jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Bo Li | Xin Li | Qing Jiang | Wang Gao
Source: Research Square (preprint, 2020-07-10)
Field: Materials Science — Materials Chemistry

An effective scheme to determine surface energy and its relation with adsorption energy Abstract Surface energy is fundamental in controlling surface properties and surface-driven processes like heterogeneous catalysis, as adsorption energy is. It is thus crucial to establish an effective scheme to determine surface energy and its relation with adsorption energy. Herein, we propose a model to quantify the effects of materials’ intrinsic characteristics on the material-dependent property and anisotropy of surface energy, based on the period number and group number of bulk atoms, and the valence-electron number, electronegativity and coordination of surface atoms. Our scheme holds for elemental crystals in both solid and liquid phases, body-centered-tetragonal intermetallics, fluorite-structure intermetallics, face-centered-cubic intermetallics, Mg-based surface alloys and semiconductor compounds, which further identifies a quantitative relation between surface energy and adsorption energy and rationalizes the material-dependent error of first-principle methods in calculating the two quantities. This model is predictive with easily accessible parameters and thus allows the rapid screening of materials for targeted properties. Relation (database) ; Scheme (mathematics) ; Energy (signal processing) ; Adsorption ; Surface (topology) ; Computer science ; Mathematics ; Statistics ; Chemistry ; Geometry ; Mathematical analysis ; Data mining ; Physical chemistry Graphene research and applications ; Chemical and Physical Properties of Materials ; Molecular Junctions and Nanostructures
Authors: Jinzhe Zeng | Linfeng Zhang | Handong Wang | Tong Zhu
Source: ChemRxiv (preprint, 2020-09-10)
Field: Materials Science — Materials Chemistry

Explore the Chemical Space of Linear Alkanes Pyrolysis via Deep Potential Generator &lt;div&gt; &lt;div&gt; &lt;div&gt; &lt;p&gt;Reactive molecular dynamics (MD) simulation is a powerful tool to study the reaction mechanism of complex chemical systems. Central to the method is the potential energy surface (PES) that can describe the breaking and formation of chemical bonds. The development of PES of both accurate and efficent has attracted significant effort in the past two decades. Recently developed Deep Potential (DP) model has the promise to bring ab initio accuracy to large-scale reactive MD simulations. However, for complex chemical reaction processes like pyrolysis, it remains challenging to generate reliable DP models with an optimal training dataset. In this work, a dataset construction scheme for such a purpose was established. The employment of a concurrent learning algorithm allows us to maximize the exploration of the chemical space while minimize the redundancy of the dataset. This greatly reduces the cost of computational resources required by ab initio calculations. Based on this method, we constructed a dataset for the pyrolysis of n-dodecane, which contains 35,496 structures. The reactive MD simulation with the DP model trained based on this dataset revealed the pyrolysis mechanism of n-dodecane in detail, and the simulation results are in good agreement with the experimental measurements. In addition, this dataset shows excellent transferability to different long-chain alkanes. These results demonstrate the advantages of the proposed method for constructing training datasets for similar systems. &lt;/p&gt; &lt;/div&gt; &lt;/div&gt; &lt;/div&gt; Transferability ; Chemical space ; Computer science ; Ab initio ; Molecular dynamics ; Redundancy (engineering) ; Potential energy surface ; Chemistry ; Computational chemistry ; Biological system ; Algorithm ; Machine learning Machine Learning in Materials Science ; Advanced Physical and Chemical Molecular Interactions ; Advanced Chemical Physics Studies
Authors: Jianjun Hu | Wenhui Yang | Rongzhi Dong | Yuxin Li | Xiang Li | Shaobo Li
Source: arXiv (Cornell University) (preprint, 2020-08-16)
Field: Materials Science — Materials Chemistry

