jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Suzanne K. Wallace | Ambroise van Roekeghem | Anton Bochkarev | Javier Carrasco | Alexander V. Shapeev | Natalio Mingo
Source: Physical Review Research (article, 2021-02-12)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Modeling the high-temperature phase coexistence region of mixed transition metal oxides from<i>ab initio</i>calculations This article describes how to calculate the solubility gap of a complex material containing two types of substitution sites, and including configurational, magnetic and vibrational entropy contributions, from first principles. Ab initio ; Configuration entropy ; Materials science ; Transition metal ; Phase transition ; Ab initio quantum chemistry methods ; Thermodynamics ; Solubility ; Condensed matter physics ; Computational chemistry ; Chemical physics ; Physical chemistry ; Chemistry ; Physics ; Molecule ; Catalysis ; Organic chemistry Magnetic and transport properties of perovskites and related materials ; Electronic and Structural Properties of Oxides ; Thermal Expansion and Ionic Conductivity
Authors: Mina Sharifi‐Bonab | Soheil Aber | Dariush Salari | Fatemeh Khodam
Source: Water Practice & Technology (article, 2021-08-16)
Field: Materials Science — Materials Chemistry

Water treatment with CoZnAl-LDH and its mixed metal oxide Abstract CoZnAl-layered double hydroxide (LDH) was synthesized by homogeneous co-precipitation. CoZnAl-Mixed Metal Oxide (MMO) was prepared by calcining the LDH. The samples' structure and morphology were studied by analytical techniques including X-ray diffraction, N2 adsorption-desorption isotherm, scanning electron microscopy and UV–visible spectroscopy. Acid orange 7 (AO7) adsorption by as-prepared samples was studied. CoZnAl-MMO showed 526.32 mg/g adsorption capacity, higher than that of CoZnAl-LDH, 243.9 mg/g. Kinetic studies confirmed the pseudo-second-order and pseudo-first-order AO7 adsorption kinetics of the LDH and MMO, respectively. AO7 adsorption onto both LDH and MMO fitted the Langmuir isotherm model well. Band gap calculation confirmed the ability of this nano-MMO to operate in the visible light region. It displayed synergetic adsorption-photocatalytic performance under visible light and the removal efficiency was about 97%. Adsorption ; Langmuir adsorption model ; Oxide ; Scanning electron microscope ; Hydroxide ; Calcination ; Photocatalysis ; Metal ; Nuclear chemistry ; Chemistry ; Visible spectrum ; Materials science ; Inorganic chemistry ; Mixed oxide ; Catalysis ; Organic chemistry Layered Double Hydroxides Synthesis and Applications ; Advanced Photocatalysis Techniques ; Adsorption and biosorption for pollutant removal
Authors: Derya Güngördü Solğun | Ümit Yıldıko | Mehmet Salih Ağırtaş
Source: Research Square (preprint, 2021-04-13)
Field: Materials Science — Materials Chemistry

Synthesis, DFT calculations, photophysical, photochemical properties of peripherally metallophthalocyanines bearing (2-(benzo[d] [1,3] dioxol-5-ylmethoxy) phenoxy) substituents Chemistry ; Photochemistry ; Bearing (navigation) ; Physics Porphyrin and Phthalocyanine Chemistry ; Photochemistry and Electron Transfer Studies ; Organic Chemistry Cycloaddition Reactions
Authors: Timothy A. Coulther | Moritz Pott | Cathleen Zeymer | Donald Hilvert | Mary Jo Ondrechen
Source: Protein Science (article, 2021-05-03)
Field: Materials Science — Materials Chemistry

