jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Juan Viguera Diez | Sara Romeo Atance | Ola Engkvist | Simon Olsson
Source: Machine Learning Science and Technology (article, 2024-04-05)
Field: Chemistry — Spectroscopy

Generation of conformational ensembles of small molecules via surrogate model-assisted molecular dynamics Abstract The accurate prediction of thermodynamic properties is crucial in various fields such as drug discovery and materials design. This task relies on sampling from the underlying Boltzmann distribution, which is challenging using conventional approaches such as simulations. In this work, we introduce surrogate model-assisted molecular dynamics (SMA-MD), a new procedure to sample the equilibrium ensemble of molecules. First, SMA-MD leverages deep generative models to enhance the sampling of slow degrees of freedom. Subsequently, the generated ensemble undergoes statistical reweighting, followed by short simulations. Our empirical results show that SMA-MD generates more diverse and lower energy ensembles than conventional MD simulations. Furthermore, we showcase the application of SMA-MD for the computation of thermodynamical properties by estimating implicit solvation free energies. Molecular dynamics ; Dynamics (music) ; Chemistry ; Nanotechnology ; Computational chemistry ; Materials science ; Physics Molecular spectroscopy and chirality ; Spectroscopy and Quantum Chemical Studies ; Protein Structure and Dynamics
Authors: Dalal Nasser Binjawhar | Fawziah A. Al‐Salmi | Ola A. Abu Ali | Maha Ali Alghamdi | Eman Fayad | Rasha Mohammed Saleem | Islam Zaki | N. A. Farouk
Source: RSC Advances (article, 2024-01-01)
Field: Chemistry — Organic Chemistry

Design, synthesis and cytotoxic activity of molecular hybrids based on quinolin-8-yloxy and cinnamide hybrids and their apoptosis inducing property The present work aims at design and synthesis of a congeneric series of small hybrids 5 and 6a-i featuring the privileged quinoline scaffold tethered with 2-(arylamido)cinnamide moiety as potential anticancer tubulin polymerization inhibitors. Most of the synthesized hybrids 5 and 6a-i significantly inhibited the growth of the HepG2 cell line, with IC<sub>50</sub> ranged from 2.46 to 41.31 μM. In particular, 2-(3,4,5-trimethoxybenzamido)-4-methoxycinnamide-quinoline hybrid 6e displayed potent IC<sub>50</sub> value toward the examined cell line, and hence chosen for further mechanistic investigations. It is noteworthy that the antiproliferative action of compound 6e highly correlated well with its ability to inhibit tubulin polymerization. In addition, the most potent hybrid 6e demonstrated a significant modification in the cellular cycle distribution, in addition to provoke of apoptotic death within the tested HepG2 cell line. Furthermore, the mechanistic approach was confirmed by a substantial upregulation in the quantity of active <i>c</i>aspase 9 by 5.81-fold relative to untreated control cells. Quinoline ; Hybrid ; Cytotoxicity ; Apoptosis ; Cytotoxic T cell ; In vitro ; Chemistry ; Sequence (biology) ; Stereochemistry ; Biology ; Biochemistry ; Organic chemistry ; Botany Synthesis and biological activity ; Cancer therapeutics and mechanisms ; Click Chemistry and Applications
Authors: Jonathan W. Zheng | Emad Al Ibrahim | Ivari Kaljurand | Ivo Leito | William H. Green
Source: Journal of Computational Chemistry (article, 2024-12-11)
Field: Chemistry — Organic Chemistry

