jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: E. M. Molnar | Emese Gál | Luiza Găină | Castelia Cristea | Luminiţa Silaghi‐Dumitrescu
Source: Molecules (article, 2020-10-04)
Field: Materials Science — Materials Chemistry

Ethyne Functionalized Meso-Phenothiazinyl-Phenyl-Porphyrins: Synthesis and Optical Properties of Free Base Versus Protonated Species Synthesis, structural characterization and photophysical properties for a series of new <i>trans</i>-A<sub>2</sub>B<sub>2</sub>- and A<sub>3</sub>B-type ethynyl functionalized <i>meso</i>-phenothiazinyl-phenyl porphyrin derivatives are described. The new compounds displayed the characteristic porphyrin absorption spectra slightly modified by weak auxochromic effects of the substituents and fluorescence emission in the range of 651-659 nm with 11-25% quantum yields. The changes recorded in the UV-vis absorption spectra in the presence of trifluoroacetic acid (TFA) are consistent with the protonation of the two internal nitrogen atoms of the free-base porphyrin (19 nm bathochromic shift of the strong Soret band and one long wave absorption maxima situated in the range of 665-695 nm). Protonation of the phenothiazine substituents required increased amounts of TFA and produced a distinct hypsochromic shift of the long wave absorption maxima. The density functional theory (DFT) calculations of a porphyrin dication pointed out a saddle-distorted porphyrin ring as the ground-state geometry. Bathochromic shift ; Hypsochromic shift ; Porphyrin ; Protonation ; Chemistry ; Photochemistry ; Dication ; Free base ; Absorption (acoustics) ; Absorption spectroscopy ; Density functional theory ; Crystallography ; Molecule ; Fluorescence ; Computational chemistry ; Physical chemistry ; Materials science ; Organic chemistry Porphyrin and Phthalocyanine Chemistry ; Photodynamic Therapy Research Studies ; Photochemistry and Electron Transfer Studies
Authors: Massimo Tosolini | João Avó | A. Jorge Parola | Gabriele Balducci | Paolo Tecilla
Source: European Journal of Inorganic Chemistry (article, 2020-09-10)
Field: Chemistry — Spectroscopy

Sterically Encumbered 4,5‐Bis(diphenylphosphino)acenaphthene Ligand and Its Ni(II), Pd(II), Pt(II), and Cu(I) Complexes A new sterically encumbered symmetrically substituted 4,5‐bis(diphenylphosphino)acenaphthene ligand ( L ) has been prepared. The ligand readily forms distorted square‐planar complexes with group 10 metal ions [Ni(II), Pd(II), Pt(II)] and a dimeric tetrahedral complex with Cu(I). The X‐ray structures of the ligand and of the complexes show a notably short distance between the two phosphorus atoms, well below than twice the van der Waals radius of P, due to the steric requirements of the rigid acenaphthene backbone. Moreover, in the complexes a stabilizing π–π interaction between two phenyl rings belonging to the two P atoms is present. The [LCuCl] 2 complex is weakly fluorescent both in solution and in the solid state with higher quantum yield as a solid where it exhibits thermally‐activated delayed fluorescence and phosphorescence. [LPdCl 2 ] and [LCuCl] 2 behave as chloride transporters across a liposomal phospholipid membrane with the Pd(II) complex displaying a very high activity. Chemistry ; Acenaphthene ; Steric effects ; Ligand (biochemistry) ; Crystallography ; Quantum yield ; Phosphorescence ; Medicinal chemistry ; Stereochemistry ; Fluorescence ; Photochemistry Molecular Sensors and Ion Detection ; Supramolecular Chemistry and Complexes ; Crystallography and molecular interactions
Authors: Laura Juhász | Krisztián Moldován | Petra Herman | Zoltán Erdélyi | István Fábián | József Kalmár | Csaba Cserháti
Source: Nanomaterials (article, 2020-06-03)
Field: Materials Science — Materials Chemistry

