jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Sarmento J. Mazivila | Alejandro C. Olivieri
Source: TrAC Trends in Analytical Chemistry (review, 2018-08-30)
Field: Chemistry — Analytical Chemistry

Chemometrics coupled to vibrational spectroscopy and spectroscopic imaging for the analysis of solid-phase pharmaceutical products: A brief review on non-destructive analytical methods Chemometrics ; Excipient ; Solubility ; Process analytical technology ; Active ingredient ; Counterfeit ; Materials science ; Spectroscopy ; Biochemical engineering ; Process engineering ; Chemistry ; Chromatography ; Organic chemistry ; Chemical engineering ; Engineering ; Physics ; Pharmacology ; Medicine Spectroscopy and Chemometric Analyses ; Crystallization and Solubility Studies ; Analytical Chemistry and Chromatography
Authors: Jasenko Zivanov | Takanori Nakane | Björn Forsberg | Dari Kimanius | Wim J. H. Hagen | Erik Lindahl | Sjors H. W. Scheres
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2018-09-19)
Field: Materials Science — Materials Chemistry

RELION-3: new tools for automated high-resolution cryo-EM structure determination Abstract Here, we describe the third major release of relion. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation and 3D-classification. Perparticle refinement of CTF parameters and correction of estimated beam tilt provides higher-resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2-0.7 Å compared to previous relion versions. Computer science ; Python (programming language) ; Algorithm ; Computational science ; Curvature ; Resolution (logic) ; OpenGL ; Gaussian ; Artificial intelligence ; Computer engineering ; Physics ; Geometry ; Mathematics ; Programming language Enzyme Structure and Function ; Advanced Electron Microscopy Techniques and Applications ; Photosynthetic Processes and Mechanisms
Authors: Yue‐Yi Peng | Hui Ma | Wei Ma | Yi‐Tao Long | He Tian
Source: Angewandte Chemie International Edition (article, 2018-02-09)
Field: Chemistry — Electrochemistry

Single‐Nanoparticle Photoelectrochemistry at a Nanoparticulate TiO<sub>2</sub>‐Filmed Ultramicroelectrode An ultrasensitive photoelectrochemical method for achieving real-time detection of single nanoparticle collision events is presented. Using a micrometer-thick nanoparticulate TiO<sub>2</sub> -filmed Au ultra-microelectrode (TiO<sub>2</sub> @Au UME), a sub-millisecond photocurrent transient was observed for an individual N719-tagged TiO<sub>2</sub> (N719@TiO<sub>2</sub> ) nanoparticle and is due to the instantaneous collision process. Owing to a trap-limited electron diffusion process as the rate-limiting step, a random three-dimensional diffusion model was developed to simulate electron transport dynamics in TiO<sub>2</sub> film. The combination of theoretical simulation and high-resolution photocurrent measurement allow electron-transfer information of a single N719@TiO<sub>2</sub> nanoparticle to be quantified at single-molecule accuracy and the electron diffusivity and the electron-collection efficiency of TiO<sub>2</sub> @Au UME to be estimated. This method provides a test for studies of photoinduced electron transfer at the single-nanoparticle level. Ultramicroelectrode ; Photocurrent ; Nanoparticle ; Thermal diffusivity ; Photoelectrochemistry ; Materials science ; Microelectrode ; Diffusion ; Electron transfer ; Nanotechnology ; Millisecond ; Electron ; Optoelectronics ; Chemistry ; Electrode ; Electrochemistry ; Photochemistry ; Physics ; Cyclic voltammetry ; Physical chemistry Electrochemical Analysis and Applications ; Electrocatalysts for Energy Conversion ; Advanced Photocatalysis Techniques
Authors: Shan Jiang | Yi Du | Marco Marcello | Edward W. Corcoran | David C. Calabro | Samantha Y. Chong | Linjiang Chen | Rob Clowes | Tom Hasell | Andrew I. Cooper
Source: Angewandte Chemie International Edition (article, 2018-06-10)
Field: Chemistry — Inorganic Chemistry

Core–Shell Crystals of Porous Organic Cages The first examples of core-shell porous molecular crystals are described. The physical properties of the core-shell crystals, such as surface hydrophobicity, CO<sub>2</sub> /CH<sub>4</sub> selectivity, are controlled by the chemical composition of the shell. This shows that porous core-shell molecular crystals can exhibit synergistic properties that out-perform materials built from the individual, constituent molecules. Shell (structure) ; Porosity ; Core (optical fiber) ; Materials science ; Nanotechnology ; Chemical engineering ; Composite material ; Engineering Metal-Organic Frameworks: Synthesis and Applications ; Covalent Organic Framework Applications ; Supramolecular Chemistry and Complexes
Authors: Thomas Defize | Jean‐Michel Thomassin | Heidi Ottevaere | Cédric Malherbe | Gauthier Eppe | Rachid Jellali | Michaël Alexandre | Christine Jérôme | Raphaël Riva
Source: Macromolecules (article, 2018-12-28)
Field: Materials Science — Polymers and Plastics

