jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Tom Kunde | Tobias Pausch | Bernd M. Schmidt
Source: Chemistry - A European Journal (article, 2021-04-14)
Field: Chemistry — Organic Chemistry

Supramolecular Alloys from Fluorinated Hybrid Tri <sup>4</sup> Di <sup>6</sup> Imine Cages To create innovative materials, efficient control and engineering of pore sizes and their characteristics, crystallinity and stability is required. Eight hybrid Tri<sup>4</sup> Di<sup>6</sup> imine cages with a tunable degree of fluorination and one fully fluorinated Tri<sup>4</sup> Di<sup>6</sup> imine cage are investigated. Although the fluorinated and the non-fluorinated building blocks used herein differ vastly in reactivity, it was possible to gain control over the outcome of the self-assembly process, by carefully controlling the feed ratio. This represents the first hybrid material based on fluorinated/hydrogenated porous organic cages (POCs). These cages with unlimited miscibility in the solid state were obtained as highly crystalline samples after recrystallization and even showed retention of the crystal lattice, forming alloys. All mixtures and the fully fluorinated Tri<sup>4</sup> Di<sup>6</sup> imine cage were analyzed by MALDI-MS, single-crystal XRD, powder XRD and in regard to thermal stability (TGA). Imine ; Crystallinity ; Materials science ; Thermal stability ; Recrystallization (geology) ; Chemical engineering ; Miscibility ; Crystal structure ; Supramolecular chemistry ; Reactivity (psychology) ; Solid-state ; Polymer chemistry ; Organic chemistry ; Chemistry ; Physical chemistry ; Polymer ; Catalysis ; Composite material Supramolecular Chemistry and Complexes ; Metal-Organic Frameworks: Synthesis and Applications ; Covalent Organic Framework Applications
Authors: Eleni K. Tsekoura | Teo Atz Dick | Porntipa Pankongadisak | Daniel Graf | Yaman Boluk | Hasan Uludağ
Source: Pharmaceuticals (article, 2021-07-12)
Field: Materials Science — Biomaterials

Delivery of Bioactive Gene Particles via Gelatin-Collagen-PEG-Based Electrospun Matrices The fabrication of fiber mats via electrospinning has been adopted in the last decades to produce high quality scaffolds for tissue engineering. However, an effective combination of electrospinning methods with gene delivery therapies remains a challenge. In this study, we describe how the delivery of gene complexes via electrospun mats that contain different volumes of gelatin (Gel), collagen (Col), and polyethylene glycol (PEG) can affect gene expression by transfected cells. Non-viral complexes were formulated by using lipid modified polyethylenimine (PEI) polymer and plasmid DNAs (pDNA) like the reporter Green Fluorescent Protein (GFP) and the therapeutically relevant Bone Morphogenetic Protein-2 (BMP-2) and electrospuned after being mixed with different volumes of Gel-Col-PEG mats and delivered to human myoblast (C2C12) and mouse osteoblast cells (MC3T3). The entrapment of GFP complexes via different homogeneous electrospun fiber mats revealed that a high fraction of collagen in the mats affected the quality of the fibers and led to reduced transfection efficiency on target cells. On the other hand, the fabrication of double-layered mats that contained collagen without complexes as a first layer and gelatin-collagen-PEG with complexes as a second layer successfully induced GFP expression and ALP activity in C2C12 cells. We conclude that this study has established the advantage of formulating multilayered bioactive collagen-based mats for gene delivery applications. Gelatin ; Gene delivery ; PEG ratio ; Polyethylene glycol ; Electrospinning ; Transfection ; Chemistry ; Tissue engineering ; Green fluorescent protein ; Self-healing hydrogels ; Biophysics ; Materials science ; Molecular biology ; Biomedical engineering ; Polymer ; Biochemistry ; Gene ; Polymer chemistry ; Biology Electrospun Nanofibers in Biomedical Applications ; RNA Interference and Gene Delivery ; Silk-based biomaterials and applications
Authors: Gabriela C. Schröder | Flora Meilleur
Source: Acta Crystallographica Section D Structural Biology (review, 2021-09-27)
Field: Materials Science — Materials Chemistry

Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed. Metalloprotein ; Chemistry ; Crystallography ; Neutron diffraction ; Protein crystallization ; Metal ; Crystal structure Enzyme Structure and Function ; Mass Spectrometry Techniques and Applications ; X-ray Spectroscopy and Fluorescence Analysis
Authors: Tom Bettens | Valentin Lacanau | Ruben Van Lommel | Tess De Maeseneer | Wouter Vandeplassche | Jolien Bertouille | Joost Brancart | Thomas Barlow | Tatiana Woller | Niko Van den Brande | Paula Moldenaers | Frank De Proft | Annemieke Madder | Richard Hoogenboom | Charlotte Martin | Steven Ballet | Mercedes Alonso
Source: Materials Advances (article, 2021-01-01)
Field: Chemistry — Physical and Theoretical Chemistry

Towards the understanding of halogenation in peptide hydrogels: a quantum chemical approach Halogenation matters! The stacking between phenylalanine side chains can be tuned by halogen atoms attached to the aromatic ring. Herein, computational data are successfully applied in the design of peptide hydrogels with increased stiffness. Halogenation ; Peptide ; Stacking ; Self-healing hydrogels ; Ring (chemistry) ; Halogen ; Chemistry ; Stiffness ; Quantum ; Quantum chemical ; Aromaticity ; Combinatorial chemistry ; Computational chemistry ; Materials science ; Polymer chemistry ; Organic chemistry ; Molecule ; Physics ; Biochemistry ; Composite material ; Alkyl ; Quantum mechanics Crystallography and molecular interactions ; Neuropeptides and Animal Physiology ; Supramolecular Self-Assembly in Materials
Authors: Venkatarao Selamneni | Sayan Kanungo | Parikshit Sahatiya
Source: Materials Advances (article, 2021-01-01)
Field: Materials Science — Materials Chemistry

Large area growth of SnS<sub>2</sub>/graphene on cellulose paper as a flexible broadband photodetector and investigating its band structure through first principles calculations This work demonstrates large-area growth of SnS<sub>2</sub> on a Gr dip-coated paper substrate and its application as an efficient broadband photodetector. Broadband ; Photodetector ; Graphene ; Optoelectronics ; Materials science ; Cellulose ; Optics ; Physics ; Nanotechnology ; Engineering ; Chemical engineering 2D Materials and Applications ; Quantum Dots Synthesis And Properties ; Chalcogenide Semiconductor Thin Films
Authors: Ana M. Reyes-Ramos | Yasmín R. Álvarez-García | Natalia Solodin | Jorge Almodóvar | Elaine T. Alarid | Wandaliz Torres‐García | Maribella Domenech
Source: ACS Biomaterials Science & Engineering (article, 2021-03-10)
Field: Materials Science — Biomaterials

