jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Pedro A. Sánchez | Ekaterina V. Novak | Elena S. Pyanzina | Sofia S. Kantorovich | Joan J. Cerdà | Tomàs Sintes
Source: Physical review. E (preprint, 2020-08-21)
Field: Chemistry — Physical and Theoretical Chemistry

Adsorption transition of a grafted ferromagnetic filament controlled by external magnetic fields Extensive Langevin dynamics simulations are used to characterize the adsorption transition of a flexible magnetic filament grafted onto an attractive planar surface. Our results identify different structural transitions at different ratios of the thermal energy to the surface attraction strength: filament straightening, adsorption, and the magnetic flux closure. The adsorption temperature of a magnetic filament is found to be higher in comparison to an equivalent nonmagnetic chain. The adsorption has been also investigated under the application of a static homogeneous external magnetic field. We found that the strength and the orientation of the field can be used to control the adsorption process, providing a precise switching mechanism. Interestingly, we have observed that the characteristic field strength and tilt angle at the adsorption point are related by a simple power law. Adsorption ; Protein filament ; Materials science ; Magnetic field ; Langevin dynamics ; Magnet ; Chemical physics ; Ferromagnetism ; Condensed matter physics ; Chemistry ; Physics ; Composite material ; Physical chemistry Advanced Physical and Chemical Molecular Interactions ; Cold Atom Physics and Bose-Einstein Condensates ; Advanced Thermodynamics and Statistical Mechanics
Authors: Yang Yang | Chendi Niu | Cedric E. Bobst | Igor A. Kaltashov
Source: ChemRxiv (preprint, 2020-12-16)
Field: Chemistry — Spectroscopy

Ionic Charge Manipulation Using Solution and Gas-Phase Chemistry to Facilitate Analysis of Highly Heterogeneous Protein Complexes in Native Mass Spectrometry Ionic signal in native MS typically populates high &lt;i&gt;m/z&lt;/i&gt; regions of mass spectra, which frequently extend beyond the precursor ion isolation limits of most commercial mass spectrometers. An approach explored in this work relies on adding supercharging reagents to protein solutions as a means of increasing the extent of multiple charging of non-covalent complexes in ESI MS without compromising their integrity. This shifts the ionic signal down the &lt;i&gt;m/z&lt;/i&gt; scale to the region where ion selection and isolation can be readily accomplished, followed by limited charge reduction of the isolated ionic population. The feasibility of the new approach is demonstrated using non-covalent complexes formed by hemoglobin with structurally heterogeneous haptoglobin. Chemistry ; Mass spectrometry ; Ionic bonding ; Covalent bond ; Ion ; Population ; Analytical Chemistry (journal) ; Reagent ; Chemical physics ; Physical chemistry ; Chromatography ; Organic chemistry Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Advanced Proteomics Techniques and Applications
Authors: Georgii Shamuilov | Katerina Domina | Vyacheslav V. Khardikov | Alexey Y. Nikitin | Vitaliy Goryashko
Source: Nanoscale (preprint, 2020-11-11)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Optical magnetic lens: towards actively tunable terahertz optics As we read this text, our eyes dynamically adjust the focal length to keep the image in focus on the retina. Similarly, in many optics applications the focal length must be dynamically tunable. In the quest for compactness and tunability, flat lenses based on metasurfaces were introduced. However, their dynamic tunability is still limited because their functionality mostly relies upon fixed geometry. In contrast, we put forward an original concept of a tunable Optical Magnetic Lens (OML) that focuses photon beams using a subwavelength-thin layer of a magneto-optical material in a non-uniform magnetic field. We applied the OML concept to a wide range of materials and found out that the effect of OML is present in a broad frequency range from microwaves to visible light. For terahertz light, OML can allow 50% relative tunability of the focal length on the picosecond time scale, which is of practical interest for ultrafast shaping of electron beams in microscopy. The OML based on magneto-optical natural bulk and 2D materials may find broad use in technologies such as 3D optical microscopy and acceleration of charged particle beams by THz beams. Terahertz radiation ; Optics ; Focal length ; Lens (geology) ; Magnetic lens ; Physics ; Picosecond ; Ultrashort pulse ; Magnetic field ; Focus (optics) ; Spherical aberration ; Materials science ; Optoelectronics ; Laser Metamaterials and Metasurfaces Applications ; Terahertz technology and applications ; Orbital Angular Momentum in Optics
Authors: A. W. Carbonari | Osmar Flávio da Silveira Leite Neto | R. N. Saxena | J. G. Correia | B. Bosch-Santos | Luciano Pereira | Juliana Schell | Anastasia Burimova | Eduardo Correa | Frederico A. Genezini | R. S. Freitas | D. Richard | Doru C. Lupascu | G. A. Cabrera-Pasca | Tatiane da Silva Nascimento Sales | Iberê Souza Ribeiro
Source: CERN Document Server (European Organization for Nuclear Research) (article, 2020-05-13)
Field: Chemistry — Inorganic Chemistry

The peculiarities of reduction and doping of vanadium oxides probed by TDPAC spectroscopy at ISOLDE Vanadium ; Doping ; Spectroscopy ; Materials science ; Metallurgy ; Optoelectronics ; Physics Radioactive element chemistry and processing ; Analytical chemistry methods development ; Nuclear Physics and Applications
Authors: Ina Poehner | Antonio Quotadamo | Joanna Panecka-Hofman | Rosaria Luciani | Matteo Santucci | Pasquale Linciano | Giacomo Landi | F. Di Pisa | Lucia Dello Iacono | Cecilia Pozzi | Stefano Mangani | Sheraz Gul | Gesa Witt | Bernhard Ellinger | Maria Kuzikov | Nuno Santarém | Anabela Cordeiro‐da‐Silva | Maria Paola Costi | Alberto Venturelli | Rebecca C. Wade
Source: ChemRxiv (preprint, 2020-11-23)
Field: Chemistry — Organic Chemistry

Multitarget, Selective Compound Design Yields Picomolar Inhibitors of a Kinetoplastid Pteridine Reductase 1 The optimization of compounds with multiple targets in the drug discovery cycle is a difficult multidimensional problem. Here, we present a systematic, multidisciplinary approach to the development of selective anti-parasitic compounds. Efficient microwave-assisted synthesis of pteridines along with iterations of crystallographic structure determination were used to validate computational docking predictions and support derivation of a structure-activity relationship for multitarget inhibition. This approach yielded compounds showing picomolar inhibition of T. brucei pteridine reductase 1 (PTR1), nanomolar inhibition of L. major PTR1, along with selective submicromolar inhibition of parasitic dihydrofolate reductase (DHFR). Moreover, by combining design for polypharmacology with a property-based on-parasite optimization, we found three compounds that exhibited micromolar EC50 values against T. brucei brucei, whilst retaining their target inhibition. Our results provide a basis for the further development of pteridine-based compounds and we expect our multitarget approach to be generally applicable to the design and optimization of anti-infective agents. Pteridine ; Dihydrofolate reductase ; