jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Lukas Tendera | Moritz Helm | Mirjam J. Krahfuß | Maximilian W. Kuntze‐Fechner | Udo Radius
Source: Chemistry - A European Journal (article, 2021-10-29)
Field: Chemistry — Organic Chemistry

Case Study of <i>N</i>‐<sup><i>i</i></sup>Pr versus <i>N</i>‐Mes Substituted NHC Ligands in Nickel Chemistry: The Coordination and Cyclotrimerization of Alkynes at [Ni(NHC)<sub>2</sub>] A case study on the effect of the employment of two different NHC ligands in complexes [Ni(NHC)<sub>2</sub> ] (NHC=<sup>i</sup> Pr<sub>2</sub> Im<sup>Me</sup> 1<sup>Me</sup> , Mes<sub>2</sub> Im 2) and their behavior towards alkynes is reported. The reaction of a mixture of [Ni<sub>2</sub> (<sup>i</sup> Pr<sub>2</sub> Im<sup>Me</sup> )<sub>4</sub> (μ-(η<sup>2</sup> : η<sup>2</sup> )-COD)] B/ [Ni(<sup>i</sup> Pr<sub>2</sub> Im<sup>Me</sup> )<sub>2</sub> (η<sup>4</sup> -COD)] B' or [Ni(Mes<sub>2</sub> Im)<sub>2</sub> ] 2, respectively, with alkynes afforded complexes [Ni(NHC)<sub>2</sub> (η<sup>2</sup> -alkyne)] (NHC=<sup>i</sup> Pr<sub>2</sub> Im<sup>Me</sup> : alkyne=MeC≡CMe 3, H<sub>7</sub> C<sub>3</sub> C≡CC<sub>3</sub> H<sub>7</sub> 4, PhC≡CPh 5, MeOOCC≡CCOOMe 6, Me<sub>3</sub> SiC≡CSiMe<sub>3</sub> 7, PhC≡CMe 8, HC≡CC<sub>3</sub> H<sub>7</sub> 9, HC≡CPh 10, HC≡C(p-Tol) 11, HC≡C(4-<sup>t</sup> Bu-C<sub>6</sub> H<sub>4</sub> ) 12, HC≡CCOOMe 13; NHC=Mes<sub>2</sub> Im: alkyne=MeC≡CMe 14, MeOOCC≡CCOOMe 15, PhC≡CMe 16, HC≡C(4-<sup>t</sup> Bu-C<sub>6</sub> H<sub>4</sub> ) 17, HC≡CCOOMe 18). Unusual rearrangement products 11 a and 12 a were identified for the complexes of the terminal alkynes HC≡C(p-Tol) and HC≡C(4-<sup>t</sup> Bu-C<sub>6</sub> H<sub>4</sub> ), 11 and 12, which were formed by addition of a C-H bond of one of the NHC N-<sup>i</sup> Pr methyl groups to the C≡C triple bond of the coordinated alkyne. Complex 2 catalyzes the cyclotrimerization of 2-butyne, 4-octyne, diphenylacetylene, dimethyl acetylendicarboxylate, 1-pentyne, phenylacetylene and methyl propiolate at ambient conditions, whereas 1<sup>Me</sup> is not a good catalyst. The reaction of 2 with 2-butyne was monitored in some detail, which led to a mechanistic proposal for the cyclotrimerization at [Ni(NHC)<sub>2</sub> ]. DFT calculations reveal that the differences between 1<sup>M</sup> <sup>e</sup> and 2 for alkyne cyclotrimerization lie in the energy profile of the initiation steps, which is very shallow for 2, and each step is associated with only a moderate energy change. The higher stability of 3 compared to 14 is attributed to a better electron transfer from the NHC to the metal to the alkyne ligand for the N-alkyl substituted NHC, to enhanced Ni-alkyne backbonding due to a smaller C<sub>NHC</sub> -Ni-C<sub>NHC</sub> bite angle, and to less steric repulsion of the smaller NHC <sup>i</sup> Pr<sub>2</sub> Im<sup>Me</sup> . Alkyne ; Diphenylacetylene ; Chemistry ; Phenylacetylene ; Medicinal chemistry ; Catalysis ; Triple bond ; Carbene ; Stereochemistry ; Double bond ; Organic chemistry N-Heterocyclic Carbenes in Organic and Inorganic Chemistry ; Organometallic Complex Synthesis and Catalysis ; Catalytic Alkyne Reactions
Authors: Beena Mol | Ansar Ereath Beeran | Prasad S. Jayaram | Prabha Prakash | Ramapurath S. Jayasree | Senoy Thomas | P. S. Baby Chakrapani | M. R. Anantharaman | M. Junaid Bushiri
Source: Journal of Materials Science Materials in Medicine (article, 2021-08-25)
Field: Materials Science — Polymers and Plastics