Contact Map based Crystal Structure Prediction using Global Optimization Crystal structure prediction is now playing an increasingly important role in discovery of new materials. Global optimization methods such as genetic algorithms (GA) and particle swarm optimization (PSO) have been combined with first principle free energy calculations to predict crystal structures given composition or only a chemical system. While these approaches can exploit certain crystal patterns such as symmetry and periodicity in their search process, they usually do not exploit the large amount of implicit rules and constraints of atom configurations embodied in the large number of known crystal structures. They currently can only handle crystal structure prediction of relatively small systems. Inspired by the knowledge-rich protein structure prediction approach, herein we explore whether known geometric constraints such as the atomic contact map of a target crystal material can help predict its structure given its space group information. We propose a global optimization based algorithm, CMCrystal, for crystal structure reconstruction based on atomic contact maps. Based on extensive experiments using six global optimization algorithms, we show that it is viable to reconstruct the crystal structure given the atomic contact map for some crystal materials but more constraints are needed for other target materials to achieve successful reconstruction. This implies that atomic interaction information learned from existing materials can be used to improve crystal structure prediction. Crystal structure prediction ; Crystal (programming language) ; Particle swarm optimization ; Exploit ; Global optimization ; Computer science ; Algorithm ; Crystal structure ; Artificial intelligence ; Chemistry ; Crystallography Machine Learning in Materials Science ; Protein Structure and Dynamics ; Computational Drug Discovery Methods
Authors: Marcelo Luís Mignoni | Victor de Aguiar Pedott | Cátia Santin Zanchett Battiston | Carolina Elisa Demaman Oro | Michèle O. de Souza | Sibele B. C. Pergher | Rogério Marcos Dallago | Roberto Fernando de Souza | Kátia Bernardo-Gusmão
Source: Revista Perspectiva (article, 2020-11-16)
Field: Chemistry — Inorganic Chemistry

Stirring effect on zeolites synthesis with different Si/Al molar ratios Using 1-Butyl-3-methylimidazolium chloride as structure-direct agent Different types of zeolites could be synthesized changing the variables in the synthesis process. This paper studies the stirring effect on zeolites synthesis at different Si/Al molar ratios (1, 8, 20, 50 and 120) using the ionic liquid 1-butyl-3-methylimidazolium chloride (BMI.Cl) as structure-direct agent. The results suggest that the ionic liquid BMI.Cl would be a highly effective directing agent for the crystallization of zeolites type A, ZSM-5, Beta and ZSM-35. The stirring effect on compositional and morphological parameters seems to be signiﬁcant. Therefore, ternary composition diagrams were plotted for the static and stirring conditions, showing the influence of stirring on the composition and morphology of the generated materials. It was possible to verify, in the ternary diagrams, the conditions for obtaining the pure ZSM-5 and ZSM-35 zeolites, as well as the different morphologies found for the same regions, when the zeolites were synthesized under static and stirring conditions. It is also observed that the zeolites ZSM-35 and Beta show a greater amount of Al2O3 (4 mol% and 1.6 mol%) only when the reaction is carried out under stirring conditions. Ionic liquid ; Molar ratio ; Ternary operation ; Crystallization ; Zeolite ; Chloride ; ZSM-5 ; Catalysis ; Chemical engineering ; Chemistry ; Composition (language) ; Inorganic chemistry ; Materials science ; Organic chemistry Zeolite Catalysis and Synthesis ; Mesoporous Materials and Catalysis ; Catalytic Processes in Materials Science
Authors: Mitali Sarkar | Pankaj Sarkar | Swagatam Sarkar | Shanku Denrah
Source: Nanoarchitectonics (article, 2020-12-29)
Field: Chemistry — Organic Chemistry