Photo-Cross-Linkable Coumarin-Based Poly(ε-caprolactone) for Light-Controlled Design and Reconfiguration of Shape-Memory Polymer Networks Photochemically cross-linked shape-memory polymer (SMP) materials have been achieved by functionalizing chain-ends of star-shaped poly(ε-caprolactone) (PCL) with 7-hydroxypropoxy-4-methylcoumarin followed by photodimerization of these end-groups. The kinetics of the network formation in function of the photosensitizer concentration has been studied by swelling experiments and rheology. Thanks to the design of a dedicated homemade mold, highly reproducible irradiation conditions have been achieved allowing to study the network formation and properties, especially the shape-memory properties, in relation to the coumarin dimerization degree as determined by Raman spectroscopy. In optimized conditions, PCL-based SMP materials exhibiting high fixity and recovery have been achieved in remarkably short irradiation time, typically 5 min. In addition, the precise control of the network cross-link density with the irradiation time, so as the high stability of the formed networks toward temperature variations was also demonstrated allowing the fine-tuning of the network properties by the irradiation process. Finally, the reversible character of the coumarin dimerization under light irradiation of appropriate wavelength has been quantified by Raman spectroscopy. The dimer photocleavage allows the photoreconfiguration of the networks offering the ability to modify the “permanent” shape of the SMP material, while preserving the excellent shape-memory properties. Materials science ; Irradiation ; Raman spectroscopy ; Polymer ; Caprolactone ; Chemical engineering ; Polymer network ; Swelling ; Photosensitizer ; Polymer chemistry ; Photochemistry ; Chemistry ; Composite material ; Copolymer ; Optics Polymer composites and self-healing ; Photochromic and Fluorescence Chemistry ; Marine Sponges and Natural Products
Authors: Sandeep Kumar Sharma | Roby Soni | Sreekumar Kurungot | S. K. Asha
Source: Macromolecules (article, 2018-01-23)
Field: Materials Science — Polymers and Plastics

Naphthalene Diimide Copolymers by Direct Arylation Polycondensation as Highly Stable Supercapacitor Electrode Materials Conjugated donor–acceptor copolymers based on naphthalene diimide (NDI) as acceptor and thiophene-terminated oligophenylenevinylene as donor moieties (P1 and P2, respectively) were synthesized using the direct (hetero) arylation (DHAP) polymerization route. Nitrile groups were introduced at the vinylene linkage in one copolymer (P2) to fine-tune its electrochemical properties. Both polymers show π–π* transition in the 300–480 nm region and intramolecular charge transfer (ICT) from thiophene to NDI in the 500–800 nm region in the absorption spectra. P2 exhibits a blue-shifted intramolecular charge transfer (ICT) band in the absorption spectrum as well as a lower reduction potential in the cyclic voltammogram compared to the analogous polymer without the nitrile substitution (P1). The two polymers were evaluated as type III supercapacitor materials by preparing composite electrodes with carbon nanotubes (CNTs) and employing 0.5 M H2SO4 as the electrolyte. Their performance was compared with that of P(NDI2OD-T2) as a reference polymer. The polymer P2 based supercapacitor exhibits a specific capacitance of 124 F/g with excellent stability up to 5000 cycles with almost 100% retention of the initial capacitance in the potential window of −0.7 to 0.5 V. Compared to P2, P1 exhibits a specific capacitance of 84 F/g, while the corresponding value for the reference polymer P(NDI2OD-T2) is 61 F/g under identical conditions. Materials science ; Supercapacitor ; Copolymer ; Polymer ; Polymer chemistry ; Triphenylamine ; Polymerization ; Thiophene ; Cyclic voltammetry ; Electrochemistry ; Chemical engineering ; Electrode ; Chemistry ; Organic chemistry ; Physical chemistry ; Composite material Conducting polymers and applications ; Organic Electronics and Photovoltaics ; Supercapacitor Materials and Fabrication
Authors: Yonghong Liu | Daliang Tang | Kuanhong Cao | Lei Yu | Jie Han | Qing Xu
Source: Journal of Catalysis (article, 2018-03-02)
Field: Chemistry — Organic Chemistry

