2024-12-09)
Field: Materials Science — Biomaterials

Pulse Electrodeposition for Carbonate-Rich Deposits from Seawater Seawater electrodeposition is gaining renewed interest in the context of sustainable development, both to build climate-resilient coastal infrastructure and for ocean-based decarbonization applications. Most of the applications benefit from CaCO3-rich deposits, but constant-voltage electrodeposition results in a mixture of CaCO3 and Mg(OH)2, especially at higher voltages where precipitation rates are more desirable. The use of pulse voltages can help control interfacial pH that dictates the precipitation reactions. Here, we explore the use of pulse electrodeposition as a function of pulse frequency and duty cycle to control deposit composition. The most CaCO3-rich deposits were obtained under 10 Hz frequency and 10% duty cycle conditions for the voltage window investigated (−0.8 V to −1.2 V vs. SCE). While pulsing the voltage increases the amount of CaCO3 deposited, the energy required per gram of CaCO3 is significantly higher (14.5×) when compared to the base case of applying a constant voltage of −0.8 V vs. SCE. Further optimization of pulse conditions, electrode materials, and system configuration could lead to finding parameters that result in exclusively carbonate deposits without compromising precipitation rates, which may prove to be more useful for corrosion protection, coastal infrastructure, and other applications in sustainable development. Duty cycle ; Seawater ; Carbonate ; Voltage ; Context (archaeology) ; Precipitation ; Pulse (music) ; Materials science ; Environmental science ; Pulse-width modulation ; Electrode ; Metallurgy ; Environmental engineering ; Chemical engineering ; Geology ; Electrical engineering ; Chemistry ; Oceanography ; Engineering ; Physics ; Meteorology Calcium Carbonate Crystallization and Inhibition ; Iron oxide chemistry and applications ; Corrosion Behavior and Inhibition
Authors: Ludmila Mahņicka-Goremikina | Māris Rundāns | Vadims Goremikins | Ruta Švinka | Visvaldis Švinka | Liga Orlova | Inna Juhņeviča
Source: Materials (article, 2024-12-17)
Field: Materials Science — Ceramics and Composites

Effect of Microsize and Nanosize TiO2 on Porous Mullite-Alumina Ceramic Prepared by Slip Casting Sintered porous mullite-alumina ceramics are obtained from the concentrated suspension of powdered raw materials such as kaolin, gamma and alpha Al<sub>2</sub>O<sub>3</sub>, and amorphous SiO<sub>2</sub>, mainly by a solid-state reaction with the presence of a liquid phase. The modification of mullite ceramic is achieved by the use of micro- and nanosize TiO<sub>2</sub> powders. The phase compositions were measured using an X-ray powder diffraction (XRD) Rigaku Ultima+ (Tokyo, Japan) and microstructures of the sintered specimens were analysed using scanning electron microscopy (SEM) Hitachi TM3000-TableTop (Tokyo, Japan). The shrinkage, bulk density, apparent porosity, and water uptake of the specimens was determined after firing using Archimedes' principle. The apparent porosity of the modified mullite ceramic is 52-69 ± 1%, water uptake is 33-40 ± 1%, pore size distributions are 0.05-0.8 μm, 0.8-10 μm and 10-1000 μm, and bulk density are variated from 1.15 ± 0.05 to 1.4 ± 0.05 g/cm<sup>3</sup>. The microsize TiO<sub>2</sub> and nanosize TiO<sub>2</sub> speed up the mullitisation process and allow the decrease in the quantity used as raw material amorphous SiO<sub>2</sub>, which was the purpose of the study. The use of nanosize TiO<sub>2</sub> additive increases the porosity of such a ceramic, decreasing the bulk density and linear thermal expansion. Mullite ; Materials science ; Porosity ; Ceramic ; Scanning electron microscope ; Amorphous solid ; Composite material ; Microstructure ; Mineralogy ; Metallurgy ; Crystallography ; Chemistry Advanced ceramic materials synthesis ; Recycling and utilization of industrial and municipal waste in materials production ; Nuclear materials and radiation effects
Authors: Gaoqiang Lv | Wenya Zhang | Xiaoyue Liu | Ji Zhang | Fei Liu | Hanping Mao | Weihong Sun | Qingyan Han | Jinxiu Song
Source: Agronomy (article, 2024-10-16)
Field: Chemistry — Analytical Chemistry

Feasibility of Nondestructive Soluble Sugar Monitoring in Tomato: Quantified and Sorted through ATR-FTIR Coupled with Chemometrics As a fast detection method, Fourier transform infrared attenuated total reflection (ATR-FTIR) spectroscopy is seldom used for monitoring soluble sugars in crops. This study aimed to demonstrate the feasibility of leveraging ATR-FTIR coupled with chemometrics to quantify and sort the contents of soluble sugar in tomatoes. Firstly, 192 tomato samples were scanned using ATR-FTIR; subsequently, a quantitative model was developed using PLSR with selected wavelength variables as inputs. Finally, a classification model was estimated through probabilistic neural network (PNN) to determine the samples. The results indicated that ATR-FTIR had successfully captured the spectra from the cellular layers of tomatoes, resulting in a robust PLSR model created by 468 selected variables with a R² value of 0.86, a RMSEP of 0.71%, a ratio of performance to relative percent deviation (RPD) of 1.87, and a ratio of prediction to interquartile range (RPIQ) of 2.1. Meanwhile, the PNN model demonstrated a high rate correct (RC) of 92.17% in identifying whether the samples with a higher soluble sugar content than the limit of detection (LOD at 2.1%). Overall, ATR-FTIR coupled with chemometrics has proven effective for non-destructive determination of soluble sugars in tomatoes, offering new insights into internal monitoring techniques for crop quality assurance. Chemometrics ; Attenuated total reflection ; Fourier transform infrared spectroscopy ; Sugar ; Analytical Chemistry (journal) ; Chemistry ; Partial least squares regression ; Chromatography ; Mathematics ; Food science ; Statistics ; Chemical engineering ; Engineering Spectroscopy and Chemometric Analyses ; Smart Agriculture and AI ; Postharvest Quality and Shelf Life Management