Collagen I Fibrous Substrates Modulate the Proliferation and Secretome of Estrogen Receptor-Positive Breast Tumor Cells in a Hormone-Restricted Microenvironment The fibril orientation of type I collagen has been shown to contribute to tumor invasion and metabolic changes. Yet, there is limited information about its impact on tumor cells' behavior in a restrictive growth environment. Restrictive growth environments are generated by the inhibition of a proliferation stimulus during therapy or as an inflammatory response to suppress tumor expansion. In this study, the impact of a type I collagen matrix orientation and fibrous architecture on cell proliferation and response to estrogen receptor (ER) therapy were examined using estrogen-dependent breast tumor cells (MCF-7 and T-47D) cultured in a hormone-restricted environment. The use of hormone-free culture media, as well as pharmacological inhibitors of ER, Tamoxifen, and Fulvestrant, were investigated as hormone restrictive conditions. Examination of cultures at 72 h showed that tumor cell proliferation was significantly stimulated (1.8-fold) in the absence of hormones on collagen fibrous substrates, but not on polycaprolactone fibrous substrates of equivalent orientation. ER inhibitors did not suppress cell proliferation on collagen fibrous substrates. The examination of reporter cells for ER signaling showed a lack of activity, thus confirming a shift toward an ER-independent proliferation mechanism. Examination of two selective inhibitors of α2β1 and α1β1 integrins showed that cell proliferation is suppressed in the presence of the α2β1 integrin inhibitor only, thereby indicating that the observed changes in tumor cell behavior are caused by a combination of integrin signaling and/or an intrinsic structural motif that is uniquely present in the collagen fibrils. Adjacent coculture studies on collagen substrates showed that tumor cells on collagen can stimulate the proliferation of cells on tissue culture plastic through soluble factors. The magnitude of this effect correlated with the increased surface anisotropy of the substrate. This sensing in fibril orientation was further supported by a differential expression pattern of secreted proteins that were identified on random and aligned orientation substrates. Overall, this study shows a new role for electrospun collagen I fibrous substrates by supporting a shift toward an ER-independent tumor cell proliferation mechanism in ER+ breast tumor cells. Integrin ; Estrogen receptor ; Fulvestrant ; Cell growth ; Tumor microenvironment ; Cancer research ; Tamoxifen ; Cell biology ; Chemistry ; Extracellular matrix ; Receptor ; Endocrinology ; Internal medicine ; Biology ; Medicine ; Biochemistry ; Cancer ; Breast cancer ; Tumor cells Collagen: Extraction and Characterization ; Cell Adhesion Molecules Research ; TGF-β signaling in diseases
Authors: Dušan Kolarski | Akiko Sugiyama | Theo Rodat | Albert M. Schulte | Christian Peifer | Kenichiro Itami | Tsuyoshi Hirota | Ben L. Feringa | Wiktor Szymański
Source: Organic & Biomolecular Chemistry (article, 2021-01-01)
Field: Materials Science — Materials Chemistry

Reductive stability evaluation of 6-azopurine photoswitches for the regulation of CKIα activity and circadian rhythms Photopharmacology develops bioactive compounds whose pharmacological potency can be regulated by light. The concept relies on the introduction of molecular photoswitches, such as azobenzenes, into the structure of bioactive compounds, such as known enzyme inhibitors. Until now, the development of photocontrolled protein kinase inhibitors proved to be challenging for photopharmacology. Here, we describe a new class of heterocyclic azobenzenes based on the longdaysin scaffold, which were designed to photo-modulate the activity of casein kinase Iα (CKIα) in the context of photo-regulation of circadian rhythms. Evaluation of a set of photoswitchable longdaysin derivatives allowed for better insight into the relationship between substituents and thermal stability of the cis-isomer. Furthermore, our studies on the chemical stability of the azo group in this type of heterocyclic azobenzenes showed that they undergo a fast reduction to the corresponding hydrazines in the presence of different reducing agents. Finally, we attempted light-dependent modulation of CKIα activity together with the accompanying modulation of cellular circadian rhythms in which CKIα is directly involved. Detailed structure-activity relationship (SAR) analysis revealed a new potent reduced azopurine with a circadian period lengthening effect more pronounced than that of its parent molecule, longdaysin. Altogether, the results presented here highlight the challenges in the development of light-controlled kinase inhibitors for the photomodulation of circadian rhythms and reveal key stability issues for using the emerging class of heteroaryl azobenzenes in biological applications. Circadian rhythm ; Rhythm ; Neuroscience ; Chemistry ; Biology ; Internal medicine ; Medicine Photochromic and Fluorescence Chemistry ; Retinal Development and Disorders ; Photoreceptor and optogenetics research
Authors: Alyn D. N. James | E. I. Harris-Lee | Alexander Hampel | Markus Aichhorn | S. B. Dugdale
Source: Physical review. B./Physical review. B (article, 2021-01-06)
Field: Materials Science — Materials Chemistry