Radio frequency plasma assisted surface modification of Fe3O4 nanoparticles using polyaniline/polypyrrole for bioimaging and magnetic hyperthermia applications Surface modification of superparamagnetic Fe<sub>3</sub>O<sub>4</sub> nanoparticles using polymers (polyaniline/polypyrrole) was done by radio frequency (r.f.) plasma polymerization technique and characterized by XRD, TEM, TG/DTA and VSM. Surface-passivated Fe<sub>3</sub>O<sub>4</sub> nanoparticles with polymers were having spherical/rod-shaped structures with superparamagnetic properties. Broad visible photoluminescence emission bands were observed at 445 and 580 nm for polyaniline-coated Fe<sub>3</sub>O<sub>4</sub> and at 488 nm for polypyrrole-coated Fe<sub>3</sub>O<sub>4</sub>. These samples exhibit good fluorescence emissions with L929 cellular assay and were non-toxic. Magnetic hyperthermia response of Fe<sub>3</sub>O<sub>4</sub> and polymer (polyaniline/polypyrrole)-coated Fe<sub>3</sub>O<sub>4</sub> was evaluated and all the samples exhibit hyperthermia activity in the range of 42-45 °C. Specific loss power (SLP) values of polyaniline and polypyrrole-coated Fe<sub>3</sub>O<sub>4</sub> nanoparticles (5 and 10 mg/ml) exhibit a controlled heat generation with an increase in the magnetic field. Polypyrrole ; Polyaniline ; Materials science ; Superparamagnetism ; Nanoparticle ; Polymerization ; Surface modification ; Chemical engineering ; Conductive polymer ; Magnetic nanoparticles ; Polymer ; Analytical Chemistry (journal) ; Nuclear chemistry ; Nanotechnology ; Magnetization ; Composite material ; Chemistry ; Magnetic field ; Organic chemistry Conducting polymers and applications ; Nanoparticle-Based Drug Delivery ; Electrospun Nanofibers in Biomedical Applications
Authors: Teodora Andrian | Sílvia Pujals | Lorenzo Albertazzi
Source: Nanoscale Advances (article, 2021-01-01)
Field: Materials Science — Biomaterials

Quantifying the effect of PEG architecture on nanoparticle ligand availability using DNA-PAINT The importance of PEG architecture on nanoparticle (NP) functionality is known but still difficult to investigate, especially at a single particle level. Here, we apply DNA Point Accumulation for Imaging in Nanoscale Topography (DNA-PAINT), a super-resolution microscopy (SRM) technique, to study the surface functionality in poly(lactide-<i>co</i>-glycolide)-poly(ethylene glycol) (PLGA-PEG) NPs with different PEG structures. We demonstrated how the length of the PEG spacer can influence the accessibility of surface chemical functionality, highlighting the importance of SRM techniques to support the rational design of functionalized NPs. PEG ratio ; Nanoparticle ; Ethylene glycol ; Rational design ; Nanotechnology ; Materials science ; Nanoscopic scale ; Surface modification ; Ligand (biochemistry) ; Colloidal gold ; DNA ; PLGA ; Resolution (logic) ; Chemical engineering ; Chemistry ; Computer science ; Engineering ; Biochemistry ; Receptor Nanoparticle-Based Drug Delivery ; Near-Field Optical Microscopy ; Advanced Fluorescence Microscopy Techniques
Authors: William Bro‐Jørgensen | Marc H. Garner | Gemma C. Solomon
Source: The Journal of Physical Chemistry A (article, 2021-09-07)
Field: Chemistry — Organic Chemistry