Analysis of electrostatic coupling throughout the laboratory evolution of a designed retroaldolase The roles of local interactions in the laboratory evolution of a highly active, computationally designed retroaldolase (RA) are examined. Partial Order Optimum Likelihood (POOL) is used to identify catalytically important amino acid interactions in several RA95 enzyme variants. The series RA95.5, RA95.5-5, RA95.5-8, and RA95.5-8F, representing progress along an evolutionary trajectory with increasing activity, is examined. Computed measures of coupling between charged states of residues show that, as evolution proceeds and higher activities are achieved, electrostatic coupling between the biochemically active amino acids and other residues is increased. In silico residue scanning suggests multiple coupling partners for the catalytic lysine K83. The effects of two predicted partners, Y51 and E85, are tested using site-directed mutagenesis and kinetic analysis of the variants Y51F and E85Q. The Y51F variants show decreases in k<sub>cat</sub> relative to wild type, with the greatest losses observed for the more evolved constructs; they also exhibit significant decreases in k<sub>cat</sub> /K<sub>M</sub> across the series. Only modest decreases in k<sub>cat</sub> /K<sub>M</sub> are observed for the E85Q variants with little effect on k<sub>cat</sub> . Computed metrics of the degree of coupling between protonation states rise significantly as evolution proceeds and catalytic turnover rate increases. Specifically, the charge state of the catalytic lysine K83 becomes more strongly coupled to those of other amino acids as the enzyme evolves to a better catalyst. Amino acid ; Lysine ; Protonation ; Chemistry ; Amino acid residue ; Coupling (piping) ; Molecular dynamics ; Stereochemistry ; Peptide sequence ; Computational chemistry ; Biochemistry ; Ion ; Materials science Enzyme Structure and Function ; Protein Structure and Dynamics ; Amino Acid Enzymes and Metabolism
Authors: Mario G. Zauchner | Stefano Dal Forno | Gábor Cśanyi | Andrew P. Horsfield | Johannes Lischner
Source: Spiral (Imperial College London) (article, 2021-10-05)
Field: Materials Science — Materials Chemistry

Predicting polarizabilities of silicon clusters using local chemical environments Calculating polarizabilities of large clusters with first-principles techniques is challenging because of the unfavorable scaling of computational cost with cluster size. To address this challenge, we demonstrate that polarizabilities of large hydrogenated silicon clusters containing thousands of atoms can be efficiently calculated with machine learning methods. Specifically, we construct machine learning models based on the smooth overlap of atomic positions (SOAP) descriptor and train the models using a database of calculated random-phase approximation polarizabilities for clusters containing up to 110 silicon atoms. We first demonstrate the ability of the machine learning models to fit the data and then assess their ability to predict cluster polarizabilities using k-fold cross validation. Finally, we study the machine learning predictions for clusters that are too large for explicit first-principles calculations and find that they accurately describe the dependence of the polarizabilities on the ratio of hydrogen to silicon atoms and also predict a bulk limit that is in good agreement with previous studies. Cluster (spacecraft) ; Silicon ; Scaling ; Limit (mathematics) ; Construct (python library) ; Statistical physics ; Computer science ; Coupled cluster ; Chemical physics ; Machine learning ; Molecular physics ; Materials science ; Computational science ; Physics ; Molecule ; Mathematics ; Quantum mechanics ; Optoelectronics Machine Learning in Materials Science ; Advanced Chemical Physics Studies ; X-ray Diffraction in Crystallography
Authors: Manuel Hoffmann | Stefan Wackerow | Amin Abdolvand | Svetlana A. Zolotovskaya
Source: Optical Materials Express (article, 2021-08-13)
Field: Materials Science — Electronic, Optical and Magnetic Materials

High performance SERS platforms via parametric optimization of the laser-assisted photodeposition of silver and gold nanoparticles Parametric optimization of the laser-assisted photocatalytic growth of Ag and Au nanoparticles for high SERS enhancement factor performance informed by design of experiment is demonstrated. The photodeposition process was divided into two phases –seeding and growth– in order to achieve the highest possible nanoparticle surface coverage for the size range from 10 to 100 nm. A substantial difference in the parameter effects between the Ag and Au seeding and growth was found. The SERS performance of the photodeposited Ag and Au nanostructures was evaluated at 532, 633 and 785 nm with thiophenol as a probe molecule. A high-enhancement broadband SERS operation was attained with Ag nanostructure grown at high laser fluences. The SERS enhancement factors of 10 5 were achieved with both Ag and Au nanostructures. Materials science ; Nanostructure ; Nanoparticle ; Thiophenol ; Nanotechnology ; Laser ; Seeding ; Optics ; Chemistry Gold and Silver Nanoparticles Synthesis and Applications ; Quantum Dots Synthesis And Properties ; Laser-Ablation Synthesis of Nanoparticles
Authors: N. Scott Bobbitt | Eric Li | Randall Q. Snurr
Source: Brazilian Journal of Chemical Engineering (article, 2021-11-10)
Field: Chemistry — Inorganic Chemistry

