jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Nikolaos Nikolopoulos | Abhijit Wickramasinghe | Gareth T. Whiting | Bert M. Weckhuysen
Source: Catalysis Science & Technology (article, 2022-12-15)
Field: Chemistry — Inorganic Chemistry

Alumina binder effects on the hydrothermal stability of shaped zeolite-based catalyst bodies The influence of hydrothermal treatments and alumina binder on the properties and catalytic performance in the methanol-to-hydrocarbon reaction of different zeolite–alumina catalyst extrudates was characterized using a combination of ex situ , in situ and operando techniques. Catalysis ; Zeolite ; Hydrothermal circulation ; Methanol ; Chemical engineering ; Hydrothermal reaction ; Hydrocarbon ; Materials science ; In situ ; Hydrothermal synthesis ; Chemistry ; Organic chemistry Zeolite Catalysis and Synthesis ; Catalysis and Hydrodesulfurization Studies ; Catalysis and Oxidation Reactions
Authors: Weihao Chen | Yang Chen | Xiao Gu | Zaizhu Chen | Chun‐Yu Ho
Source: Nature Communications (article, 2022-09-20)
Field: Chemistry — Inorganic Chemistry

(NHC)Pd(II) hydride-catalyzed dehydroaromatization by olefin chain-walking isomerization and transfer-dehydrogenation Transition-metal-catalyzed homogeneous dehydrogenation and isomerization are common organic molecular activation reactions. Palladium hydrides are good olefin isomerization catalysts but are usually short-lived species under redox-active dehydrogenation conditions. Here, we show that Pd-H in the presence of an N-heterocyclic carbene ligand and an alkene regulator enables transfer-dehydroaromatization, avoiding the homo-disproportionation pathway. The desired product is obtained with up to 99:1 selectivity, and the exo-to-endo olefin isomerization can be carried out in one pot. In contrast to previously reported methods that rely on the efficient removal of Pd-H, the approach reported herein benefits from the steric effects of the N-heterocyclic carbene and the choice of alkene to regulate the competing reactivity of allylic C‒H activation and hydropalladation. This method circumvents the challenges associated with tedious olefin separation and a low exo-to-endo olefin isomerization ratio and expands the scope to include challenging endo- and exo-cyclic olefins under mild, neutral, and oxidant-free conditions. Overall, herein, we provide a strategy to synthesize (hetero)aromatic compounds via chemoselective dehydrogenation of cyclic alkenes over ketones and the dehydrogenative Diels-Alder reaction of a cyclic enamine. Isomerization ; Dehydrogenation ; Chemistry ; Olefin fiber ; Alkene ; Catalysis ; Photochemistry ; Allylic rearrangement ; Steric effects ; Combinatorial chemistry ; Organic chemistry Asymmetric Hydrogenation and Catalysis ; Catalytic C–H Functionalization Methods ; Catalytic Cross-Coupling Reactions
Authors: Stefan Habermehl | Carina Schlesinger | Martin U. Schmidt
Source: Acta Crystallographica Section B Structural Science Crystal Engineering and Materials (article, 2022-03-16)
Field: Materials Science — Materials Chemistry

Structure determination from unindexed powder data from scratch by a global optimization approach using pattern comparison based on cross-correlation functions A method of ab initio crystal structure determination from powder diffraction data for organic and metal-organic compounds, which does not require prior indexing of the powder pattern, has been developed. Only a reasonable molecular geometry is required, needing knowledge of neither unit-cell parameters nor space group. The structures are solved from scratch by a global fit to the powder data using the new program FIDEL-GO (`FIt with DEviating Lattice parameters - Global Optimization'). FIDEL-GO uses a similarity measure based on cross-correlation functions, which allows the comparison of simulated and experimental powder data even if the unit-cell parameters deviate strongly. The optimization starts from large sets of random structures in various space groups. The unit-cell parameters, molecular position and orientation, and selected internal degrees of freedom are fitted simultaneously to the powder pattern. The optimization proceeds in an elaborate multi-step procedure with built-in clustering of duplicate structures and iterative adaptation of parameter ranges. The best structures are selected for an automatic Rietveld refinement. Finally, a user-controlled Rietveld refinement is performed. The procedure aims for the analysis of a wide range of `problematic' powder patterns, in particular powders of low crystallinity. The method can also be used for the clustering and screening of a large number of possible structure candidates and other application scenarios. Examples are presented for structure determination from unindexed powder data of the previously unknown structures of the nanocrystalline phases of 4,11-difluoro-, 2,9-dichloro- and 2,9-dichloro-6,13-dihydro-quinacridone, which were solved from powder patterns with 14-20 peaks only, and of the coordination polymer dichloro-bis(pyridine-N)copper(II). Powder diffraction ; Global optimization ; Rietveld refinement ; Cluster analysis ; Position (finance) ; Ab initio ; Scratch ; Similarity (geometry) X-ray Diffraction in Crystallography ; Crystallography and molecular interactions ; Advanced NMR Techniques and Applications
Authors: Jonathan G. Coldstream | Philip J. Camp | D. Phillips | Peter J. Dowding
Source: Soft Matter (article, 2022-01-01)
Field: Materials Science — Materials Chemistry