Probing the support effect at the molecular level in the polyaniline-supported palladium nanoparticle-catalyzed Ullmann reaction of aryl iodides Chemistry ; Catalysis ; Aryl ; Palladium ; Polyaniline ; Nanoparticle ; Ullmann reaction ; Combinatorial chemistry ; Organic chemistry ; Photochemistry ; Nanotechnology ; Polymer Catalytic Cross-Coupling Reactions ; Sulfur-Based Synthesis Techniques ; Catalytic C–H Functionalization Methods
Authors: Dina Ibrahim Abouelamaiem | María José Mostazo‐López | Guanjie He | Drasti Patel | Tobias P. Neville | Ivan P. Parkin | Dolores Lozano‐Castelló | Emilia Morallón | Diego Cazorla‐Amorós | Ana Jorge Sobrido | Rongfang Wang | Shan Ji | Maria‐Magdalena Titirici | Paul R. Shearing | Dan J. L. Brett
Source: Journal of Energy Storage (article, 2018-08-25)
Field: Materials Science — Electronic, Optical and Magnetic Materials

New insights into the electrochemical behaviour of porous carbon electrodes for supercapacitors Activated carbons, with different surface chemistry and porous textures, were used to study the mechanism of electrochemical hydrogen and oxygen evolution in supercapacitor devices. Cellulose precursor materials were activated with different potassium hydroxide (KOH) ratios, and the electrochemical behaviour was studied in 6 M KOH electrolyte. In situ Raman spectra were collected to obtain the structural changes of the activated carbons under severe electrochemical oxidation and reduction conditions, and the obtained data were correlated to the cyclic voltammograms obtained at high anodic and cathodic potentials. Carbon-hydrogen bonds were detected for the materials activated at high KOH ratios, which form reversibly under cathodic conditions. The influence of the specific surface area, narrow microporosity and functional groups in the carbon electrodes on their chemical stability and hydrogen capture mechanism in supercapacitor applications has been revealed. Supercapacitor ; Electrochemistry ; Electrolyte ; Potassium hydroxide ; Activated carbon ; Materials science ; Raman spectroscopy ; Inorganic chemistry ; Chemical engineering ; Electrode ; Cathodic protection ; Carbon fibers ; Chemistry ; Organic chemistry ; Adsorption ; Composite material ; Physical chemistry Supercapacitor Materials and Fabrication ; Conducting polymers and applications ; Electrocatalysts for Energy Conversion
Authors: Chang Liu | Béla Tuzson | Philipp Scheidegger | Herbert Looser | Bernhard Bereiter | Manuel Gräf | Morten Hundt | Оleg Aseev | D. J. H. C. Maas | Lukas Emmenegger
Source: Review of Scientific Instruments (article, 2018-06-01)
Field: Chemistry — Spectroscopy

Laser driving and data processing concept for mobile trace gas sensing: Design and implementation High precision mobile sensing of multi-species gases is greatly demanded in a wide range of applications. Although quantum cascade laser absorption spectroscopy demonstrates excellent field-deployment capabilities for gas sensing, the implementation of this measurement technique into sensor-like portable instrumentation still remains challenging. In this paper, two crucial elements, the laser driving and data acquisition electronics, are addressed. Therefore, we exploit the benefits of the time-division multiplexed intermittent continuous wave driving concept and the real-time signal pre-processing capabilities of a commercial System-on-Chip (SoC, Red Pitaya). We describe a re-designed current driver that offers a universal solution for operating a wide range of multi-wavelength quantum cascade laser device types and allows stacking for the purpose of multiple laser configurations. Its adaptation to the various driving situations is enabled by numerous field programmable gate array (FPGA) functionalities that were developed on the SoC, such as flexible generation of a large variety of synchronized trigger signals and digital inputs/outputs (DIOs). The same SoC is used to sample the spectroscopic signal at rates up to 125 MS/s with 14-bit resolution. Additional FPGA functionalities were implemented to enable on-board averaging of consecutive spectral scans in real-time, resulting in optimized memory bandwidth and hardware resource utilisation and autonomous system operation. Thus, we demonstrate how a cost-effective, compact, and commercial SoC can successfully be adapted to obtain a fully operational research-grade laser spectrometer. The overall system performance was examined in a spectroscopic setup by analyzing low pressure absorption features of CO<sub>2</sub> at 4.3 μm. Computer science ; Field-programmable gate array ; Quantum cascade laser ; Gate array ; Laser ; Computer hardware ; Embedded system ; Electronic engineering ; Optics ; Physics Spectroscopy and Laser Applications ; Laser Design and Applications ; Atmospheric Ozone and Climate
Authors: L. Weston | C. Stampfl
Source: Physical Review Materials (article, 2018-08-21)
Field: Materials Science — Materials Chemistry

