jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Andreas Mecklenfeld | G. Raabe
Source: ADMET & DMPK (article, 2020-06-28)
Field: Materials Science — Materials Chemistry

GAFF/IPolQ-Mod+LJ-Fit: Optimized force field parameters for solvation free energy predictions Rational drug design featuring explicit solubility considerations can greatly benefit from molecular dynamics simulations, as they allow for the prediction of the Gibbs free energy of solvation and thus relative solubilities. In our previous work (A. Mecklenfeld, G. Raabe. J. Chem. Theory Comput. <b>13</b> no. 12 (2017) 6266-6274), we have compared solvation free energy results obtained with the General Amber Force Field (GAFF) and its default restrained electrostatic potential (RESP) partial charges to those obtained by modified implicitly polarized charges (IPolQ-Mod) for an implicit representation of impactful polarization effects. In this work, we have adapted Lennard-Jones parameters for GAFF atom types in combination with IPolQ-Mod to further improve the accuracies of solvation free energy and liquid density predictions. We thereby focus on prominent atom types in common drugs. For the refitting, 357 respectively 384 systems were considered for free energies and densities and validation was performed for 142 free energies and 100 densities of binary mixtures. By the in-depth comparison of simulation results for default GAFF, GAFF with IPolQ-Mod and our new set of parameters, which we label GAFF/IPolQ-Mod+LJ-Fit, we can clearly highlight the improvements of our new model for the description of both relative solubilities and fluid phase behaviour. Solvation ; Force field (fiction) ; Thermodynamics ; Implicit solvation ; Chemistry ; Molecular dynamics ; Gibbs free energy ; Thermodynamic integration ; Work (physics) ; Statistical physics ; Computational chemistry ; Physics ; Molecule ; Quantum mechanics Crystallization and Solubility Studies ; Computational Drug Discovery Methods ; Analytical Chemistry and Chromatography
Authors: Andy S. Anker | Emil T. S. Kjær | Erik B. Dam | Simon J. L. Billinge | Kirsten M. Ø. Jensen | Raghavendra Selvan
Source: ChemRxiv (preprint, 2020-07-17)
Field: Materials Science — Materials Chemistry

Characterising the Atomic Structure of Mono-Metallic Nanoparticles from X-Ray Scattering Data Using Conditional Generative Models The development of new nanomaterials for energy technologies is dependent on understanding the intricate relation between material properties and atomic structure. It is, therefore, crucial to be able to routinely characterise the atomic structure in nanomaterials, and a promising method for this task is Pair Distribution Function (PDF) analysis. The PDF can be obtained through Fourier transformation of x-ray total scattering data, and represents a histogram of all interatomic distances in the sample. Going from the distance information in the PDF to a chemical structure is an unassigned distance geometry problem (uDGP), and solving this is often the bottleneck in nanostructure analysis. In this work, we propose to use a Conditional Variational Autoencoder (CVAE) to automatically solve the uDGP to obtain valid chemical structures from PDFs. We use a simple model system of hypothetical mono-metallic nanoparticles containing up to 100 atoms in the face centered cubic (FCC) structure as a proof of concept. The model is trained to predict the assigned distance matrix (aDM) from a simulated PDF of the structure as the conditional input. We introduce a novel representation of structures by projecting them inside a unit sphere and adding additional anchor points or satellites to help in the reconstruction of the chemical structure. The performance of the CVAE model is compared to a Deterministic Autoencoder (DAE) showing that both models are able to solve the uDGP reasonably well. We further show that the CVAE learns a structured and meaningful latent embedding space which can be used to predict new chemical structures. Autoencoder ; Conditional probability distribution ; Computer science ; Conditional probability ; Representation (politics) ; Statistical physics ; Algorithm ; Biological system ; Artificial neural network ; Artificial intelligence ; Mathematics ; Physics X-ray Diffraction in Crystallography ; Machine Learning in Materials Science ; Electron and X-Ray Spectroscopy Techniques
Authors: Bo Pang | Tian Han | Ying Wu
Source: arXiv (Cornell University) (preprint, 2020-10-19)
Field: Materials Science — Materials Chemistry