Quantification of the Helicality of Helical Molecular Orbitals The frontier molecular orbital (MO) topology of linear carbon molecules, such as polyynes, can be visually identified as helices.However, there is no clear way to quantify the helical curvature of these -MOs, and it is thus challenging to quantify correlations between the helical curvature and molecular properties.In this paper, we develop a method that enables us to compute the helical curvature of MOs based on their nodal planes.Using this method, we define a robust way of quantifying the helical nature of MOs (helicality) by their deviation from a perfect helix.We explore several limiting cases, including polyynes, metallacumulenes, cyclic allenes, and spiroconjugated systems, where the change in helical curvature is subtle yet clearly highlighted with this method.For example, we show that strain only has a minor effect on the helicality of the frontier orbitals of cycloallenes and that the MOs of spiroconjugated systems are close to perfect helices around the spiro-carbon.Our work provides a well-defined method for assessing orbital helicality beyond visual inspection of MO isosurfaces, thus paving the way for future studies of how the helicality of -MOs affects molecular properties. Curvature ; Molecular orbital ; Atomic orbital ; Limiting ; Helix (gastropod) ; Physics ; Topology (electrical circuits) ; Molecule ; Materials science ; Computer science ; Mathematics ; Geometry ; Combinatorics ; Quantum mechanics ; Biology ; Engineering Synthesis and Properties of Aromatic Compounds ; Fullerene Chemistry and Applications ; Catalysis and Oxidation Reactions
Authors: Andrey A. Koverga | Elizabeth Flórez | Carlos Jimenez‐Orozco | José A. Rodríguez
Source: Physical Chemistry Chemical Physics (article, 2021-01-01)
Field: Materials Science — Materials Chemistry

Spot the difference: hydrogen adsorption and dissociation on unsupported platinum and platinum-coated transition metal carbides Hydrogenation reactions are involved in several processes in heterogeneous catalysis. Platinum is the best-known catalyst; however, there are limitations to its practical use. Therefore, it is necessary to explore alternative materials and transition metal carbides (TMCs) have emerged as potential candidates. We explore the possibility of using cheap TMCs as supports for a Pt monolayer, aiming to reduce the amount of the noble metal in the catalyst without a significant loss of its activity towards H<sub>2</sub> dissociation. Hence, analyzing H<sub>2</sub> dissociation from a fundamental point of view is a necessary step towards a further practical catalyst. By means of periodic DFT calculations, we analyze H<sub>2</sub> adsorption and dissociation on Pt/β-Mo<sub>2</sub>C and Pt/α-WC surfaces, as a function of hydrogen surface coverage (<i>Θ</i><sub>H</sub>), resembling a more realistic model of a catalyst. H<sub>2</sub> dissociation rates were analyzed as a function of the reaction temperature. The results show that Pt/C-WC and Pt/Mo-Mo<sub>2</sub>C have a Pt-like behavior for H<sub>2</sub> dissociation at <i>Θ</i><sub>H</sub> > 1/2 ML. At a particular temperature of 298 K, Pt/C-WC and Pt/Mo-Mo2C have low energy barriers for H<sub>2</sub>* → 2H* (0.13 and 0.11 eV, respectively), close to the value of Pt (0.06 eV). For the highest coverage, <i>i.e. Θ</i><sub>H</sub> = 1, Pt/C-WC has a lower activation energy and a higher reaction rate than Pt. Finally, the H<sub>2</sub> dissociation rate is higher in Pt/Mo-Mo<sub>2</sub>C than in Pt when increasing the temperature above 298 K. Our results put Pt/C-WC and Pt/Mo-Mo<sub>2</sub>C under the spotlight as potential catalysts for H<sub>2</sub> dissociation, with a similar performance to Pt, paving the way for further experimental and/or theoretical studies, addressing the capability of Pt/TMC as practical catalysts in hydrogenation reactions. Platinum ; Transition metal ; Dissociation (chemistry) ; Hydrogen ; Carbide ; Adsorption ; Inorganic chemistry ; Materials science ; Metal ; Chemistry ; Physical chemistry ; Metallurgy ; Catalysis ; Organic chemistry Catalytic Processes in Materials Science ; Catalysis and Hydrodesulfurization Studies ; Nanomaterials for catalytic reactions
Authors: Denis Alikin | А. С. Абрамов | A. P. Turygin | Anton V. Ievlev | V. I. Pryakhina | D. V. Karpinsky | Qingyuan Hu | Li Jin | V. Ya. Shur | Alexander Tselev | Andréi L. Kholkin
Source: Small Methods (article, 2021-12-29)
Field: Materials Science — Materials Chemistry