Machine learning the band gap properties of kesterite <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi mathvariant="normal">I</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:mtext>−</mml:mtext><mml:mi>II</mml:mi><mml:mtext>−</mml:mtext><mml:mi>IV</mml:mi><mml:mtext>−</mml:mtext><mml:msub><mml:mi mathvariant="normal">V</mml:mi><mml:mn>4</mml:mn></mml:msub></mml:mrow></mml:math> quaternary compounds for photovoltaics applications Kesterite ${\mathrm{I}}_{2}\text{\ensuremath{-}}\mathrm{II}\text{\ensuremath{-}}\mathrm{IV}\text{\ensuremath{-}}{\mathrm{V}}_{4}$ semiconductors are promising solar absorbers for photovoltaics applications. The band gap and its character, either direct or indirect, are fundamental properties determining photovoltaic-device efficiency. We use a combination of accurate first-principles calculations and machine learning to predict the properties of the band gap for a large number of kesterite ${\mathrm{I}}_{2}\text{\ensuremath{-}}\mathrm{II}\text{\ensuremath{-}}\mathrm{IV}\text{\ensuremath{-}}{\mathrm{V}}_{4}$ semiconductors. In determining the magnitude of the fundamental gap, we compare results for a number of machine-learning models, and achieve a root mean squared error as low as 283 meV; the best results are achieved using support-vector regression with a radial-bias kernel. This error is well within the uncertainty of even the most advanced first-principles methods for calculating semiconductor band gaps. Predicting the direct-indirect property of the band gap is more challenging. After significant feature engineering, we are able to train a classifier that predicts the nature of the band gap with an accuracy of 89% using logistic regression. Using these trained models, the band gap properties of 1568 kesterite ${\mathrm{I}}_{2}\text{\ensuremath{-}}\mathrm{II}\text{\ensuremath{-}}\mathrm{IV}\text{\ensuremath{-}}{\mathrm{V}}_{4}$ compounds are predicted. We find 717 compounds with band gaps in the range 0.5--2.5 eV that can potentially act as solar absorbers and 242 materials with a band gap in the ``optimum range'' of 1.2--1.8 eV. The stability of these 242 compounds is assessed by calculating the energy above hull using the Materials Project database, and the band gaps are verified using hybrid functional calculations; in the end, we identify 25 compounds that are expected to be synthesizable and have a band gap in the range 1.2--1.8 eV---most of which are previously unexplored. These results will be useful in the materials engineering of efficient photovoltaic devices. Kesterite ; Band gap ; Semiconductor ; Photovoltaics ; Hybrid functional ; Direct and indirect band gaps Machine Learning in Materials Science ; Chalcogenide Semiconductor Thin Films ; Chemical and Physical Properties of Materials
Authors: Elham Nematinia | Saman Abdanan Mehdizadeh
Source: Journal of Food Measurement & Characterization (article, 2018-02-24)
Field: Chemistry — Analytical Chemistry

Assessment of egg freshness by prediction of Haugh unit and albumen pH using an artificial neural network Haugh unit ; Correlation coefficient ; Artificial neural network ; Yolk ; Conjugate gradient method ; Mathematics ; Pearson product-moment correlation coefficient ; Coefficient of determination ; Artificial intelligence ; Statistics ; Pattern recognition (psychology) ; Chemistry ; Computer science ; Food science ; Algorithm ; Biology ; Body weight ; Feed conversion ratio Spectroscopy and Chemometric Analyses ; Animal Nutrition and Physiology ; Meat and Animal Product Quality
Authors: Panagiotis Barmpalexis | Anna Karagianni | Ioannis Nikolakakis | Kyriakos Kachrimanis
Source: Journal of Pharmaceutical and Biomedical Analysis (article, 2018-06-04)
Field: Materials Science — Materials Chemistry