Learning Latent Space Energy-Based Prior Model for Molecule Generation Deep generative models have recently been applied to molecule design. If the molecules are encoded in linear SMILES strings, modeling becomes convenient. However, models relying on string representations tend to generate invalid samples and duplicates. Prior work addressed these issues by building models on chemically-valid fragments or explicitly enforcing chemical rules in the generation process. We argue that an expressive model is sufficient to implicitly and automatically learn the complicated chemical rules from the data, even if molecules are encoded in simple character-level SMILES strings. We propose to learn latent space energy-based prior model with SMILES representation for molecule modeling. Our experiments show that our method is able to generate molecules with validity and uniqueness competitive with state-of-the-art models. Interestingly, generated molecules have structural and chemical features whose distributions almost perfectly match those of the real molecules. Representation (politics) ; Computer science ; Chemical space ; Simple (philosophy) ; String (physics) ; Generative model ; Theoretical computer science ; Uniqueness ; Space (punctuation) ; Energy (signal processing) ; Character (mathematics) ; Generative grammar ; Artificial intelligence ; Mathematics ; Theoretical physics ; Physics ; Chemistry ; Drug discovery ; Quantum mechanics Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Protein Structure and Dynamics
Authors: Nasir Abdus- Salam | Abiola Victoria Ikudayisi-Ugbe | Fabian Audu Ugbe
Source: Acta Scientifica Malaysia (article, 2020-11-17)
Field: Chemistry — Analytical Chemistry

ADSORPTIVE REMOVAL OF METHYLENE BLUE FROM SYNTHETIC WASTEWATER USING DATE PALM SEEDS, GOETHITE AND THEIR COMPOSITE The adsorption of Methylene Blue (MB) onto Raw Date-palm Seeds (RDS), Thermally Activated Carbon (TAC), Chemically Activated Carbon (CAC), Goethite (GT) and their Composite (COM) were studied using batch equilibrium technique. Variations of sorptive properties such as initial solution concentration, pH, adsorbent dosage, contact time and temperature had a remarkable influence on the adsorption processes. The data fitted well tested isotherm models in the order; Langmuir (R2 = 0.942 and 0.963) &gt; Freundlich (0.886 and 0.948) &gt; Temkin (0.869 and 0.83) for GT and COM respectively. That of CAC and TAC was best described by Freundlich and Langmuir models respectively while RDS showed very poor fittings. Pseudo-second order and film diffusion models best described the adsorption kinetics. The adsorption was feasible, spontaneous (∆G &lt; 0) and exothermic (except MB-CAC with ∆H being positive). The combined results of isotherm, kinetics and thermodynamic studies suggested a combined chemisorptions and physisorptions processes. Also, the kinetic modeling suggested that intra-particle and film diffusions occurred simultaneously and/or in combination with other processes in the mechanism of adsorption. Freundlich equation ; Adsorption ; Activated carbon ; Methylene blue ; Langmuir ; Chemistry ; Goethite ; Langmuir adsorption model ; Nuclear chemistry ; Composite number ; Kinetics ; Chemical engineering ; Chromatography ; Materials science ; Organic chemistry ; Composite material ; Catalysis Spectroscopy and Chemometric Analyses ; Dye analysis and toxicity ; Date Palm Research Studies
Authors: Xuewei Zhao | Hua Zhang | Wangming Li | Xingke Li | Wen Fan | Yanyan Zhang
Source: Journal of Food Process Engineering (article, 2020-06-29)
Field: Materials Science — Materials Chemistry

Langmuir‐diffusion model: Its modification and further application to glutinous rice flour particles Abstract When the Langmuir‐diffusion model was applied to a continuous multistep dynamic vapor adsorption, an initial desorption of bound water was predicted for the relative humidity (RH) steps except the first. The desorption is physically meaningless. The model was modified with assuming probability ratio ( β / γ ) continuity between the boundary and field equations. The β / γ was calculated from the Park isotherm model. According to our modifying methodology, two parameter selection strategies exist while conducting parameter optimization: β as parameter while γ calculated using the β / γ ratio; γ as parameter while β calculated. These two strategies can result to almost identical total, free and bound water concentration evolution, nearly equal diffusivity, and qualitatively similar variation trends of both γ and β with free water concentration. Application of the modified model to the adsorption of glutinous rice flour revealed that the well‐documented bell‐like diffusivity vs RH curve did not hold for the free water. Practical Applications The Fickian law assumes that all water molecules diffuse equally. As we all know, at least two water populations with different mobilities coexist in most food materials. The Langmuir‐diffusion model assumes that the water molecules exist in free and bound states and that the free molecules may bond at certain sorption sites while diffusing. The modified version of the Langmuir‐diffusion model proposed here can be used to describe a continuous multistep vapor adsorption and deepen our understanding of moisture transfer mechanisms. This information can be applied in optimizing both the quality of food product and the economics of many food processes involving water transfer. Thermal diffusivity ; Langmuir ; Desorption ; Langmuir adsorption model ; Thermodynamics ; Adsorption ; Chemistry ; Diffusion ; Bound water ; Sorption ; Mass transfer ; Water vapor ; Relative humidity ; Molecule ; Fick's laws of diffusion ; Physical chemistry ; Chromatography ; Organic chemistry ; Physics Material Dynamics and Properties ; Food Drying and Modeling ; Granular flow and fluidized beds
Authors: Chaima Zouzou | М. Кеддам | B. Bouarour | Adam Piasecki | Andrzej Miklaszewski | M. Kulka
Source: Annales de Chimie Science des Matériaux (article, 2020-03-15)
Field: Materials Science — Materials Chemistry