Gradient copolymers<i>versus</i>block copolymers: self-assembly in solution and surface adsorption The structures of amphiphilic block and gradient copolymers in solution and adsorbed onto surfaces are surveyed using molecular-dynamics simulations. A bead-spring model is used to identify the general effects of the different architectures: block and gradient copolymers have equal numbers of solvophilic and solvophobic beads, and the gradient copolymer is represented by a linear concentration profile along the chain. Each type of isolated copolymer forms a structure with a globular head of solvophobic beads, and a coil-like tail of solvophilic beads. The radius of gyration of a gradient copolymer is found to be much more sensitive to temperature than that of a block copolymer due to an unravelling mechanism. At finite concentrations, both gradient and block copolymers self-assemble into micelles, with the gradient copolymers again showing a larger temperature dependence. The micelles are characterised using simulated scattering profiles, which compare favourably to existing experimental data. The adsorption of copolymers onto structureless surfaces is modelled with an attractive potential that is selective for the solvophobic beads, and the surface structures are characterised using the average height of the molecules, and the proportion of beads adsorbed. Both types of copolymer form adsorbed films with persistent micelle-like structures, but the gradient copolymers show a stronger dependence on the strength of the surface interactions and the temperature. Coarse-grained, bead-spring models allow a rapid survey and comparison of the block and gradient architectures, and the results set the scene for future work with atomistic simulations. A superficial but favourable comparison is made between the results from the bead-spring models, and atomistic simulations of a butyl prop-2-enoate/prop-2-enoic acid (butyl acrylate/acrylic acid) copolymer in <i>n</i>-dodecane at room temperature. Copolymer ; Adsorption ; Self-assembly ; Block (permutation group theory) ; Chemical engineering ; Materials science ; Surface (topology) ; Polymer chemistry ; Polymer science ; Chemical physics ; Chemistry ; Nanotechnology ; Physical chemistry ; Polymer ; Geometry ; Composite material ; Mathematics ; Engineering Block Copolymer Self-Assembly ; Advanced Polymer Synthesis and Characterization ; Polymer Surface Interaction Studies
Authors: Shivan Bissesar | Davita M. E. van Raamsdonk | Dáire Gibbons | René M. Williams
Source: Molecules (article, 2022-01-28)
Field: Chemistry — Physical and Theoretical Chemistry

Spin Orbit Coupling in Orthogonal Charge Transfer States: (TD-)DFT of Pyrene—Dimethylaniline The conformational dependence of the matrix element for spin-orbit coupling and of the electronic coupling for charge separation are determined for an electron donor-acceptor system containing a pyrene acceptor and a dimethylaniline donor. Different kinetic and energetic aspects that play a role in the spin-orbit charge transfer intersystem crossing (SOCT-ISC) mechanism are discussed. This includes parameters related to initial charge separation and the charge recombination pathways using the Classical Marcus Theory of electron transfer. The spin-orbit coupling, which plays a significant role in charge recombination to the triplet state, can be probed by (TD)-DFT, using the latter as a tool to understand and predict the SOCT-ISC mechanism. The matrix elements for spin-orbit coupling for acetone and 4-thio-thymine are used for benchmarking. (Time Dependent-) Density Functional Theory (DFT and TD-DFT) calculations are applied using the quantum chemical program Amsterdam Density Functional (ADF). Intersystem crossing ; Density functional theory ; Chemistry ; Spin–orbit interaction ; Charge (physics) ; Triplet state ; Coupling (piping) ; Marcus theory ; Dimethylaniline ; Spin (aerodynamics) ; Molecular physics ; Excited state ; Chemical physics ; Computational chemistry ; Atomic physics ; Photochemistry ; Materials science ; Physics ; Condensed matter physics ; Thermodynamics ; Quantum mechanics ; Reaction rate constant ; Kinetics Photochemistry and Electron Transfer Studies ; Porphyrin and Phthalocyanine Chemistry ; Molecular Junctions and Nanostructures
Authors: Vignesh K. Manivasagam | M. Sankar | Caterina Bartomeu Garcia | Jithin Vishnu | Kaushik Chatterjee | Satyam Suwas | Geetha Manivasagam | Thomas J. Webster
Source: In vitro models (article, 2022-05-02)
Field: Materials Science — Biomaterials