Artificial neural networks (ANNs) and partial least squares (PLS) regression in the quantitative analysis of cocrystal formulations by Raman and ATR-FTIR spectroscopy Partial least squares regression ; Cocrystal ; Chemistry ; Fourier transform infrared spectroscopy ; Analytical Chemistry (journal) ; Attenuated total reflection ; Raman spectroscopy ; Spectroscopy ; Chemometrics ; Mean squared error ; Principal component regression ; Linear regression ; Chromatography ; Infrared spectroscopy ; Mathematics ; Statistics ; Organic chemistry ; Optics Crystallization and Solubility Studies ; Spectroscopy and Chemometric Analyses ; Crystallography and molecular interactions
Authors: Enrico Berardo | Lukas Turcani | Marcin Miklitz | Kim E. Jelfs
Source: Chemical Science (article, 2018-01-01)
Field: Chemistry — Inorganic Chemistry

An evolutionary algorithm for the discovery of porous organic cages The chemical and structural space of possible molecular materials is enormous, as they can, in principle, be built from any combination of organic building blocks. Here we have developed an evolutionary algorithm (EA) that can assist in the efficient exploration of chemical space for molecular materials, helping to guide synthesis to materials with promising applications. We demonstrate the utility of our EA to porous organic cages, predicting both promising targets and identifying the chemical features that emerge as important for a cage to be shape persistent or to adopt a particular cavity size. We identify that shape persistent cages require a low percentage of rotatable bonds in their precursors (<20%) and that the higher topicity building block in particular should use double bonds for rigidity. We can use the EA to explore what size ranges for precursors are required for achieving a given pore size in a cage and show that 16 Å pores, which are absent in the literature, should be synthetically achievable. Our EA implementation is adaptable and easily extendable, not only to target specific properties of porous organic cages, such as optimal encapsulants or molecular separation materials, but also to any easily calculable property of other molecular materials. Porosity ; Drug discovery ; Computer science ; Algorithm ; Chemistry ; Biology ; Bioinformatics ; Organic chemistry Metal-Organic Frameworks: Synthesis and Applications ; Supramolecular Chemistry and Complexes ; Supramolecular Self-Assembly in Materials
Authors: Cristina Nastasă | Dan Cristian Vodnar | Ioana Ionuț | Anca Stana | Daniela Benedec | Radu Tamaian | Ovidiu Oniga | Brînduşa Tiperciuc
Source: International Journal of Molecular Sciences (article, 2018-01-11)
Field: Chemistry — Organic Chemistry

Antibacterial Evaluation and Virtual Screening of New Thiazolyl-Triazole Schiff Bases as Potential DNA-Gyrase Inhibitors The global spread of bacterial resistance to drugs used in therapy requires new potent and safe antimicrobial agents. DNA gyrases represent important targets in drug discovery. Schiff bases, thiazole, and triazole derivatives are considered key scaffolds in medicinal chemistry. Fifteen thiazolyl-triazole Schiff bases were evaluated for their antibacterial activity, measuring the growth inhibition zone diameter, the minimum inhibitory concentration (MIC), and the minimum bactericidal concentration (MBC), against Gram-positive (<i>Staphylococcus aureus</i>, <i>Listeria monocytogenes</i>) and Gram-negative (<i>Escherichia coli</i>, <i>Salmonella typhimurium</i>, <i>Pseudomonas aeruginosa</i>) bacteria. The inhibition of <i>S. aureus</i> and <i>S. typhimurium</i> was modest. Compounds <b>B1</b>, <b>B2</b>, and <b>B9</b> showed a similar effect as ciprofloxacin, the antimicrobial reference, against <i>L. monocytogenes</i>. <b>B10</b> displayed a better effect. Derivatives <b>B1</b>, <b>B5</b>-<b>7</b>, <b>B9</b>, and <b>B11</b>-<b>15</b> expressed MIC values lower than the reference, against <i>L. monocytogenes</i>. <b>B5</b>, <b>B6</b>, and <b>B11</b>-<b>15</b> strongly inhibited the growth of <i>P. aeruginosa</i>. All compounds were subjected to an in silico screening of the ADMET (absorption, distribution, metabolism, elimination, toxicity) properties. Molecular docking was performed on the gyrA and gyrB from <i>L. monocytogenes</i>. The virtual screening concluded that thiazolyl-triazole Schiff base <b>B8</b> is the best <i>drug-like</i> candidate, satisfying requirements for both safety and efficacy, being more potent against the bacterial gyrA than ciprofloxacin. DNA gyrase ; Virtual screening ; Chemistry ; Triazole ; DNA ; Combinatorial chemistry ; Schiff base ; 1,2,4-Triazole ; Biochemistry ; Stereochemistry ; Medicinal chemistry ; Escherichia coli ; Organic chemistry ; Drug discovery Synthesis and biological activity ; Click Chemistry and Applications ; Synthesis and Characterization of Heterocyclic Compounds