Characterization and Boronizing Kinetics of EN-GJL-250 Lamellar Gray Cast Iron The aim of the present study is to generate the boride coatings at the surface of the lamellar gray cast iron . This material was hardened by pack-boriding in the powders mixture of 50% B4C, 49.5% Al2O3 and 0.5% AlF3 at 800, 900 and 1000C for 4, 6 and 8 h. The produced borided layers were characterized by Scanning electron microscopy (SEM) and XRD analysis. The boriding kinetics of EN-GJL-250 lamellar gray cast iron was also investigated. Based on the experimental data, the value of activation energy for boron diffusion was calculated as 163.86 kJ mol-1 for the EN-GJL-250 cast iron by using the integral diffusion model. The regression model based on the design of experiments (DOE) was also employed in order to predict the total boride layer thickness as a function of boriding parameters (the treatment time and the boriding temperature). The experimental values of total boride layer thickness were in agreement with the results from the regression model. Cast iron ; Lamellar structure ; Kinetics ; Metallurgy ; Materials science ; Characterization (materials science) ; Gray (unit) ; Art ; Medicine ; Nanotechnology ; Physics ; Nuclear medicine Metal Alloys Wear and Properties ; Powder Metallurgy Techniques and Materials ; Metal and Thin Film Mechanics
Authors: Gülbanu Koyundereli Çılgı | Metin Ak
Source: Journal of Molecular Structure (article, 2020-07-09)
Field: Materials Science — Materials Chemistry

Thermal degradation kinetics and thermodynamics of maleimide-sytrene based alternating copolymer: A comparative investigation of monomer and polymer structures Copolymer ; Monomer ; Chemistry ; Maleimide ; Polymer chemistry ; Polymer ; Thermal decomposition ; Kinetics ; Activation energy ; Thiophene ; Decomposition ; Styrene ; Thermodynamics ; Physical chemistry ; Organic chemistry Thermal and Kinetic Analysis ; Synthesis and properties of polymers ; Polymer Nanocomposites and Properties
Authors: Özge Yalçın | Nilay Baylan | Süheyla Çehreli
Source: International Journal of Environmental & Analytical Chemistry (article, 2020-12-15)
Field: Chemistry — Electrochemistry

An antiparkinsonism drug entacapone removal from water onto Amberlite IRA-67: kinetic, thermodynamics, optimisation studies and determination by Ultra Performance Liquid Chromatography (UPLC) Entacapone is a drug used for Parkinson’s disease treatment. The contamination of water resources by this active drug ingredient affects the human health, environment and ecosystem. In the present research, adsorption properties of entacapone were investigated by using Amberlite IRA-67 as an adsorbent. The quantity of entacapone before and after adsorption was analysed by a sensitive, simple and rapid ultra performance liquid chromatography (UPLC) method. Adsorption characteristics factors, including initial entacapone concentration in the solution (20–100 ppm), contact time (30–240 min), adsorbent dosage (0.01–0.03 g), pH (2–10), and temperature (25–45 °C) were examined. The adsorption isotherm models (Langmuir, Freundlich, and Temkin), and kinetic models (Lagergren pseudo-first order, Ho pseudo-second order, Elovich, and Weber-Morris intra particle model) were also investigated to characterise the adsorption mechanism. ™Furthermore, thermodynamic analysis was employed to explain the adsorption behaviour. Langmuir isotherm model showed the best compliance to the adsorption data with R2 value of 0.9801. The maximum adsorption capacity was obtained as 86.21 mg.g−1 from the Langmuir isotherm model. The kinetic data for entacapone adsorption on Amberlite IRA-67 were well characterised by Weber-Morris intra-particle diffusion model with R2 value of 0.9793. Besides, an optimisation and modelling study was performed by response surface methodology (RSM).The optimum adsorption parameters were obtained as 99.57 ppm of initial entacapone concentration in the solution, a pH of 5.83, and a temperature of 34.82 °C. Under these optimum conditions, the experimental and predicted adsorption capacity values were acquired to be 89.91 mg.g−1 and 84.53 mg.g−1.This adsorption researc™h demonstrated that Amberlite IRA-67 is an influential adsorbent for the uptake of antiparkinsonism drug entacapone from the water. Amberlite ; Entacapone ; Chromatography ; Chemistry ; High-performance liquid chromatography ; Kinetic energy ; Thermodynamics ; Adsorption ; Organic chemistry Electrochemical Analysis and Applications ; Analytical Chemistry and Chromatography ; Analytical chemistry methods development
Authors: Biljana Koturević | Borivoj Adnadjević | Jelena Jovanović
Source: Process Safety and Environmental Protection (article, 2020-11-02)
Field: Chemistry — Organic Chemistry