Optimization and Feasibility of Alizarin Red S Retention on Iron- Loaded Cellulose Nanocomposite Bead Iron(III) loaded cellulose nanocomposite bead, synthesized through sol-gel method, was characterized by Fourier transform infra-red spectroscopy, field emission scanning electron microscopy, energy dispersive spectroscopy, atomic force microscopy, tunneling electron microscopy, and tested for adsorptive removal of alizarin red S from aqueous solution. The influence of variables such as pH, contact time, initial dye concentration, adsorbent dose and temperature for dye retention were investigated in batch operation. The process was optimized by employing response surface methodology following full factorial and central composite design. The maximum adsorption of 97% was observed at an optimum condition of pH 3.0, dose of 2.0 gdm-3 and shaking time of 45 mins corresponding to the dye concentration of 100 mgdm-3 at 303 K. Correlation of cooperative influences of the significant variables and the extent of dye adsorption were represented by a second order polynomial equation. The mutual interactions of the significant variables were presented by 3D response surface and 2D contour plots in the design space. The adsorption was better described by Langmuir isotherm and pseudo second order kinetics. The process was spontaneous (-∆G°, 48.19 kJmol-1 ), feasible (∆S°, 0.284 Jmol -1 K-1 ) and endothermic (∆H°, 71.62 kJmol-1 ). The adsorbent can be regenerated with NaOH (10.0 × 10-2 M) and recycled for reuse, at least for five successive operations. Adsorption ; Langmuir adsorption model ; Endothermic process ; Cellulose ; Aqueous solution ; Response surface methodology ; Fourier transform infrared spectroscopy ; Nanocomposite ; Materials science ; Scanning electron microscope ; Analytical Chemistry (journal) ; Chemical engineering ; Chemistry ; Nuclear chemistry ; Composite material ; Chromatography ; Organic chemistry Nanomaterials for catalytic reactions ; Adsorption and biosorption for pollutant removal ; Extraction and Separation Processes
Authors: Radhi Muhammed Mizher
Source: Nanoarchitectonics (article, 2020-02-12)
Field: Chemistry — Electrochemistry

Electrochemical Characterization of Redox FeII/FeIII Mediated by ZrO2NPs/GCE Using Cyclic Voltammetry In this article, experimental methods based on cyclic voltammetric technique were used to study the electrochemical analysis of a new modified electrode with zirconium dioxide molecules on the glassy carbon electrode (ZrO2NPs/GCE) to characterize iron ions K4[Fe(CN)6]. These methods also allowed the study of current peaks for oxidation reduction of Fe(II)/Fe(III) using potassium chloride (KCl) solution as electrolytes at different concentration, pH, scanning rates, and stability (reliability) of which these parameters are important in assessing oxidation properties. Also, the diffusion coefficient values of oxidation-reduction reaction for iron ions on the new sensor (ZrO2 NPs/GCE) was determined using Randles-Seveik equation as Dfa = 2.03 ×10-5 cm2 /sec and Dfc = 7.12 × 10-5 cm2 /sec, respectively. It was found the modified electrode ZrO2NPs/GCE acts as a good sensor with high detection limit of iron ions in electrolyte. It can be used the modified electrode in different electrochemical applications because of its higher conductivity. Electrochemistry ; Cyclic voltammetry ; Redox ; Supporting electrolyte ; Inorganic chemistry ; Electrolyte ; Electrode ; Chemistry ; Detection limit ; Diffusion ; Glassy carbon ; Chloride ; Analytical Chemistry (journal) ; Materials science ; Physical chemistry Electrochemical Analysis and Applications ; Conducting polymers and applications ; Analytical Chemistry and Sensors
Authors: Mohammad Atif Faiz Afzal | Andrea Browning | Alexander Goldberg | Mathew D. Halls | Jacob Gavartin | Tsuguo Morisato | Thomas F. Hughes | David J. Giesen | Joseph E. Goose
Source: ChemRxiv (preprint, 2020-12-04)
Field: Materials Science — Materials Chemistry