<scp> p <i>K</i> <sub>a</sub> </scp> prediction in non‐aqueous solvents Acid dissociation constants ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics><mml:mrow><mml:mi>p</mml:mi> <mml:msub><mml:mi>K</mml:mi> <mml:mi>a</mml:mi></mml:msub> </mml:mrow> <mml:annotation>$$ \mathrm{p}{K}_{\mathrm{a}} $$</mml:annotation></mml:semantics> </mml:math> ) are widely measured and studied, most typically in water. Comparatively few datasets and models for non-aqueous <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics><mml:mrow><mml:mi>p</mml:mi> <mml:msub><mml:mi>K</mml:mi> <mml:mi>a</mml:mi></mml:msub> </mml:mrow> <mml:annotation>$$ \mathrm{p}{K}_{\mathrm{a}} $$</mml:annotation></mml:semantics> </mml:math> values exist. In this work, we demonstrate how the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics><mml:mrow><mml:mi>p</mml:mi> <mml:msub><mml:mi>K</mml:mi> <mml:mi>a</mml:mi></mml:msub> </mml:mrow> <mml:annotation>$$ \mathrm{p}{K}_{\mathrm{a}} $$</mml:annotation></mml:semantics> </mml:math> in one solvent can be accurately determined using reference data in another solvent, corrected by solvation energy calculations from the COSMO-RS method. We benchmark this approach in 10 different solvents, and find that <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics><mml:mrow><mml:mi>p</mml:mi> <mml:msub><mml:mi>K</mml:mi> <mml:mi>a</mml:mi></mml:msub> </mml:mrow> <mml:annotation>$$ \mathrm{p}{K}_{\mathrm{a}} $$</mml:annotation></mml:semantics> </mml:math> values calculated in six solvents deviate from experimental data on average by less than 1 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics><mml:mrow><mml:mi>p</mml:mi> <mml:msub><mml:mi>K</mml:mi> <mml:mi>a</mml:mi></mml:msub> </mml:mrow> <mml:annotation>$$ \mathrm{p}{K}_{\mathrm{a}} $$</mml:annotation></mml:semantics> </mml:math> unit. We observe comparable performance on a more diverse test set including amino acids and drug molecules, with higher error for large molecules. The model performance in four other solvents is worse, with one MAE exceeding 3 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics><mml:mrow><mml:mi>p</mml:mi> <mml:msub><mml:mi>K</mml:mi> <mml:mi>a</mml:mi></mml:msub> </mml:mrow> <mml:annotation>$$ \mathrm{p}{K}_{\mathrm{a}} $$</mml:annotation></mml:semantics> </mml:math> units; we discuss how such errors arise due to both model error and inconsistency in obtaining experimental data. Finally, we demonstrate how this technique can be used to estimate the proton transfer energy between different solvents, and use this to report a value of the proton's solvation energy in formamide, a quantity that does not have a consensus value in literature. Aqueous solution ; Chemistry ; Computational chemistry ; Physical chemistry Free Radicals and Antioxidants ; Computational Drug Discovery Methods ; Chemistry and Chemical Engineering
Authors: Panagiotis Krokidas | M.E. Kainourgiakis | Theodore Steriotis | George Giannakopoulos
Source: Physical Chemistry Chemical Physics (article, 2024-01-01)
Field: Chemistry — Inorganic Chemistry

Inverse design of ZIFs through artificial intelligence methods We report a tool combining a biologically inspired evolutionary algorithm with machine learning to design fine-tuned zeolitic-imidazolate frameworks (ZIFs), a sub-family of MOFs, for desired sets of diffusivities of species <i>i</i> (<i>D</i><sub><i>i</i></sub>) and <i>D</i><sub><i>i</i></sub>/<i>D</i><sub><i>j</i></sub> of any given mixture of species <i>i</i> and <i>j</i>. We display the efficacy and validitiy of our tool, by designing ZIFs that meet industrial performance criteria of permeability and selectivity, for CO<sub>2</sub>/CH<sub>4</sub>, O<sub>2</sub>/N<sub>2</sub> and C<sub>3</sub>H<sub>6</sub>/C<sub>3</sub>H<sub>8</sub> mixtures. Inverse ; Zeolitic imidazolate framework ; Computer science ; Artificial intelligence ; Evolutionary algorithm ; Biological system ; Nanotechnology ; Materials science ; Chemistry ; Mathematics ; Metal-organic framework ; Biology Metal-Organic Frameworks: Synthesis and Applications ; Machine Learning in Materials Science ; X-ray Diffraction in Crystallography
Authors: Valerija Gruzinova | Valentin Romanovski
Source: Waste and Biomass Valorization (article, 2024-12-11)
Field: Chemistry — Organic Chemistry