Comparative kinetic analysis of total hypericin extraction from Hypericum perforatum flowers carried out under simultaneous external physical field and cooling reaction system operational conditions Hypericin ; Extraction (chemistry) ; Hypericum perforatum ; Kinetic energy ; Chemistry ; Analytical Chemistry (journal) ; Chromatography ; Materials science ; Thermodynamics ; Physics Microwave-Assisted Synthesis and Applications ; Analytical Chemistry and Chromatography ; Synthesis of Organic Compounds
Authors: Long Wang | Xingyuan Huang | Duyang Wang
Source: e-Polymers (article, 2020-01-01)
Field: Materials Science — Polymers and Plastics

Solubility and diffusion coefficient of supercritical CO <sub>2</sub> in polystyrene dynamic melt Abstract The solubility and diffusion coefficient of supercritical CO 2 in polystyrene (PS) dynamic melt were studied by using a new constant pressure experimental device. By comparing the experimental results with those of other researchers, the validity of the experimental device and the reliability of the calculated results are verified. The solubility and diffusion coefficient of supercritical CO 2 in polystyrene dynamic melts at different temperatures and pressures were obtained. The numerical calculation method, dissolution process, and experimental results are analyzed and compared with that of the static melt. Finally, the effects of stirring speed, pressure, and temperature fluctuation on the solubility and diffusion coefficient are also analyzed. Supercritical fluid ; Solubility ; Diffusion ; Polystyrene ; Dissolution ; Materials science ; Thermodynamics ; Chemistry ; Polymer ; Composite material ; Physical chemistry Polymer Foaming and Composites ; Phase Equilibria and Thermodynamics ; Injection Molding Process and Properties
Authors: Douglas Read | Colin H. Sillerud | Joshua J. Whiting | Komandoor E. Achyuthan
Source: Journal of Chromatographic Science (article, 2020-02-04)
Field: Chemistry — Inorganic Chemistry

Metal-Organic Framework Stationary Phases for One- and Two-Dimensional Micro-Gas Chromatographic Separations of Light Alkanes and Polar Toxic Industrial Chemicals Despite promising advances with metal-organic frameworks (MOFs) as stationary phases for chromatography, the application of MOFs for one- and two-dimensional micro-gas chromatography (μGC and μGC × μGC) applications has yet to be shown. We demonstrate for the first time, μGC columns coated with two different MOFs, HKUST-1 and ZIF-8, for the rapid separation of high volatility light alkane hydrocarbons (natural gas) and determined the partition coefficients for toxic industrial chemicals, using μGC and μGC × μGC systems. Complete separation of natural gas components, methane through pentane, was completed within 1 min, with sufficient resolution to discriminate n-butane from i-butane. Layer-by-layer controlled deposition cycles of the MOFs were accomplished to establish the optimal film thickness, which was validated using GC (sorption thermodynamics), quartz-crystal microbalance gravimetric analysis and scanning electron microscopy. Complete surface coverage was not observed until after ~17 deposition cycles. Propane retention factors with HKUST-1-coated μGC and a state-of-the-art polar, porous-layer open-tubular (PLOT) stationary phase were approximately the same at ~7.5. However, with polar methanol, retention factors with these two stationary phases were 748 and 59, respectively, yielding methanol-to-propane selectivity factors of ~100 and ~8, respectively, a 13-fold increase in polarity with HKUST-1. These studies advance the applications of MOFs as μGC stationary phase. Chemistry ; Butane ; Propane ; Gas chromatography ; Chromatography ; Gravimetric analysis ; Methanol ; Metal-organic framework ; Alkane ; Pentane ; Flame ionization detector ; Analytical Chemistry (journal) ; Two-dimensional gas ; Adsorption ; Hydrocarbon ; Organic chemistry Metal-Organic Frameworks: Synthesis and Applications ; Gas Sensing Nanomaterials and Sensors ; Analytical Chemistry and Chromatography
Authors: O. A. Kyzyma
Source: Ukrainian Journal of Physics (article, 2020-08-26)
Field: Chemistry — Organic Chemistry