Synthesis and Stabilization of Support-Free Mesoporous Gold Nanoparticles Porous gold nanoparticles (PGNs) are usually prepared in an immobilized form on a solid substrate, which is not practical in many applications. In this work, a simple method is reported for the preparation and stabilization of mesoporous gold particles of a few hundred nanometers in size in aqueous suspension. Nanoparticles of Ag-Au alloy were fabricated on CaF 2 and Si/SiO 2 substrates by the solid-state dewetting method. Silver was selectively dissolved (dealloyed), and the resulting porous gold nanoparticles were chemically removed from the substrate either in a concerted step with dealloying, or in a subsequent step. Nitric acid was used for the one-step dealloying and detachment of the particles from CaF 2 substrate. The consecutive use of HNO 3 and HF resulted in the dealloying and the subsequent detachment of the particles from Si/SiO 2 substrate. The PGNs were recovered from the aqueous suspensions by centrifugation. The Au content of the suspensions was monitored by using elemental analysis (ICP-OES), and recovery was optimized. The morphology and the optical characteristics of the support-free PGNs were analyzed by scanning electron microscopy (SEM), dynamic light scattering spectroscopy (DLS), and near-infrared spectrophotometry (NIR). The obtained PGNs are spherical disk-shaped with a mean particle size of 765 ± 149 nm. The suspended, support-free PGNs display an ideally narrow dipole plasmon peak at around 1450 nm in the NIR spectral region. Thus, the new colloidal PGNs are ideal candidates for biomedical applications, for instance photothermal therapy. Materials science ; Dynamic light scattering ; Dewetting ; Nanoparticle ; Colloidal gold ; Substrate (aquarium) ; Chemical engineering ; Nanotechnology ; Scanning electron microscope ; Colloid ; Mesoporous material ; Aqueous solution ; Photothermal therapy ; Particle (ecology) ; Chemistry ; Thin film ; Organic chemistry ; Composite material Nanoporous metals and alloys ; Gold and Silver Nanoparticles Synthesis and Applications ; Pickering emulsions and particle stabilization
Authors: Thomas Voigtmann | Miriam Siebenbürger | Christian P. Amann | Stefan U. Egelhaaf | Sebastian Fritschi | Matthias Krüger | Marco Laurati | Kevin J. Mutch | K. Samwer
Source: Colloid & Polymer Science (article, 2020-04-26)
Field: Materials Science — Materials Chemistry

Rheology of colloidal and metallic glass formers Abstract Colloidal hard-sphere suspensions are convenient experimental models to understand soft matter, and also by analogy the structural-relaxation behavior of atomic or small-molecular fluids. We discuss this analogy for the flow and deformation behavior close to the glass transition. Based on a mapping of temperature to effective hard-sphere packing, the stress–strain curves of typical bulk metallic glass formers can be quantitatively compared with those of hard-sphere suspensions. Experiments on colloids give access to the microscopic structure under deformation on a single-particle level, providing insight into the yielding mechanisms that are likely also relevant for metallic glasses. We discuss the influence of higher-order angular signals in connection with non-affine particle rearrangements close to yielding. The results are qualitatively explained on the basis of the mode-coupling theory. We further illustrate the analogy of pre-strain dependence of the linear-elastic moduli using data on PS-PNiPAM suspensions. Rheology ; Materials science ; Colloid ; Atomic packing factor ; Relaxation (psychology) ; Particle (ecology) ; Deformation (meteorology) ; Chemical physics ; Physics ; Composite material ; Chemistry ; Crystallography ; Physical chemistry Material Dynamics and Properties ; Theoretical and Computational Physics ; Metallic Glasses and Amorphous Alloys
Authors: Khairul Alam | Kabusure M. Kabusure | Benjamin O. Asamoah | Tarmo Nuutinen | Marian Baah | Sughra Mohamed | Antti Matikainen | Janne Heikkinen | Heikki Rekola | M. Roussey | Markku Kuittinen | Tommi K. Hakala
Source: Nanoscale (article, 2020-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Double resonant plasmonic lattices for Raman studies We demonstrate radiation induced enhancement of both the in coupling of Raman excitation wavelength and Raman signal in plasmonic nanoparticle lattices. Rectangular nanoparticle lattices show two independently controllable lattice resonances, which we tune to be resonant with both the Raman excitation wavelength and the Raman transitions of rhodamine 6G molecules. We demonstrate that these narrow and intense resonances produced by the nanoparticle lattices allow for Raman transition specific enhancements. The system allows for independent tuning of both resonance conditions, enabling an efficient and versatile platform for Raman studies of various molecules. Raman spectroscopy ; Plasmon ; Materials science ; Optoelectronics ; Nanotechnology ; Optics ; Physics Gold and Silver Nanoparticles Synthesis and Applications ; Plasmonic and Surface Plasmon Research ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: Konstantin O. Nagornov | Anton N. Kozhinov | Édith Nicol | Oleg Yu. Tsybin | David Touboul | Alain Brunelle | Yury O. Tsybin
Source: Journal of the American Society for Mass Spectrometry (article, 2020-09-23)
Field: Chemistry — Spectroscopy