High-Throughput Molecular Dynamics Simulations and Validation of Thermophysical Properties of Polymers Recent advances in graphics-processing-unit (GPU) hardware and improved efficiencies of atomistic simulation programs allow the screening of a large number of polymers to predict properties that require running and analyzing long Molecular Dynamics (MD) trajectories of large molecular systems. This paper outlines an efficient MD cooling simulation workflow based on GPU MD simulation and the refined Optimized Potentials for Liquids Simulation (OPLS) OPLS3e force field to calculate glass transition temperatures (Tg) of 315 polymers for which experimental values were reported by Bicerano.1 We observed good agreement of predicted Tg values with experimental observation across a wide range of polymers, which confirms the clear utility of the described workflow. During the stepwise cooling simulation for the calculation of Tg, a subset of polymers clearly showed an ordered structure developing as the temperature decreased. Such polymers have a point of discontinuity on the specific volume vs. temperature plot, which we associated with the melting temperature (Tm). We demonstrate the distinction between crystallized and amorphous polymers by examining polyethylene. Linear polyethylene shows a discontinuity in the specific volume vs. temperature plot, but we do not observe the discontinuity for branched polyethylene simulations. Molecular dynamics ; Polymer ; Glass transition ; Polyethylene ; Materials science ; Amorphous solid ; Volume (thermodynamics) ; Thermodynamics ; Computer science ; Statistical physics ; Chemistry ; Physics ; Crystallography ; Computational chemistry Material Dynamics and Properties ; Phase Equilibria and Thermodynamics ; Theoretical and Computational Physics
Authors: Mikołaj Sacha | Mikołaj Błaż | Piotr Byrski | Paweł Dąbrowski-Tumański | Mikołaj Chromiński | Rafał Loska | Paweł Włodarczyk-Pruszyński | Stanisław Jastrzȩbski
Source: arXiv (Cornell University) (preprint, 2020-06-27)
Field: Materials Science — Materials Chemistry

Molecule Edit Graph Attention Network: Modeling Chemical Reactions as\n Sequences of Graph Edits The central challenge in automated synthesis planning is to be able to\ngenerate and predict outcomes of a diverse set of chemical reactions. In\nparticular, in many cases, the most likely synthesis pathway cannot be applied\ndue to additional constraints, which requires proposing alternative chemical\nreactions. With this in mind, we present Molecule Edit Graph Attention Network\n(MEGAN), an end-to-end encoder-decoder neural model. MEGAN is inspired by\nmodels that express a chemical reaction as a sequence of graph edits, akin to\nthe arrow pushing formalism. We extend this model to retrosynthesis prediction\n(predicting substrates given the product of a chemical reaction) and scale it\nup to large datasets. We argue that representing the reaction as a sequence of\nedits enables MEGAN to efficiently explore the space of plausible chemical\nreactions, maintaining the flexibility of modeling the reaction in an\nend-to-end fashion, and achieving state-of-the-art accuracy in standard\nbenchmarks. Code and trained models are made available online at\nhttps://github.com/molecule-one/megan.\n Computer science ; Chemical space ; Retrosynthetic analysis ; Encoder ; Graph ; Formalism (music) ; Theoretical computer science ; Edit distance ; Artificial intelligence ; Chemistry ; Drug discovery Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Advanced Graph Neural Networks
Authors: Verónica Sáez-Jiménez | Željka Sanader Maršić | Matteo Lambrughi | Jae Ho Shin | Robin van Havere | Elena Papaleo | Lisbeth Olsson | Valeria Mapelli
Source: PLoS ONE (article, 2020-05-21)
Field: Materials Science — Materials Chemistry