Applying design principles to improve hydrogen storage capacity in nanoporous materials Hydrogen storage ; Gravimetric analysis ; Hydrogen ; Nanoporous ; Materials science ; Energy storage ; Bar (unit) ; Chemical engineering ; Process engineering ; Chemistry ; Nanotechnology ; Thermodynamics ; Organic chemistry ; Physics ; Engineering Metal-Organic Frameworks: Synthesis and Applications ; Covalent Organic Framework Applications ; Membrane Separation and Gas Transport
Authors: Sophia Kurdziel | Joshua L. Lansford | Dionisios G. Vlachos
Source: The Journal of Physical Chemistry C (article, 2021-09-03)
Field: Materials Science — Materials Chemistry

Prediction of Transition-State Scaling Relationships and Universal Transition-State Vibrational and Entropic Correlations for Dehydrogenations Linear scaling relationships (LSRs) and Brønsted–Evans–Polanyi (BEP) or transition-state scaling (TSS) relations aid with the prediction of electronic energies. However, temperature effects and pre-exponentials are often taken as constants across metal surfaces or a homologous series. Vibrational scaling relationships (VSRs) offer a way to determine such parameters. Transition-state VSRs (TSVSRs) between local minima and transition states of AHX (A = C, N, O) surface diffusions correlate with BEP relations and broaden to thermochemical property scaling. Using density functional theory, we extend TSVSRs to AHX dehydrogenation reactions on transition-metal surfaces, relating vibrational modes of local minima to transition states. We first predict the slopes of the TSS relations by incorporating bond angles using the Slater–Koster structure factors and hybridization through crystal orbital overlap population analysis and energy overlap integrals between adsorbates and metal surfaces. Additionally, we uncover universal thermochemical property scaling, enabling the estimation of entropies and temperature corrections to enthalpies across a homologous series. We demonstrate both significant vibrational corrections in reactions with low intrinsic electronic barriers and considerable variation in the pre-exponential of a simple dehydrogenation reaction across metals and AHX adsorbates. Scaling ; Maxima and minima ; Chemistry ; Transition metal ; Statistical physics ; Thermodynamics ; Physics ; Mathematics ; Geometry Machine Learning in Materials Science ; Advanced Chemical Physics Studies ; Catalysis and Oxidation Reactions
Authors: Rasha Atwi | Ying Chen | Kee Sung Han | Karl T. Mueller | Vijayakumar Murugesan | Nav Nidhi Rajput
Source: Research Square (preprint, 2021-10-04)
Field: Chemistry — Spectroscopy

An automated framework for high-throughput predictions ofNMR chemical shifts within liquid solutions Abstract Identifying stable speciation in multicomponent liquid solutions is of fundamental importance to areas ranging from electrochemistry to organic chemistry and biomolecular systems. However, elucidating this complex solvation environment is a daunting task even when using advanced experimental and computational techniques. Here, we introduce a fully automated, high-throughput computational framework for the accurate and robust prediction of stable species present in liquid solutions by computing the nuclear magnetic resonance (NMR) chemical shifts of molecules. The framework automatically extracts and categorizes hundreds of thousands of atomic clusters from classical molecular dynamics (CMD) simulations to identify the most stable speciation in the solution and calculate their NMR chemical shifts via DFT calculations. Additionally, the framework creates an output database of computed chemical shifts for liquid solutions across a wide chemical and parameter space. This task can be infeasible experimentally and challenging using conventional computational methods. To demonstrate the capabilities of our framework, we compare our computational results to experimental measurements for a complex test case of magnesium bis(trifluoromethanesulfonyl)imide Mg(TFSI)2 salt in dimethoxyethane (DME) solvent, which is a common electrolyte system for Mg-based batteries. Our extensive benchmarking and analysis of the Mg2+ solvation structural evolutions reveal critical factors such as the effect of force field parameters that influence the accuracy of NMR chemical shift predictions in liquid solutions. Furthermore, we show how the framework reduces the efforts of performing and managing over 300 13C and 600 1H DFT chemical shift predictions to a single submission procedure. By enabling more efficient and accurate high-throughput computations of NMR chemical shifts, our approach can accelerate theory-guided design of liquid solutions for various applications. Chemical shift ; Solvation ; Chemical space ; Chemistry ; Computer science ; Molecule ; Chemical physics ; Computational chemistry ; Drug discovery ; Physical chemistry Advanced NMR Techniques and Applications ; NMR spectroscopy and applications ; Solid-state spectroscopy and crystallography
Authors: Mohamed Abboud
Source: Research Square (preprint, 2021-11-29)
Field: Materials Science — Materials Chemistry