Surface-modified WE43 magnesium alloys for reduced degradation and superior biocompatibility Biocompatibility ; Materials science ; Magnesium ; Surface modification ; Wetting ; Osteoblast ; Surface roughness ; Chemical engineering ; Metallurgy ; Chemistry ; Composite material ; In vitro ; Biochemistry Magnesium Alloys: Properties and Applications ; Bone Tissue Engineering Materials ; Orthopaedic implants and arthroplasty
Authors: Alexander Kettner | Matthias Noll | Carola Griehl
Source: Applied Microbiology and Biotechnology (article, 2022-01-01)
Field: Materials Science — Biomaterials

In situ quantification of poly(3-hydroxybutyrate) and biomass in Cupriavidus necator by a fluorescence spectroscopic assay Fluorescence spectroscopy offers a cheap, simple, and fast approach to monitor poly(3-hydroxybutyrate) (PHB) formation, a biodegradable polymer belonging to the biodegradable polyester class polyhydroxyalkanoates. In the present study, a fluorescence and side scatter-based spectroscopic setup was developed to monitor in situ biomass, and PHB formation of biotechnological applied Cupriavidus necator strain. To establish PHB quantification of C. necator, the dyes 2,2-difluoro-4,6,8,10,12-pentamethyl-3-aza-1-azonia-2-boranuidatricyclo[7.3.0.03,7]dodeca-1(12),4,6,8,10-pentaene (BODIPY<sup>493/503</sup>), ethyl 5-methoxy-1,2-bis(3-methylbut-2-enyl)-3-oxoindole-2-carboxylate (LipidGreen2), and 9-(diethylamino)benzo[a]phenoxazin-5-one (Nile red) were compared with each other. Fluorescence staining efficacy was obtained through 3D-excitation-emission matrix and design of experiments. The coefficients of determination were ≥ 0.98 for all three dyes and linear to the high-pressure liquid chromatography obtained PHB content, and the side scatter to the biomass concentration. The fluorescence correlation models were further improved by the incorporation of the biomass-related side scatter. Afterward, the resulting regression fluorescence models were successfully applied to nitrogen-deficit, phosphor-deficit, and NaCl-stressed C. necator cultures. The highest transferability of the regression models was shown by using LipidGreen2. The novel approach opens a tailor-made way for a fast and simultaneous detection of the crucial biotechnological parameters biomass and PHB content during fermentation. KEY POINTS: • Intracellular quantification of PHB and biomass using fluorescence spectroscopy. • Optimizing fluorescence staining conditions and 3D-excitation-emission matrix. • PHB was best obtained by LipidGreen2, followed by BODIPDY<sup>493/503</sup> and Nile red. Cupriavidus necator ; Fluorescence ; Fluorescence spectroscopy ; Nile red ; Polyhydroxyalkanoates ; Chemistry ; Biomass (ecology) ; Fluorescamine ; Fermentation ; Chromatography ; Biochemistry ; Bacteria ; Biology biodegradable polymer synthesis and properties ; Microplastics and Plastic Pollution ; Enzyme Catalysis and Immobilization
Authors: Sarah M. Somers | Jordana Gilbert‐Honick | In Young Choi | Emily K.W. Lo | Hotae Lim | Shaquielle Dias | Kathryn R. Wagner | Hai‐Quan Mao | Patrick Cahan | Gabsang Lee | Warren L. Grayson
Source: Bioengineering (article, 2022-11-15)
Field: Materials Science — Biomaterials