Structure-function investigation of 3-methylaspartate ammonia lyase reveals substrate molecular determinants for the deamination reaction The enzymatic reactions leading to the deamination of β-lysine, lysine, or 2-aminoadipic acid are of great interest for the metabolic conversion of lysine to adipic acid. Enzymes able to carry out these reactions are not known, however ammonia lyases (EC 4.3.1.-) perform deamination on a wide range of substrates. We have studied 3-methylaspartate ammonia lyase (MAL, EC 4.3.1.2) as a potential candidate for protein engineering to enable deamination towards β-lysine, that we have shown to be a competitive inhibitor of MAL. We have characterized MAL activity, binding and inhibition properties on six different compounds that would allow to define the molecular determinants necessary for MAL to deaminate our substrate of interest. Docking calculations showed that β-lysine as well as the other compounds investigated could fit spatially into MAL catalytic pocket, although they probably are weak or very transient binders and we identified molecular determinants involved in the binding of the substrate. The hydrophobic interactions formed by the methyl group of 3-methylaspartic acid, together with the presence of the amino group on carbon 2, play an essential role in the appropriate binding of the substrate. The results showed that β-lysine is able to fit and bind in MAL catalytic pocket and can be potentially converted from inhibitor to substrate of MAL upon enzyme engineering. The characterization of the binding and inhibition properties of the substrates tested here provide the foundation for future and more extensive studies on engineering MAL that could lead to a MAL variant able to catalyse this challenging deamination reaction. Deamination ; Oxidative deamination ; Lysine ; Chemistry ; Enzyme ; Stereochemistry ; Biochemistry ; Substrate (aquarium) ; Amino acid ; Active site ; Lyase ; Combinatorial chemistry ; Biology Enzyme Structure and Function ; Amino Acid Enzymes and Metabolism ; Biochemical and Molecular Research
Authors: Marcin Maździarz
Source: Preprints.org (preprint, 2020-12-21)
Field: Materials Science — Materials Chemistry

Transferability of Molecular Potentials for 2D Molybdenum Disulphide An ability of different molecular potentials to reproduce the properties of 2D molybdenum disulphide polymorphs is examined. Structural and mechanical properties, as well as phonon dispersion of the 2H, 1T and 1T&amp;rsquo; single-layer MoS2 (SL MoS2) phases, were obtained using density functional theory (DFT) and molecular statics calculations (MS) with Stillinger-Weber, REBO, SNAP, and ReaxFF interatomic potentials. Quantitative systematic comparison and discussion of the results obtained are reported. Molybdenum ; Transferability ; Density functional theory ; Molecular dynamics ; Molybdenum disulfide ; Chemical physics ; Chemistry ; Computational chemistry ; Materials science ; Inorganic chemistry 2D Materials and Applications ; MXene and MAX Phase Materials ; Boron and Carbon Nanomaterials Research
Authors: I Alexa | M Ignat | R Popovic | M Aliabadi | K Morshedzadeh | H Soheyli | B Alireza | H Bahman | R Reza | S Almuhamed | N Khenoussi | M Bonne | L Schacher | B Lebeau | D Adolphe | J Brendle | A An | J Guo | E.-J Lee | S Jeong | Zhaoy | Z Wang | T Leiknes | A Badiei | B Laurent | C Nicolas | Mohammadi Ziarani | Gh | H Bahrambeygi | N Sabetzadeh | A Rabbi | K Nasouri | A Shoushtari | M Babaei | F Boorboorajdari | M Behzad | M Burleigh | S Dai | E Hagaman | L Lin | E Da'na | A Sayari | S Devaraju | M Vengatesan | M Selvi | Ashok Kumar | A Hamerton | I Go | J Alagar | M | B Erdem | S Erdem | A tak | C Yavru | R kszoglu | S Garcia-Segura | S Dosta | J Guilemany | E Brillas | H Gulbeyidursun | Y Arzu | Y Jiang | Y Sun | H Liu | F Zho | H Yin | A Kaur | S Vats | S Rekhi | A Bhardwaj | J Goel | R Tanwar | K Gaur | A Khataee | M Zarei | G Dehghan | S Lin | R Juang | R Liversidge | G Lloyd | D Wase | C Forster | S Munusamy | R Apama | S Nadavala | A Kaflou | I Nilsson | A Moller | B Mattiasson | M Rubindamayugi | U Welander
Source: Global NEST Journal (article, 2020-11-09)
Field: Chemistry — Organic Chemistry