Narrow Aperture Detection Electrodes ICR Cell with Quadrupolar Ion Detection for FT-ICR MS at the Cyclotron Frequency Ion signal detection at the true (unperturbed) cyclotron frequency instead of the conventional reduced cyclotron frequency has remained a formidable challenge since the inception of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Recently, routine FT-ICR MS at the true cyclotron frequency has become a reality with the implementation of ICR cells with narrow aperture detection electrodes (NADEL). Here, we describe the development and implementation of the next generation of these cells, namely, a 2xNADEL ICR cell, which comprises four flat detect and four ∼45° cylindrical excite electrodes, enabling independent ion excitation and quadrupolar ion detection. The performance of the 2xNADEL ICR cell was evaluated on two commercial FT-ICR MS platforms, 10 T LTQ FT from Thermo Scientific and 9.4 T SolariX XR from Bruker Daltonics. The cells provided accurate mass measurements in the analyses of singly and multiply charged peptides (root-mean-square, RMS, mass error <i>Δm</i>/<i>m</i> of 90 ppb), proteins (<i>Δm</i>/<i>m</i> = 200 ppb), and petroleum fractions (<i>Δm</i>/<i>m</i> < 200 ppb). Due to the reduced influence of measured frequency on the space charge and external (trapping) electric fields, the 2xNADEL ICR cells exhibited stable performance in a wide range of trapping potentials (1-20 V). Similarly, in a 13 h rat brain MALDI imaging experiment, the RMS mass error did not exceed 600 ppb even for low signal-to-noise ratio analyte peaks. Notably, the same set of calibration constants was applicable to Fourier spectra in all pixels, reducing the need for recalibration at the individual pixel level. Overall, these results support further experimental development and fundamentals investigation of this promising technology. Fourier transform ion cyclotron resonance ; Chemistry ; Ion cyclotron resonance ; Cyclotron ; Analytical Chemistry (journal) ; Mass spectrometry ; Ion ; Chromatography Mass Spectrometry Techniques and Applications ; Analytical Chemistry and Chromatography ; Ion-surface interactions and analysis
Authors: Lina Takemaru | Gongrui Guo | Ping Zhu | Wayne A. Hendrickson | Seán McSweeney | Qun Liu
Source: Journal of Applied Crystallography (article, 2020-01-14)
Field: Materials Science — Materials Chemistry

<i>PyMDA</i>: microcrystal data assembly using Python The recent developments at microdiffraction X-ray beamlines are making microcrystals of macromolecules appealing subjects for routine structural analysis. Microcrystal diffraction data collected at synchrotron microdiffraction beamlines may be radiation damaged with incomplete data per microcrystal and with unit-cell variations. A multi-stage data assembly method has previously been designed for microcrystal synchrotron crystallography. Here the strategy has been implemented as a Python program for microcrystal data assembly (<i>PyMDA</i>). <i>PyMDA</i> optimizes microcrystal data quality including weak anomalous signals through iterative crystal and frame rejections. Beyond microcrystals, <i>PyMDA</i> may be applicable for assembling data sets from larger crystals for improved data quality. Python (programming language) ; Computer graphics (images) ; Computer science ; Programming language ; Materials science Enzyme Structure and Function ; Protein Structure and Dynamics ; Advanced Proteomics Techniques and Applications
Authors: Sujit Bidhar | N. Simos | David J. Senor | P. Hurh
Source: Nuclear Materials and Energy (article, 2020-06-15)
Field: Materials Science — Materials Chemistry