Optimizing Oil-Contaminated Wastewater Purification with Polypropylene Thread Waste Abstract The increasing generation of oil-containing wastewater poses significant environmental challenges, necessitating the development of effective and sustainable filtration materials. Polypropylene thread scraps, a waste product from textile manufacturing, present a potential low-cost alternative to industrially produced polypropylene fibrous filters. This study evaluates the filtration properties of these scraps to determine their viability for oil product removal from wastewater. The polypropylene thread scraps exhibited promising physical characteristics: a fiber diameter range of 10–120 μm, bulk density between 100 and 200 kg/m 3 , total porosity of 78–89%, and a specific surface area of 75 m 2 /kg. Their hydrophobic nature is comparable to that of commercial polypropylene filter materials. Experimental studies demonstrated that the thread scraps could effectively remove oil products at a 70% efficiency, with a maximum specific wastewater volume of 8 L/g. The oil capacity for oil products was measured at 51.1 mg/g, which decreased to 36.2 mg/g after regeneration by washing with hot water at 70 °C. The optimal filtration parameters were identified as a material packing density of 65 kg/m 3 , filtration speed of 3.5 m/h, and a loading height of 1.5 m, achieving removal efficiencies of 82.0% for oil products and 91.5% for suspended solids. Polypropylene thread scraps demonstrate significant potential as a sustainable filtration material for oil-containing wastewater, offering comparable performance to industrial filters. Their ability to be regenerated and reused further enhances their cost-effectiveness and environmental benefits. This research supports the use of polypropylene thread scraps as a viable solution for wastewater treatment, contributing to waste reduction and improved environmental management. Graphical abstract Wastewater ; Contamination ; Waste management ; Polypropylene ; Thread (computing) ; Environmental science ; Pulp and paper industry ; Chemistry ; Engineering ; Organic chemistry ; Biology Inorganic and Organometallic Chemistry ; Water Quality Monitoring and Analysis ; Environmental and Analytical Chemistry Studies
Authors: Georgia D. Ioannou | Christos N. Christou | Katerina A. Ioannou | Atalanti Christou | Ioannis J. Stavrou | Theodora Krasia‐Christoforou | Constantina P. Kapnissi‐Christodoulou
Source: Journal of Food Processing and Preservation (article, 2024-01-01)
Field: Materials Science — Biomaterials

Innovative Chitosan Edible Coating Incorporated With a Natural Deep Eutectic Solvent and <i>Aloe vera</i> for Extending the Blackberry Shelf Life Biodegradable and nontoxic chitosan edible coatings offer a promising alternative to conventional plastic food packaging materials. Recently, there has been significant interest in incorporating green plasticizers into these coatings. Accordingly, response surface methodology was employed to optimize a chitosan coating formulation that integrates Aloe vera extracts and a deep eutectic solvent (choline chloride–citric acid) as a plasticizer. The selection of the optimized formulation was related to quality characteristics of coated blackberries including their weight loss, pH, total phenolic content, total anthocyanin content, and antioxidant activity after 7 days of cold storage. The models demonstrated a high level of significance between the responses and independent variables, with p value less than 0.0001. The optimal coating formulation for blackberry fruits was identified as 2.05% ( v / v ) aloe rind extract, 1.1% ( w / w ) aloe gel extract, and 15% ( w / w ) choline chloride–citric acid. The developed film was characterized by ATR‐FTIR and SEM for its intermolecular interactions and surface morphology, respectively, demonstrating good combability of polymer matrix with the plasticizer and aloe extracts. The optimized film was compared to a pure chitosan film in regard to their physical and mechanical properties. The alternative plasticizer choline chloride–citric acid improved the flexibility of the edible packaging by enhancing its mechanical properties, such as tensile strength, elongation at rupture, and elastic modulus. Additionally, the incorporation of this plasticizer and plant extracts slightly increased the transparency of the film. The coating was then applied to blackberry fruits in order to investigate the potential of the developed coating formulation to maximize the shelf life of food products. The results indicated the ability of the coating to extend shelf life and maintain the quality of the fruits. Aloe vera ; Shelf life ; Chitosan ; Eutectic system ; Deep eutectic solvent ; Coating ; Food science ; Chemistry ; Botany ; Biology ; Organic chemistry Nanocomposite Films for Food Packaging ; Phytochemicals and Antioxidant Activities ; Postharvest Quality and Shelf Life Management
Authors: A. B. Pawar | P. William | Milind V. Kulkarni | Debdas Roy | N Yogeesh
Source: Journal of Nano- and Electronic Physics (article, 2024-01-01)
Field: Materials Science — General Materials Science