Exploring Charged Defects in Ferroelectrics by the Switching Spectroscopy Piezoresponse Force Microscopy Monitoring the charged defect concentration at the nanoscale is of critical importance for both the fundamental science and applications of ferroelectrics. However, up-to-date, high-resolution study methods for the investigation of structural defects, such as transmission electron microscopy, X-ray tomography, etc., are expensive and demand complicated sample preparation. With an example of the lanthanum-doped bismuth ferrite ceramics, a novel method is proposed based on the switching spectroscopy piezoresponse force microscopy (SSPFM) that allows probing the electric potential from buried subsurface charged defects in the ferroelectric materials with a nanometer-scale spatial resolution. When compared with the composition-sensitive methods, such as neutron diffraction, X-ray photoelectron spectroscopy, and local time-of-flight secondary ion mass spectrometry, the SSPFM sensitivity to the variation of the electric potential from the charged defects is shown to be equivalent to less than 0.3 at% of the defect concentration. Additionally, the possibility to locally evaluate dynamics of the polarization screening caused by the charged defects is demonstrated, which is of significant interest for further understanding defect-mediated processes in ferroelectrics. Piezoresponse force microscopy ; Materials science ; Ferroelectricity ; Microscopy ; Nanoscopic scale ; X-ray photoelectron spectroscopy ; Nanometre ; Bismuth ferrite ; Spectroscopy ; Transmission electron microscopy ; Analytical Chemistry (journal) ; Optoelectronics ; Dielectric ; Nanotechnology ; Optics ; Nuclear magnetic resonance ; Chemistry ; Multiferroics ; Physics Ferroelectric and Piezoelectric Materials ; Electronic and Structural Properties of Oxides ; Multiferroics and related materials
Authors: M. Pathania | T. Tosi | Charlotte Millership | Fumiya Hoshiga | Rhodri M. L. Morgan | Paul S. Freemont | Angelika Gründling
Source: Journal of Biological Chemistry (article, 2021-10-21)
Field: Materials Science — Materials Chemistry

Structural basis for the inhibition of the Bacillus subtilis c-di-AMP cyclase CdaA by the phosphoglucomutase GlmM Cyclic-di-adenosine monophosphate (c-di-AMP) is an important nucleotide signaling molecule that plays a key role in osmotic regulation in bacteria. c-di-AMP is produced from two molecules of ATP by proteins containing a diadenylate cyclase (DAC) domain. In Bacillus subtilis, the main c-di-AMP cyclase, CdaA, is a membrane-linked cyclase with an N-terminal transmembrane domain followed by the cytoplasmic DAC domain. As both high and low levels of c-di-AMP have a negative impact on bacterial growth, the cellular levels of this signaling nucleotide are tightly regulated. Here we investigated how the activity of the B. subtilis CdaA is regulated by the phosphoglucomutase GlmM, which has been shown to interact with the c-di-AMP cyclase. Using the soluble B. subtilis CdaA<sub>CD</sub> catalytic domain and purified full-length GlmM or the GlmM<sub>F369</sub> variant lacking the C-terminal flexible domain 4, we show that the cyclase and phosphoglucomutase form a stable complex in vitro and that GlmM is a potent cyclase inhibitor. We determined the crystal structure of the individual B. subtilis CdaA<sub>CD</sub> and GlmM homodimers and of the CdaA<sub>CD</sub>:GlmM<sub>F369</sub> complex. In the complex structure, a CdaA<sub>CD</sub> dimer is bound to a GlmM<sub>F369</sub> dimer in such a manner that GlmM blocks the oligomerization of CdaA<sub>CD</sub> and formation of active head-to-head cyclase oligomers, thus suggesting a mechanism by which GlmM acts as a cyclase inhibitor. As the amino acids at the CdaA<sub>CD</sub>:GlmM interphase are conserved, we propose that the observed mechanism of inhibition of CdaA by GlmM may also be conserved among Firmicutes. Phosphoglucomutase ; Bacillus subtilis ; Adenylate kinase ; Biology ; Cyclase ; Chemistry ; Biochemistry ; Molecular biology ; Genetics ; Enzyme ; Bacteria Enzyme Structure and Function ; Biochemical and Molecular Research ; Bacterial Genetics and Biotechnology
Authors: Kevin M. Blum | Lauren Roby | Jacob C. Zbinden | Yu‐Chun Chang | Gabriel Mirhaidari | James W. Reinhardt | Tai Yi | Jenny C. Barker | Christopher K. Breuer
Source: Scientific Reports (article, 2021-04-13)
Field: Materials Science — Biomaterials