Engineering Skeletal Muscle Grafts with PAX7::GFP-Sorted Human Pluripotent Stem Cell-Derived Myogenic Progenitors on Fibrin Microfiber Bundles for Tissue Regeneration Tissue engineering strategies that combine human pluripotent stem cell-derived myogenic progenitors (hPDMs) with advanced biomaterials provide promising tools for engineering 3D skeletal muscle grafts to model tissue development in vitro and promote muscle regeneration in vivo. We recently demonstrated (i) the potential for obtaining large numbers of hPDMs using a combination of two small molecules without the overexpression of transgenes and (ii) the application of electrospun fibrin microfiber bundles for functional skeletal muscle restoration following volumetric muscle loss. In this study, we aimed to demonstrate that the biophysical cues provided by the fibrin microfiber bundles induce hPDMs to form engineered human skeletal muscle grafts containing multinucleated myotubes that express desmin and myosin heavy chains and that these grafts could promote regeneration following skeletal muscle injuries. We tested a genetic PAX7 reporter line (PAX7::GFP) to sort for more homogenous populations of hPDMs. RNA sequencing and gene set enrichment analyses confirmed that PAX7::GFP-sorted hPDMs exhibited high expression of myogenic genes. We tested engineered human skeletal muscle grafts derived from PAX7::GFP-sorted hPDMs within in vivo skeletal muscle defects by assessing myogenesis, engraftment and immunogenicity using immunohistochemical staining. The PAX7::GFP-sorted groups had moderately high vascular infiltration and more implanted cell association with embryonic myosin heavy chain (eMHC) regions, suggesting they induced pro-regenerative microenvironments. These findings demonstrated the promise for the use of PAX7::GFP-sorted hPDMs on fibrin microfiber bundles and provided some insights for improving the cell-biomaterial system to stimulate more robust in vivo skeletal muscle regeneration. Regeneration (biology) ; Cell biology ; Progenitor cell ; Induced pluripotent stem cell ; Tissue engineering ; Stem cell ; Microfiber ; Fibrin ; Anatomy ; Skeletal muscle ; Regenerative medicine ; Biology ; Chemistry ; Embryonic stem cell ; Immunology ; Biochemistry Electrospun Nanofibers in Biomedical Applications ; 3D Printing in Biomedical Research ; Tissue Engineering and Regenerative Medicine
Authors: Emmanuelle M. D. Allouche | Raphaël Simonet‐Davin | Jérôme Waser
Source: Chemistry - A European Journal (article, 2022-02-09)
Field: Chemistry — Organic Chemistry

<i>N</i>‐Terminal Selective C−H Azidation of Proline‐Containing Peptides: a Platform for Late‐Stage Diversification A methodology for the C-H azidation of N-terminal proline-containing peptides was developed employing only commercially available reagents. Peptides bearing a broad range of functionalities and containing up to 6 amino acids were selectively azidated at the carbamate-protected N-terminal residue in presence of the numerous other functional groups present on the molecules. Post-functionalizations of the obtained aminal compounds were achieved: cycloaddition reactions or C-C bond formations via a sequence of imine formation/nucleophilic addition were performed, offering an easy access to diversified peptides. Chemistry ; Residue (chemistry) ; Carbamate ; Imine ; Proline ; Stereochemistry ; Cycloaddition ; Aminal ; Combinatorial chemistry ; Reagent ; Nucleophile ; Total synthesis ; Amino acid ; Organic chemistry ; Biochemistry ; Catalysis Synthesis and Catalytic Reactions ; Chemical Synthesis and Analysis ; Oxidative Organic Chemistry Reactions
Authors: Andreas Dreuw | Thomas Fransson
Source: Physical Chemistry Chemical Physics (article, 2022-01-01)
Field: Materials Science — Surfaces, Coatings and Films

Using core-hole reference states for calculating X-ray photoelectron and emission spectra For the calculation of core-ionization energies (IEs), X-ray photoelectron spectra (XPS), and X-ray emission spectra (XES), a commonly applied approach is to use non-<i>Aufbau</i> reference states with a core-hole as either final (IE and XPS) or initial (XES) state. However, such reference states can introduce numerical instabilities in post-HF methods, relating to the denominator of the energy corrections involved. This may become arbitrarily close to zero if a negative virtual orbital is present, <i>e.g.</i> a core-hole, leading to near-singularities. The resulting instabilities lead to severe convergence issues of the calculation schemes and, in addition, can strongly affect both energies and intensities, with oscillator strengths seen to reach values up to 4 × 10<sup>7</sup>. For the <i>K</i>-edge we propose freezing the highest-energy virtual orbitals which contribute to any denominator below a threshold of 0.1 Hartree. Stable and reliable spectra are then produced, with minimal influence due to freezing energetically high-lying virtual orbitals (typically removing <5% of the total number of MOs). The developed protocol is here tested for Møller-Plesset perturbation theory and for the algebraic diagrammatic construction scheme for the polarization propagator, and it is also relevant for coupled cluster theory and other related methods. X-ray ; Spectral line ; Core (optical fiber) ; X-ray photoelectron spectroscopy ; Atomic physics ; Emission spectrum ; Materials science ; Physics ; Chemistry ; Nuclear magnetic resonance ; Optics ; Quantum mechanics Electron and X-Ray Spectroscopy Techniques ; X-ray Spectroscopy and Fluorescence Analysis ; Crystallography and Radiation Phenomena
Authors: Clayton Forssén | Isak Silander | Johan Zakrisson | Martin Zelán | Ove Axner
Source: Journal of Optics (article, 2022-01-25)
Field: Chemistry — Spectroscopy