Failure investigation of nuclear grade POCO graphite target in high energy neutrino physics through numerical simulation In many high energy physics neutrino beamlines, targets are made up of isotropic POCO graphite grade for production of neutrinos for high energy particle physics research and are bombarded with highly energetic pulsed proton beam. The pulsed proton beam with a small beam size creates thermal stress waves as well as radiation damage such as displacement damage, void formation, swelling, and gas formation amongst others. As a result, after a few years of operation one of the longest operated targets appears to have undergone bulk swelling and fractured along the beam centerline. A complex interaction of dynamic loading due to beam, material degradation due to irradiation are thought to have caused such a failure. Here, we present a numerical simulation to capture the combined effects of swelling and the dynamic effect of thermal stress waves due to beam heating, to explain the failure of target. An empirical formula has been developed to take into account swelling as a function of temperature and proton fluence and has been implemented in a commercial finite element code. Extensive X-ray diffraction (XRD) were performed on graphite samples from the failed target to understand the lattice parameter changes due to irradiation and build a valid empirical model. Simulation results show that swelling plays a major role in elevating the stress state in the material exceeding the failure strength while the pulsed beam heating also introduces fatigue loading that would explain brittle fracture emanating from inside of the material and propagating outward. Such empirical formulations will help in identifying the threshold values of critical parameters to extend the service life of future multi-megawatt neutrino targets and targets in other accelerator environments. Graphite ; Materials science ; Beam (structure) ; Neutrino ; Nuclear graphite ; Irradiation ; Isotropy ; Swelling ; Proton ; Physics ; Nuclear physics ; Nuclear engineering ; Composite material ; Optics Graphite, nuclear technology, radiation studies ; Radiation Therapy and Dosimetry ; Muon and positron interactions and applications
Authors: Jos Oomens | Lisanne J. M. Kempkes | Thijs P. J. Geurts | Luuk van Dijk | Jonathan Martens | Giel Berden | P. B. Armentrout
Source: Journal of the American Society for Mass Spectrometry (article, 2020-09-02)
Field: Chemistry — Spectroscopy

Water Loss from Protonated XxxSer and XxxThr Dipeptides Gives Oxazoline—Not Oxazolone—Product Ions Neutral loss of water and ammonia are often significant fragmentation channels upon collisional activation of protonated peptides. Here, we deploy infrared ion spectroscopy to investigate the dehydration reactions of protonated AlaSer, AlaThr, GlySer, GlyThr, PheSer, PheThr, ProSer, ProThr, AsnSer, and AsnThr, focusing on the question of the structure of the resulting [M + H - H<sub>2</sub>O]<sup>+</sup> fragment ion and the site from which H<sub>2</sub>O is expelled. In all cases, the second residue of the selected peptides contains a hydroxyl moiety, so that H<sub>2</sub>O loss can potentially occur from this side-chain, as an alternative to loss from the C-terminal free acid of the dipeptide. Infrared action spectra of the product ions along with quantum-chemical calculations unambiguously show that dehydration consistently produces fragment ions containing an oxazoline moiety. This contrasts with the common oxazolone structure that would result from dehydration at the C-terminus analogous to the common b/y dissociation forming regular b<sub>2</sub>-type sequence ions. The oxazoline product structure suggests a reaction mechanism involving water loss from the Ser/Thr side-chain with concomitant nucleophilic attack of the amide carbonyl oxygen at its β-carbon, forming an oxazoline ring. However, an extensive quantum-chemical investigation comparing the potential energy surfaces for three entirely different dehydration reaction pathways indicates that it is actually the backbone amide oxygen atom that leaves as the water molecule. Chemistry ; Oxazolone ; Protonation ; Moiety ; Oxazoline ; Amide ; Side chain ; Photochemistry ; Molecule ; Stereochemistry ; Ion ; Organic chemistry Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Analytical Chemistry and Chromatography
Authors: Naveen Datt
Source: Plant Pathology & Quarantine (article, 2020-01-01)
Field: Chemistry — Inorganic Chemistry