A Novel Biological Approach to Copper Nanoparticles Synthesis: Characterization and its Application Against Phytopathogenic Fungi Abstract In nanotechnology, fungi have been identified as excellent candidates for the synthesis of nanoparticles, thus presenting a cleaner alternative to produce new materials with a wide range of potential applications in biomedicine and industry. In this respect, A novel biological approach Penicillium olsonii have demonstrated excellent synthesis capacity to produce copper nanoparticles (CuNPs). Their properties were determined by ultraviolet-visible (UV-Vis) absorption spectrum, Fourier transform infrared spectroscopy (FT-IR), and Scanning Electron Microscopy (SEM) images. UV-Vis spectra with characteristic absorption peak was observed at 565nm. Biomolecules mediating the synthesis and stabilizing the nanobactericides was studied with FTIR that showed different functional groups. SEM investigations confirmed that size of CuNPs were varied from 6-26 nm. The antifungal activity of CuNPs was evaluated by testing against three phytopathogenic fungi including Fusarium oxysporum , Fusarium solani and Curvularia curvulatat with growth inhibition 86.25, 32.92 and 68.42%, respectively at 200ppm. F. oxysporum was more affected by CuNPs followed by C. curvulata and F. solani . The present work demonstrated that it is possible to perform the biogenic synthesis of CuNPs using P. olsonii as appropriate fungicide. Fourier transform infrared spectroscopy ; Nanoparticle ; Biomolecule ; Fusarium oxysporum ; Nuclear chemistry ; Scanning electron microscope ; Fusarium solani ; Materials science ; Absorption spectroscopy ; Copper ; Nanotechnology ; Chemistry ; Chemical engineering ; Botany ; Biology ; Metallurgy ; Optics ; Composite material ; Physics Nanoparticles: synthesis and applications ; Nanocomposite Films for Food Packaging
Authors: Haw‐Ming Huang | Ping-Han Wu | Po-Chien Chou | Wen-Tien Hsiao | Hsin‐Ta Wang | Hsin-Pei Chiang | Chi‐Ming Lee | Shwu-Huey Wang | Yu‐Cheng Hsiao
Source: International Journal of Nanomedicine (article, 2021-05-31)
Field: Materials Science — Biomaterials

Enhancement of T2* Weighted MRI Imaging Sensitivity of U87MG Glioblastoma Cells Using γ-Ray Irradiated Low Molecular Weight Hyaluronic Acid-Conjugated Iron Nanoparticles Overall, the present results suggest that LMWHA-IONPs fabricated in this study provide an effective MRI contrast agent for improving the diagnosis of early stage glioblastoma in MRI examinations. Biocompatibility ; Viability assay ; Materials science ; Hyaluronic acid ; Nanoprobe ; Nanoparticle ; Biophysics ; Chemistry ; Cell ; Nanotechnology ; Medicine ; Biochemistry Nanoparticle-Based Drug Delivery ; Nanoplatforms for cancer theranostics ; Lanthanide and Transition Metal Complexes
Authors: Mel O’Leary | Aliaksandr Baidak | Martyn Barnes | Thomas Donoclift | Christopher P. Emerson | Catarina Figueira | Oliver Fox | Annette Kleppe | Aaron McCulloch | Darryl Messer | Robin M. Orr | F. J. Currell
Source: Scientific Reports (article, 2021-11-24)
Field: Chemistry — Inorganic Chemistry

First observation of radiolytic bubble formation in unstirred nano-powder sludges and a consistent model thereof Experiments involving the irradiation of water contained within magnesium hydroxide and alumina nanoparticle sludges were conducted and culminated in observations of an increased yield of molecular hydrogen when compared to the yield from the irradiation of bulk water. We show that there is a relationship linking this increased yield to the direct nanoscale ionization mechanism in the nanoparticles, indicating that electron emission from the nanoparticles drives new radiative pathways in the water. Because the chemical changes in these sludges are introduced by irradiation only, we have a genuinely unstirred system. This feature allows us to determine the diffusivity of the dissolved gas. Using the measured gas production rate, we have developed a method for modelling when hydrogen bubble formation will occur within the nanoparticle sludges. This model facilitates the determination of a consistent radiolytic consumption rate coinciding with the observations of bubble formation. Thus, we demonstrate a nanoscale radiation effect directly influencing the formation of molecular hydrogen. Radiolysis ; Yield (engineering) ; Hydrogen ; Bubble ; Nanoparticle ; Chemical engineering ; Irradiation ; Materials science ; Chemistry ; Nanoscopic scale ; Nanotechnology ; Aqueous solution ; Physical chemistry ; Organic chemistry ; Composite material Radioactive element chemistry and processing ; Nuclear Physics and Applications ; Nuclear materials and radiation effects
Authors: Andreas S. Kalogirou | Michael P. East | Tuomo Laitinen | Chad Torrice | Kaitlyn Maffuid | David H. Drewry | Panayiotis A. Koutentis | Gary L. Johnson | Daniel J. Crona | Christopher R. M. Asquith
Source: Molecules (article, 2021-09-29)
Field: Chemistry — Organic Chemistry