Liquid Systems with Fullerenes in Organic Solvents and Aqueous Media The unique properties of nanocarbon materials – in particular, fullerenes – has led in recent years to the expansion of the spectrum of their application in various fields of the industry, including the chemical, energy, and pharmaceutical ones. The use of fullerenes in new industries poses new challenges to the scientific and research community. Thus, new methods of obtaining biocompatible liquid systems with small-sized monodisperse fullerene aggregates are still being sought. The paper focuses on the properties of fullerene solutions in mixtures of organic solvents, which serve as a basis for the development of new methods for synthesizing the aqueous liquid systems with fullerenes. Fullerene ; Materials science ; Aqueous solution ; Dispersity ; Nanotechnology ; Aqueous medium ; Chemical engineering ; Organic chemistry ; Chemistry ; Polymer chemistry Fullerene Chemistry and Applications ; Carbon Nanotubes in Composites ; Laser-Ablation Synthesis of Nanoparticles
Authors: Leonid Dorogin | M. V. Dorogov | Sergei Vlassov | А. А. Викарчук | А. Е. Романов
Source: Reviews on advanced materials and technologies (article, 2020-01-01)
Field: Materials Science — Materials Chemistry

Whisker Growth and Cavity Formation at the Microscale We discuss a recent progress in research on micro-/nanoscale metal and oxide whiskers. It is common to define whiskers as quasi-one-dimensional (elongated) solid objects that formed on a surface of a crystalline material by growth from its base. Whisker growth is often accompanied by formation of cavities and cracks in the bulk of material. This fact did facilitate the advancing of various explanations on the mass transfer for whisker growth. First theoretical models of metal whiskers growth were based on the theory of crystal lattice defects and on the assumption of inherent mechanical stresses in the material that "push" the whisker out. However, those models were not applicable to all variety of whisker growth observed. There are more complex cases of whiskers, such as oxide whiskers that formed in chemical reactions, such as oxidation during annealing in air or a synthetic reaction in a liquid. Theoretical modelling of the complex cases is still a challenging task at the border of chemical kinetics and materials science. Oxide whiskers are usually considered separately from metal whiskers, thus the fundamental interlink between the two cases might be lost. The goal of the present review is to collect the most prominent observations and theoretical explanations of whisker growth for both single phase and compound objects into a single document. Whisker ; Microscale chemistry ; Materials science ; Nanotechnology ; Metallurgy ; Psychology ZnO doping and properties ; Nanowire Synthesis and Applications ; Electronic and Structural Properties of Oxides
Authors: Hares Wahdat | Matthias Gerst | Stephan Möbius | Jörg Adams
Source: Journal of Applied Polymer Science (article, 2020-01-15)
Field: Materials Science — Polymers and Plastics

Interdiffusion during film formation of ionically cross‐linked acrylics investigated with Förster resonance energy transfer (FRET) ABSTRACT Polymer interdiffusion is crucial to obtain continuous films from aqueous polymer dispersions. Here, interdiffusion in films from dispersions of acrylates which were ionically cross‐linked prior to film formation was studied by Förster resonance energy transfer analysis. Dispersions of copolymers of n‐butyl acrylate, methacrylic acid, and zinc dimethacrylate (ZnDMA) were investigated. ZnDMA was used as a co‐monomer to ionically cross link the polymers during the synthesis. Ionic cross‐linking does not prevent interdiffusion even at high gel contents. Interdiffusion data were compared with results of tensile tests on final films. Films of ionically cross‐linked polymers fracture at both higher stress and strain than films of covalently cross‐linked polymers. Further interdiffusion studies addressed effects of temperature and humidity. Both increased temperature and humidity accelerate interdiffusion of ionically cross‐linked polymers. Thus, using ZnDMA allows for preparing dispersions which can form continuous films. Also, no volatile organic compounds are released during the film formation. © 2020 The Authors. Journal of Applied Polymer Science published by Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2020 , 137 , 48972. Polymer ; Materials science ; Copolymer ; Polymer chemistry ; Chemical engineering ; Cross-link ; Acrylate ; Monomer ; Composite material Polymer crystallization and properties ; Polymer Foaming and Composites ; Polymer composites and self-healing