Sex and Tamoxifen confound murine experimental studies in cardiovascular tissue engineering Tissue engineered vascular grafts hold promise for the creation of functional blood vessels from biodegradable scaffolds. Because the precise mechanisms regulating this process are still under investigation, inducible genetic mouse models are an important and widely used research tool. However, here we describe the importance of challenging the baseline assumption that tamoxifen is inert when used as a small molecule inducer in the context of cardiovascular tissue engineering. Employing a standard inferior vena cava vascular interposition graft model in C57BL/6 mice, we discovered differences in the immunologic response between control and tamoxifen-treated animals, including occlusion rate, macrophage infiltration and phenotype, the extent of foreign body giant cell development, and collagen deposition. Further, differences were noted between untreated males and females. Our findings demonstrate that the host-response to materials commonly used in cardiovascular tissue engineering is sex-specific and critically impacted by exposure to tamoxifen, necessitating careful model selection and interpretation of results. Tamoxifen ; Context (archaeology) ; Medicine ; Tissue engineering ; Bioinformatics ; Biology ; Pathology ; Internal medicine ; Biomedical engineering Electrospun Nanofibers in Biomedical Applications ; RNA Interference and Gene Delivery ; Tissue Engineering and Regenerative Medicine
Authors: Daniel Andres‐Penares | Mojtaba Karimi Hábil | Alejandro Molina‐Sánchez | Carlos J. Zapata-Rodrı́guez | Juan P. Martínez‐Pastor | Juan F. Sánchez‐Royo
Source: Communications Materials (article, 2021-05-26)
Field: Materials Science — Materials Chemistry

Out-of-plane trion emission in monolayer WSe2 revealed by whispering gallery modes of dielectric microresonators Abstract The manipulation of light emitted by two-dimensional semiconductors grounds forthcoming technologies in the field of on-chip communications. However, these technologies require from the so elusive out-of-plane photon sources to achieve an efficient coupling of radiated light into planar devices. Here we propose a versatile spectroscopic method that enables the identification of the out-of-plane component of dipoles. The method is based on the selective coupling of light emitted by in-plane and out-of-plane dipoles to the whispering gallery modes of spherical dielectric microresonators, in close contact to them. We have applied this method to demonstrate the existence of dipoles with an out-of-plane orientation in monolayer WSe 2 at room temperature. Micro-photoluminescent measurements, numerical simulations based on finite element methods, and ab-initio calculations have identified trions as the source responsible for this out-of-plane emission, opening new routes for realizing on-chip integrated systems with applications in information processing and quantum communications. Dipole ; Whispering-gallery wave ; Trion ; Whispering gallery ; Dielectric ; Optoelectronics ; Plane (geometry) ; Planar ; Coupling (piping) ; Semiconductor ; Materials science ; Monolayer ; Optics ; Physics ; Photoluminescence ; Nanotechnology ; Resonator ; Computer science ; Geometry ; Quantum mechanics 2D Materials and Applications ; Photonic and Optical Devices ; Molecular Junctions and Nanostructures
Authors: Edwin Lazo | Stephen Antonelli | Jun Aishima | H. J. Bernstein | Dileep Bhogadi | Martin R. Fuchs | Nicolas Guichard | Seán McSweeney | Stuart Myers | Kun Qian | Dieter K. Schneider | Grace Shea-McCarthy | John M. Skinner | Robert M. Sweet | Lin Yang | Jean Jakoncic
Source: Journal of Synchrotron Radiation (article, 2021-08-23)
Field: Materials Science — Materials Chemistry