Study of Removal of Direct Black ANBN dye from Aqueous Solution by Chitosan-Functionalized Mesoporous (SBA-15) Composites Synthesized by Electrospinning Method &lt;p&gt;In this research, capability of adsorption of modified chitosan Nano composites with functionalized mesoporous silica which synthesized by electrospinning method in the removal of direct black ANBN dye has been studied. Silicate mesoporous were functionalized during synthesis process and then the intended Nano fibers were produced by using of electrospinning device. Synthesized Nano fibers were recognized by analyzing the FT-IR, XRD, FE-SEM, and TEM and tension test. The removal of direct black ANBN dye from aqueous solution in a continuous system was done by this adsorbent by studying the effects of some parameters such as type and amount of adsorbent, pH, initial concentration of colored solution and contact time; And at the end finding appropriate isotherms for direct black dye adsorption was done. The result show that simple CTS/SBA-15 have the best removal efficiency in 40 min of contact time, in acidic pH, with 0.05 gr adsorbent and 60 mg/L initial concentration. By examining the adsorption isotherms, it has been clearly defined [that] Removal of this dye follows Freundlich model. In order to compare accurately and evaluate the efficiency of the synthesized sample, the adsorption of Direct Black ANBN was investigated by two different adsorbents: CTS/SBA-15 and Chitosan. According to the results, CTS/SBA-15 Nano fibers have suitable efficiency for removal of direct black ANBN dye.&lt;/p&gt;&#x0D; Electrospinning ; Adsorption ; Chitosan ; Aqueous solution ; Materials science ; Mesoporous material ; Freundlich equation ; Chemical engineering ; Nanofiber ; Composite material ; Nuclear chemistry ; Chemistry ; Organic chemistry ; Polymer ; Catalysis Synthesis of Tetrazole Derivatives ; Brain Tumor Detection and Classification
Authors: Yoshikata Koga | Kei Hasegawa | H. Lee | Keisuke Kameda | Yuta Iida | Manabu Ihara
Source: Fuel Cells (article, 2020-12-01)
Field: Materials Science — Materials Chemistry

Determination with a Genetic Algorithm of Reactant Coverages on H<sub>2</sub>/H<sub>2</sub>O Electrodes Based on Electrochemical Kinetics Under Reversible SOFC/EC Operation▴ Abstract A scheme to quantify surface coverages of reactants at triple phase boundary (TPB) by electrochemical measurements was constructed to evaluate the electrode performance of solid oxide fuel cells and electrolysis cells (SOFC/EC). The developments of electrode requires that the intrinsic properties of materials separated from the effect of geometric structure of the electrode. The proposed reaction model at TPB of H 2 /H 2 O electrodes is composed of competitive adsorptions and Langmure‐type surface reactions under the relationship between oxygen activity ( a O ) and the electrode potential. To determine the reaction constant ( k a ) and four adsorption equilibrium constants at TPB ( K H , K H2O , K O and K OH ), a mashine learning approach with a genetic algorithm as an optimization method and the experimental data of reversible SOFC/ECs with different H 2 /H 2 O partial pressures as the learning data was developed. As a result, even though all experimental curves of the current density vs. a O in SOFC operation were fitted by numerous sets of the five constants, the coverages under different conditions could be uniquely determined. Results suggest that TPB at 900 °C was almost vacant with a small amount of H 2 O in SOEC operation, and was not vacant and the OH coverage increased with increasing a O in SOFC operation. Electrochemistry ; Triple phase boundary ; Electrode ; Electrolysis ; Analytical Chemistry (journal) ; Adsorption ; Oxide ; Materials science ; Solid oxide fuel cell ; Chemistry ; Electrolyte ; Physical chemistry ; Chromatography ; Metallurgy Advancements in Solid Oxide Fuel Cells ; Electrocatalysts for Energy Conversion ; Fuel Cells and Related Materials