Key transboundary plant pests of Coconut [Cocos nucifera] in the Pacific Island Countries – a biosecurity perspective The movement of plant pests and diseases from one continent or country to another bypassing physical boundary is as ancient a menace as the drift of people themselves. Many of these species pose a direct threat to food security with progressive socio-economic perils affecting the livelihoods of people. The National Plant Protection Organisation of a country is vested with legislative powers to prevent the incursion of such species through the implementation of proactive measures such as risk assessments, monitoring, surveillance and controlling human-aided pathways. The unfortunate event of an unwanted incursion brings with it challenges of early detection and immediate implementation of eradication measures which are further compounded by capability gaps and funding constraints. The success of eradication is more than often determined by quick execution of appropriate emergency response measures and flexibility to scale operations when needed. Even with extensive and exhaustive eradication efforts applied, many-a-times the National Plant Protection Organizations face unfavourable results. Coconut is an extremely important subsistence as well as an economic plant for almost all island nations in the Pacific. In this view, existing transboundary pests of coconut in the Pacific Islands basin, namely Coconut Rhinoceros Beetle-Guam biotype, Coconut Lethal Yellowing phytoplasma and the Coconut Cadang-Cadang viroid pose more than a significant threat to countries free of these pests and which have put regional National Plant Protection Organizations on high alert. Biosecurity ; Cocos nucifera ; Key (lock) ; Geography ; Perspective (graphical) ; Agroforestry ; Biology ; Ecology ; Horticulture ; Art Coconut Research and Applications ; Date Palm Research Studies
Authors: Theodore A. Uyeno | A. J. Clark
Source: Canadian Journal of Zoology (article, 2020-10-21)
Field: Materials Science — Biomaterials

On the fit of skins with a particular focus on the biomechanics of loose skins of hagfishes There is a considerable diversity in how skins fit. Here, we review the function of both tight and loose skins and note that the latter are poorly understood. Analysis of loose skin examples suggest five functional categories: (I) freedom of movement, (II) surface area enhancement, (III) increased structural extensibility, (IV) lubrication, and (V) maladaptive examples arising through sexual or artificial selection. We investigate the skins of hagfishes as a model for understanding loose skin function by examining its structure using histology, standardized puncture resistance testing using the ASTM F1306 protocol, and the effect of internal pressure using a simple inflated balloon model. Skins of hagfishes are composed of multiple layers of cross-helically wound connective tissue fibers of a 45° angle to the longitudinal axis, resulting in a skin that functions as fabric cut “on the bias”. Hagfish skins are relatively yielding; however, skin looseness adds a “structural extensibility” that may allow hagfishes to compensate for low puncture resistance. Physical balloon models, with stiff cores that limit length changes, show that only low pressures allow short loop radii without local buckling. Hagfishes represent ideal organisms for studying loose skin function because their skins seem to fit in all functionally adaptive categories. Biology ; Extensibility ; Anatomy ; Biomechanics ; Biological system ; Computer science Silk-based biomaterials and applications ; Neurobiology and Insect Physiology Research ; Cellular Mechanics and Interactions
Authors: Anthony Wang | Steven Kauwe | Ryan Murdock | Taylor D. Sparks
Source: ChemRxiv (preprint, 2020-02-20)
Field: Materials Science — Materials Chemistry

Compositionally-Restricted Attention-Based Network for Materials Property Prediction &lt;div&gt;In this paper, we demonstrate a novel application of the Transformer self-attention mechanism. Our network, the Compositionally-Restricted Attention-Based network, referred to as CrabNet, explores the area of structure-agnostic materials property predictions when only a chemical formula is provided.&lt;/div&gt;&lt;div&gt;Our results show that CrabNet's performance matches or exceeds current best practice methods on nearly all of 28 total benchmark datasets. We also demonstrate how CrabNet's architecture lends itself towards model interpretability by showing different visualization approaches that are made possible by its design.&lt;/div&gt;&lt;div&gt;We feel confident that CrabNet, and its attention-based framework, will be of keen interest to future materials informatics researchers. &lt;/div&gt;&lt;div&gt;&lt;br&gt;&lt;/div&gt;&lt;div&gt;For trained model weights, please see: http://doi.org/10.5281/zenodo.4633866&lt;/div&gt; Interpretability ; Benchmark (surveying) ; Computer science ; Informatics ; Property (philosophy) ; Visualization ; Artificial intelligence ; Transformer ; Machine learning ; Cartography ; Engineering ; Geography Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Advanced Graph Neural Networks