Exploration of Composition-Microstructure Relations in Polymer Nanocomposites: Intelligent Honey Journal of Nano- and Electronic Physics. Scientific journal. ISSN: 2077-6772. Journal abbreviation: J. Nano- Electron. Phys. No page charges. All articles are freely available on-line. Issued 4 times per year. Publisher: Sumy State University. (Sumy, Ukraine) Microstructure ; Nanocomposite ; Composition (language) ; Polymer ; Materials science ; Chemical engineering ; Composite material ; Art ; Engineering ; Literature Material Properties and Applications ; Adsorption, diffusion, and thermodynamic properties of materials
Authors: Yutong Zhou | Lvchao Qiu | Zongchao Xu | Shixuan Huang | Jingkai Nie | Hang Yin | Feng Tu | Z.D. Zhao
Source: Polymers (article, 2024-04-24)
Field: Materials Science — Materials Chemistry

Thermal Oxidative Aging and Service Life Prediction of Commercial Ethylene–Propylene–Diene Monomer Spacer Damping Composites for High–Voltage Transmission Lines The aging behavior and life prediction of rubber composites are crucial for ensuring high-voltage transmission line safety. In this study, commercially available ethylene-propylene-diene monomer (EPDM) spacer composites were chosen and investigated to elucidate the structure and performance changes under various aging conditions. The results showed an increased C=O peak intensity with increasing aging time, suggesting intensified oxidation of ethylene and propylene units. Furthermore, the surface morphology of commercial EPDM composites displayed increased roughness and aggregation after aging. Furthermore, hardness, modulus at 100% elongation, and tensile strength of commercial EPDM composites exhibited a general increase, while elongation at break decreased. Additionally, the damping performance decreased significantly after aging, with a 20.6% reduction in loss factor (20 °C) after aging at 100 °C for 672 h. With increasing aging time and temperature, the compression set gradually rose due to the irreversible movement of the rubber chains under stress. A life prediction model was developed based on a compression set to estimate the lifetime of rubber composites for spacer bars. The results showed that the product's life was 8.4 years at 20 °C. Therefore, the establishment of a life prediction model for rubber composites can provide valuable technical support for spacer product services. Diene ; Materials science ; Composite material ; Monomer ; Ethylene ; Service life ; Thermal ; Ethylene propylene rubber ; Oxidative phosphorylation ; Transmission (telecommunications) ; Polymer ; Electrical engineering ; Organic chemistry ; Natural rubber ; Chemistry ; Engineering ; Copolymer High voltage insulation and dielectric phenomena ; Thermal Analysis in Power Transmission ; Smart Materials for Construction
Authors: Siyun Li | T. Luo | Zhenlong Chao | Longtao Jiang | Huimin Han | Bingzhuo Han | Shanqi Du | Mingqi Liu
Source: Materials (review, 2024-04-18)
Field: Materials Science — Materials Chemistry

A Review of Dynamic Mechanical Behavior and the Constitutive Models of Aluminum Matrix Composites Aluminum matrix composites (AMMCs) have demonstrated substantial potential in the realm of armor protection due to their favorable properties, including low density, high specific stiffness, and high specific strength. These composites are widely employed as structural components and frequently encounter high strain rate loading conditions, including explosions and penetrations during service. And it is crucial to note that under dynamic conditions, these composites exhibit distinct mechanical properties and failure mechanisms compared to static conditions. Therefore, a thorough investigation into the dynamic mechanical behavior of aluminum matrix composites and precise constitutive equations are imperative to advance their application in armor protection. This review aims to explore the mechanical properties, strengthening the mechanism and deformation damage mechanism of AMMCs under high strain rate. To facilitate a comprehensive understanding, various constitutive equations are explored, including phenomenological constitutive equations, those with physical significance, and those based on artificial neural networks. This article provides a critical review of the reported work in this field, aiming to analyze the main challenges and future development directions of aluminum matrix composites in the field of protection. Constitutive equation ; Materials science ; Composite material ; Stiffness ; Matrix (chemical analysis) ; Armour ; Micromechanics ; Deformation (meteorology) ; Structural engineering ; Composite number ; Finite element method ; Engineering High-Velocity Impact and Material Behavior ; Aluminum Alloys Composites Properties ; Advanced ceramic materials synthesis
Authors: Thanh Tung Pham | Thanh Ba Nguyen | Dam Sao | Lien Le Phuong Nguyen | László Baranyai
Source: Agriculture (review, 2024-10-10)
Field: Chemistry — Analytical Chemistry