Wave functions, electronic localization, and bonding properties for correlated materials beyond the Kohn-Sham formalism Many-body theories such as dynamical mean field theory (DMFT) have enabled the description of the electron-electron correlation effects that are missing in current density functional theory (DFT) calculations. However, there has been relatively little focus on the wave functions from these theories. We present the methodology of the newly developed elk-triqs interface and how to calculate the DFT with DMFT ($\mathrm{DFT}+\mathrm{DMFT}$) wave functions, which can be used to calculate $\mathrm{DFT}+\mathrm{DMFT}$ wave-function-dependent quantities. We illustrate this by calculating the electron localization function (ELF) in monolayer ${\mathrm{SrVO}}_{3}$ and ${\mathrm{CaFe}}_{2}{\mathrm{As}}_{2}$, which provides a means of visualizing their chemical bonds. Monolayer ${\mathrm{SrVO}}_{3}$ ELFs are sensitive to the charge redistribution between the DFT, one-shot $\mathrm{DFT}+\mathrm{DMFT}$, and fully charge self-consistent $\mathrm{DFT}+\mathrm{DMFT}$ calculations. In both tetragonal and collapsed tetragonal ${\mathrm{CaFe}}_{2}{\mathrm{As}}_{2}$ phases, the ELF changes weakly with correlation-induced charge redistribution of the hybridized As $p$ and Fe $d$ states. Nonetheless, the interlayer As-As bond in the collapsed tetragonal structure is robust to the changes at and around the Fermi level. Wave function ; Kohn–Sham equations ; Tetragonal crystal system ; Density functional theory ; Electronic correlation ; Physics ; Condensed matter physics ; Electronic structure ; Electron localization function ; Fermi level ; Monolayer ; Electron ; Molecular physics ; Chemistry ; Quantum mechanics ; Materials science ; Nanotechnology Electronic and Structural Properties of Oxides ; Iron-based superconductors research ; Magnetic and transport properties of perovskites and related materials
Authors: Laia Vicens | Giorgio Olivo | Miguel Costas
Source: Angewandte Chemie International Edition (article, 2021-12-02)
Field: Chemistry — Inorganic Chemistry

Remote Amino Acid Recognition Enables Effective Hydrogen Peroxide Activation at a Manganese Oxidation Catalyst Precise delivery of a proton plays a key role in O<sub>2</sub> activation at iron oxygenases, enabling the crucial O-O cleavage step that generates the oxidizing high-valent metal-oxo species. Such a proton is delivered by acidic residues that may either directly bind the iron center or lie in its second coordination sphere. Herein, a supramolecular strategy for enzyme-like H<sub>2</sub> O<sub>2</sub> activation at a biologically inspired manganese catalyst, with a nearly stoichiometric amount (1-1.5 equiv) of a carboxylic acid is disclosed. Key for this strategy is the incorporation of an α,ω-amino acid in the second coordination sphere of a chiral catalyst via remote ammonium-crown ether recognition. The properly positioned carboxylic acid function enables effective activation of hydrogen peroxide, leading to catalytic asymmetric epoxidation. Modulation of both amino acid and catalyst structure can tune the efficiency and the enantioselectivity of the reaction, and a study on the oxidative degradation pathway of the system is presented. Hydrogen peroxide ; Manganese ; Catalysis ; Chemistry ; Inorganic chemistry ; Combinatorial chemistry ; Organic chemistry Metal-Catalyzed Oxygenation Mechanisms ; Electrochemical sensors and biosensors ; Electrocatalysts for Energy Conversion
Authors: Philipp Haines | Ramandeep Kaur | Max Martin | Martin B. Minameyer | Stefan Frühwald | Simon Bönisch | Dominik Lungerich | Frank Hampel | Andreas Görling | Thomas Drewello | Norbert Jux | Dirk M. Guldi
Source: Advanced Energy Materials (article, 2021-03-11)
Field: Chemistry — Organic Chemistry