Robotic sample changers for macromolecular X-ray crystallography and biological small-angle X-ray scattering at the National Synchrotron Light Source II Here we present two robotic sample changers integrated into the experimental stations for the macromolecular crystallography (MX) beamlines AMX and FMX, and the biological small-angle scattering (bioSAXS) beamline LiX. They enable fully automated unattended data collection and remote access to the beamlines. The system designs incorporate high-throughput, versatility, high-capacity, resource sharing and robustness. All systems are centered around a six-axis industrial robotic arm coupled with a force torque sensor and in-house end effectors (grippers). They have the same software architecture and the facility standard EPICS-based BEAST alarm system. The MX system is compatible with SPINE bases and Unipucks. It comprises a liquid nitrogen dewar holding 384 samples (24 Unipucks) and a stay-cold gripper, and utilizes machine vision software to track the sample during operations and to calculate the final mount position on the goniometer. The bioSAXS system has an in-house engineered sample storage unit that can hold up to 360 samples (20 sample holders) which keeps samples at a user-set temperature (277 K to 300 K). The MX systems were deployed in early 2017 and the bioSAXS system in early 2019. Beamline ; Goniometer ; Software ; Synchrotron ; Grippers ; Sample (material) ; Robotic arm ; Computer hardware ; Computer science ; Materials science ; Optics ; Mechanical engineering ; Physics ; Engineering ; Operating system Enzyme Structure and Function ; Protein Structure and Dynamics ; Biochemical and Molecular Research
Authors: Marjan Hadian-Jazi | Alireza Sadri | Anton Barty | Oleksandr Yefanov | M. Galchenkova | D. Oberthüer | Dana Komadina | W. Brehm | Henry Kirkwood | Grant Mills | Raphaël de Wijn | Romain Letrun | Marco Kloos | Mohammad Vakili | Luca Gelisio | Connie Darmanin | Adrian P. Mancuso⋈ | Henry N. Chapman | Brian Abbey
Source: Journal of Applied Crystallography (article, 2021-09-13)
Field: Materials Science — Materials Chemistry

Data reduction for serial crystallography using a robust peak finder A peak-finding algorithm for serial crystallography (SX) data analysis based on the principle of 'robust statistics' has been developed. Methods which are statistically robust are generally more insensitive to any departures from model assumptions and are particularly effective when analysing mixtures of probability distributions. For example, these methods enable the discretization of data into a group comprising inliers (<i>i.e.</i> the background noise) and another group comprising outliers (<i>i.e.</i> Bragg peaks). Our robust statistics algorithm has two key advantages, which are demonstrated through testing using multiple SX data sets. First, it is relatively insensitive to the exact value of the input parameters and hence requires minimal optimization. This is critical for the algorithm to be able to run unsupervised, allowing for automated selection or 'vetoing' of SX diffraction data. Secondly, the processing of individual diffraction patterns can be easily parallelized. This means that it can analyse data from multiple detector modules simultaneously, making it ideally suited to real-time data processing. These characteristics mean that the robust peak finder (RPF) algorithm will be particularly beneficial for the new class of MHz X-ray free-electron laser sources, which generate large amounts of data in a short period of time. Reduction (mathematics) ; Data reduction ; Algorithm ; Discretization ; Computer science ; Statistics ; Probability and statistics ; Mathematics ; Mathematical analysis ; Geometry Crystallization and Solubility Studies ; X-ray Diffraction in Crystallography ; Computational Drug Discovery Methods