A Review of the Application of the Laser-Light Backscattering Imaging Technique to Agricultural Products Growing concerns about food safety and waste have increased consumer demand for high-quality agricultural products, particularly at the postharvest stage. This demand has prompted the development of non-destructive methods to assess or inspect the internal quality of fruits and vegetables. The backscattering imaging technique, also known as diffuse reflectance imaging, is considered a highly promising approach. Numerous studies have focused on practical applications, using laser light at selected wavelengths to develop quick multispectral methods. Due to the rapid interaction of photons with biological tissue, together with the highly computational performance of machine vision, backscattering imaging can offer a valuable alternative to traditional methods. Its primary benefits include quick measurements without chemical sample preparation, easy integration with high-throughput automatic quality control, and reduced waste, since this non-destructive technique does not damage samples. This review presents a comprehensive overview of backscattering imaging, including the measurement geometry, data analysis, and design considerations for vision systems. Additionally, it explores this technique’s advantages, challenges, and accuracy, as demonstrated using various case studies. Agriculture ; Laser ; Environmental science ; Optics ; Remote sensing ; Geography ; Physics ; Biology ; Ecology Spectroscopy and Chemometric Analyses
Authors: Wenjie Zhang | Shan Wang | Hong Guo
Source: Polymers (article, 2024-12-31)
Field: Materials Science — Biomaterials

Study on the Aging Effects of Relative Humidity on the Primary Chemical Components of Palm Leaf Manuscripts Palm Leaf Manuscripts represent a significant component of the world's cultural heritage. Investigating their primary chemical components and understanding the transformations these materials undergo under environmental influences are crucial for elucidating their material characteristics and aging mechanisms and developing effective strategies for preventive conservation. This study utilized infrared absorption spectroscopy and X-ray diffraction analysis to examine changes in the primary chemical components of Palm Leaf Manuscripts under varying relative humidity conditions over extended periods. The findings reveal that dry environments lead to surface cracking, while humid environments promote mold growth, both of which contribute to the degradation of the primary chemical components. These degradative processes reduce cellulose crystallinity and thermal stability. The deterioration is particularly severe under high humidity, with hemicellulose degrading faster and more extensively than cellulose under the same conditions. After 200 days of aging at 10% RH and 90% RH, cellulose degradation reached 19.82% and 54.40%, respectively, while hemicellulose degradation was 34.78% and 64.28%. Correspondingly, the relative crystallinity of cellulose decreased by 8.01% and 13.11%. In contrast, samples maintained at 50% RH exhibited minimal deterioration, with cellulose and hemicellulose degrading by only 4.08% and 13.55%, respectively, and a 6.61% reduction in cellulose crystallinity. These results suggest that a relative humidity of 50% is optimal for the preservation of Palm Leaf Manuscripts. This study offers significant insights into the ageing mechanisms and preventive conservation of Palm Leaf Manuscripts, as well as other cellulose-based organic heritage materials. Cellulose ; Hemicellulose ; Crystallinity ; Relative humidity ; Materials science ; Humidity ; Chemistry ; Composite material ; Organic chemistry ; Geography Advanced Cellulose Research Studies ; Cultural Heritage Materials Analysis ; Lignin and Wood Chemistry
Authors: Sabyasachi Chakraborty | Eduardo Mayo Yanes | Renana Gershoni‐Poranne
Source: Beilstein Journal of Organic Chemistry (article, 2024-07-31)
Field: Chemistry — Organic Chemistry

Hetero-polycyclic aromatic systems: A data-driven investigation of structure–property relationships Polycyclic aromatic systems (PASs) are pervasive compounds that have a substantial impact in chemistry and materials science. Although their specific structure-property relationships hold the key to the design of new functional molecules, a detailed understanding of these relationships remains elusive. To elucidate these relationships, we performed a data-driven investigation of the newly generated COMPAS-2 dataset, which contains ~500k molecules consisting of 11 types of aromatic and antiaromatic rings and ranging in size from one to ten rings. Our analysis explores the effects of electron count, geometry, atomic composition, and heterocyclic composition on a range of electronic molecular properties of PASs. Chemistry ; Property (philosophy) ; Polycyclic aromatic hydrocarbon ; Computational chemistry ; Combinatorial chemistry ; Organic chemistry Synthesis and Properties of Aromatic Compounds ; Computational Drug Discovery Methods ; Crystallography and molecular interactions