Synthesis and Evaluation of Novel 1,2,6-Thiadiazinone Kinase Inhibitors as Potent Inhibitors of Solid Tumors A focused series of substituted 4<i>H</i>-1,2,6-thiadiazin-4-ones was designed and synthesized to probe the anti-cancer properties of this scaffold. Insights from previous kinase inhibitor programs were used to carefully select several different substitution patterns. Compounds were tested on bladder, prostate, pancreatic, breast, chordoma, and lung cancer cell lines with an additional skin fibroblast cell line as a toxicity control. This resulted in the identification of several low single digit micro molar compounds with promising therapeutic windows, particularly for bladder and prostate cancer. A number of key structural features of the 4<i>H</i>-1,2,6-thiadiazin-4-one scaffold are discussed that show promising scope for future improvement. Prostate cancer ; Cancer research ; Kinase ; Cell culture ; Fibroblast ; Chemistry ; Medicine ; Cancer ; Internal medicine ; Biology ; Biochemistry Quinazolinone synthesis and applications ; Synthesis and biological activity ; Click Chemistry and Applications
Authors: Joakim Brorsson | Anders E. C. Palmqvist | Paul Erhart
Source: The Journal of Physical Chemistry C (article, 2021-10-12)
Field: Materials Science — Materials Chemistry

First-Principles Study of Order–Disorder Transitions in Pseudobinary Clathrates It has been recently demonstrated that the pseudoternary Ba8AlxGayGe46-x-y clathrate undergoes an order-disorder transition with increasing temperature that can be observed via site occupation factors (SOFs) and manifests itself, e.g., in electrical transport properties. Here, we generalize this result and analyze the characteristics of this order-disorder transition in the pseudobinary clathrates Ba8GaxGe46-x, Ba8GaxSi46-x, Ba8AlxGe46-x, and Ba8AlxSi46-x. To this end, we employ atomistic simulations that combine alloy cluster expansions trained against density functional theory calculations with Wang-Landau and ensemble Monte Carlo simulations. The simulations show that all four systems studied here display order-disorder transitions for at least some composition range. Based on an extensive literature survey, we also provide evidence for signatures of the transition in earlier experimental studies that to the best of our knowledge have hitherto not been related to such transitions. The predicted transition temperatures are lower for Ba8GaxGe46-x and Ba8GaxSi46-x than for Ba8AlxGe46-x and Ba8AlxSi46-x, although it appears that the simulations underestimate the transition temperatures for Ga-containing systems compared to the experiment. This nonetheless provides a sensible explanation for why the experimentally determined Al SOFs agree better with the simulated higherature disordered configurations, while the Ga SOFs more closely agree with the simulated ground-state configurations. As a result of stronger interactions, the SOFs vary substantially, especially near the stoichiometric 16:30 composition, providing an indication of why it has proved difficult to synthesize Ba8AlxGe46-x and Ba8AlxSi46-x samples at this ratio. The present study thereby yields detailed atomic-scale insights into the ordering in inorganic clathrates that, given the connection to transport properties established earlier, are not only useful from a fundamental perspective but also relevant for applications. Stoichiometry ; Clathrate hydrate ; Cluster (spacecraft) ; Statistical physics ; Order (exchange) ; Condensed matter physics ; Materials science ; Monte Carlo method ; Thermodynamics ; Chemistry ; Physics ; Hydrate ; Physical chemistry ; Mathematics ; Computer science ; Statistics Advanced Thermoelectric Materials and Devices ; Thermal Expansion and Ionic Conductivity ; Magnetic and transport properties of perovskites and related materials