An optical pascal in Sweden Abstract By measuring the refractivity and the temperature of a gas, its pressure can be assessed from fundamental principles. The highest performing instruments are based on Fabry–Perot cavities where a laser is used to probe the frequency of a cavity mode, which is shifted in relation to the refractivity of the gas in the cavity. Recent activities have indicated that such systems can demonstrate an extended uncertainty in the 10 ppm (parts-per-million or 10 −6 ) range. As a means to reduce the influence of various types of disturbances (primarily drifts and fluctuations) a methodology based on modulation, denoted gas modulation refractometry (GAMOR), has recently been developed. Systems based on this methodology are in general high-performance, e.g. they have demonstrated precision in the sub-ppm range, and they are sturdy. They can also be made autonomous, allowing for automated and unattended operation for virtually infinite periods of time. To a large degree, the development of such instruments depends on the access to modern photonic components, e.g. narrow line-width lasers, electro- and acousto-optic components, and various types of fiber components. This work highlights the role of such modern devices in GAMOR-based instrumentation and provides a review on the recent development of such instruments in Sweden that has been carried out in a close collaboration between a research institute and the Academy. It is shown that the use of state-of-the-art photonic devices allows sturdy, automated and miniaturized instrumentation that, for the benefit of industry, can serve as standards for pressure and provide fast, unattended, and calibration-free pressure assessments at a fraction of the present cost. Instrumentation (computer programming) ; Optics ; Photonics ; Laser ; Modulation (music) ; Refractometry ; Computer science ; Optoelectronics ; Materials science ; Physics ; Refractive index ; Acoustics Spectroscopy and Laser Applications ; Scientific Measurement and Uncertainty Evaluation ; Advanced Sensor Technologies Research
Authors: Eric S. Muckley | Rama K. Vasudevan | Bobby G. Sumpter | Rigoberto C. Advíncula | Ilia N. Ivanov
Source: ACS Applied Materials & Interfaces (article, 2022-12-28)
Field: Materials Science — Materials Chemistry

Machine Intelligence-Centered System for Automated Characterization of Functional Materials and Interfaces Classic design of experiment relies on a time-intensive workflow that requires planning, data interpretation, and hypothesis building by experienced researchers. Here, we describe an integrated, machine-intelligent experimental system which enables simultaneous dynamic tests of electrical, optical, gravimetric, and viscoelastic properties of materials under a programmable dynamic environment. Specially designed software controls the experiment and performs on-the-fly extensive data analysis and dynamic modeling, real-time iterative feedback for dynamic control of experimental conditions, and rapid visualization of experimental results. The system operates with minimal human intervention and enables time-efficient characterization of complex dynamic multifunctional environmental responses of materials with simultaneous data processing and analytics. The system provides a viable platform for artificial intelligence (AI)-centered material characterization, which, when coupled with an AI-controlled synthesis system, could lead to accelerated discovery of multifunctional materials. Workflow ; Characterization (materials science) ; Computer science ; Analytics ; Visualization ; Software ; Artificial intelligence ; Materials science ; Nanotechnology ; Data mining Machine Learning in Materials Science ; Force Microscopy Techniques and Applications ; Analytical Chemistry and Sensors
Authors: Zeyu Ma | Bo Wang | Lei Tao
Source: Molecules (review, 2022-11-15)
Field: Chemistry — Organic Chemistry

Stepping Further from Coupling Tools: Development of Functional Polymers via the Biginelli Reaction Multicomponent reactions (MCRs) have been used to prepare polymers with appealing functions. The Biginelli reaction, one of the oldest and most famous MCRs, has sparked new scientific discoveries in polymer chemistry since 2013. Recent years have seen the Biginelli reaction stepping further from simple coupling tools; for example, the functions of the Biginelli product 3,4-dihydropyrimidin-2(1H)-(thi)ones (DHPM(T)) have been gradually exploited to develop new functional polymers. In this mini-review, we mainly summarize the recent progress of using the Biginelli reaction to identify polymers for biomedical applications. These polymers have been documented as antioxidants, anticancer agents, and bio-imaging probes. Moreover, we also provide a brief introduction to some emerging applications of the Biginelli reaction in materials and polymer science. Finally, we present our perspectives for the further development of the Biginelli reaction in polymer chemistry. Biginelli reaction ; Polymer ; Coupling reaction ; Chemistry ; Combinatorial chemistry ; Nanotechnology ; Computer science ; Materials science ; Organic chemistry ; Thiourea ; Catalysis Multicomponent Synthesis of Heterocycles ; Synthesis and biological activity ; Synthesis and Characterization of Heterocyclic Compounds