Screening Nanographene‐Mediated Inter(Porphyrin) Communication to Optimize Inter(Porphyrin–Fullerene) Forces Abstract Multifunctional molecular materials comprising porphyrins and fullerenes have served as perfect prototypes to study key aspects of natural photosynthesis starting at light harvesting and energy transfer processes all the way to charge separation, charge shift, and charge recombination. Herein, hexa‐ peri ‐hexabenzocoronenes (HBCs) are explored, decorated with one, two, and six porphyrins at their peripheral positions, within the context of replicating key steps of photosynthesis. The major focus of the investigations is to screen inter(porphyrin) communications across the HBC platform as a function of the substitution pattern and to optimize the intermolecular forces with fullerenes. To this end, the ground‐ and excited‐state features are investigated in the absence of C 60 and C 70 by employing an arsenal of spectroscopic methods. Further insights into inter(porphyrin) communications come from time‐dependent density‐functional theory (TDDFT) calculations. In the presence of C 60 and C 70 , X‐ray crystallography, steady‐state and time‐resolved spectroscopy, and mass spectrometry corroborate exceptionally strong inter(porphyrin–fullerene) interactions in the solid, liquid, and gas phases. The experiments are backed‐up with DFT calculations of the geometrically optimized and energetically stable complex configuration. Porphyrin ; Fullerene ; Materials science ; Time-dependent density functional theory ; Density functional theory ; Intermolecular force ; Context (archaeology) ; Chemical physics ; Excited state ; Spectroscopy ; Ground state ; Artificial photosynthesis ; Nanotechnology ; Photochemistry ; Molecule ; Computational chemistry ; Atomic physics ; Chemistry ; Organic chemistry ; Physics ; Catalysis ; Photocatalysis Fullerene Chemistry and Applications ; Porphyrin and Phthalocyanine Chemistry ; Carbon Nanotubes in Composites
Authors: S. R. Burke | Matthias E. Möbius | Tuomo Hjelt | Jukka A. Ketoja | Stefan Hutzler
Source: SN Applied Sciences (article, 2021-01-24)
Field: Materials Science — Polymers and Plastics

Analysis of the foam-forming of non-woven lightweight fibrous materials using X-ray tomography Abstract Foam-forming has in the past predominantly been used to create two-dimensional sheet-like fibrous materials. Allowing the foam to drain freely and decay under gravity, rather than applying a vacuum to remove it rapidly, we can produce lightweight three-dimensional fibrous structures from cellulose fibres, of potential use for thermal and acoustic insulation. $$\mu$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>μ</mml:mi> </mml:math> CT scanning of the fibrous materials enable us to determine both void size distributions and also distributions of fibre orientations. Through image analysis and uniaxial compression testing, we find that the orientation of the fibres, rather than the size of the voids, determine the compressive strength of the material. The fibrous samples display a layering of the fibres perpendicular to the direction of drainage of the precursor liquid foam. This leads to an anisotropy of the compressive behaviour of the samples. Varying the initial liquid fraction of the foam allows for tuning of the compressive strength. We show an increase in over seven times can be achieved for samples of the same density (13 kg.m -3 ). Graphic abstract Materials science ; Metal foam ; X-ray ; Tomography ; Composite material ; Computed tomography ; Porosity ; Optics ; Radiology ; Medicine ; Physics Textile materials and evaluations ; Additive Manufacturing and 3D Printing Technologies ; Cellular and Composite Structures
Authors: Antoine Hoguin | Achal Rastogi | Chris Bowler | Leı̈la Tirichine
Source: Scientific Reports (article, 2021-02-03)
Field: Materials Science — Biomaterials

Genome-wide analysis of allele-specific expression of genes in the model diatom Phaeodactylum tricornutum Recent advances in next generation sequencing technologies have allowed the discovery of widespread autosomal allele-specific expression (aASE) in mammals and plants with potential phenotypic effects. Extensive numbers of genes with allele-specific expression have been described in the diatom Fragilariopsis cylindrus in association with adaptation to external cues, as well as in Fistulifera solaris in the context of natural hybridization. However, the role of aASE and its extent in diatoms remain elusive. In this study, we investigate allele-specific expression in the model diatom Phaeodactylum tricornutum by the re-analysis of previously published whole genome RNA sequencing data and polymorphism calling. We found that 22% of P. tricornutum genes show moderate bias in allelic expression while 1% show nearly complete monoallelic expression. Biallelic expression associates with genes encoding components of protein metabolism while moderately biased genes associate with functions in catabolism and protein transport. We validated candidate genes by pyrosequencing and found that moderate biases in allelic expression were less stable than monoallelically expressed genes that showed consistent bias upon experimental validations at the population level and in subcloning experiments. Our approach provides the basis for the analysis of aASE in P. tricornutum and could be routinely implemented to test for variations in allele expression under different environmental conditions. Phaeodactylum tricornutum ; Biology ; Genetics ; Allele ; Gene ; Pyrosequencing ; Gene expression ; Transcriptome ; Subcloning ; Diatom ; Context (archaeology) ; Ecology Diatoms and Algae Research ; Advanced Proteomics Techniques and Applications ; Algal biology and biofuel production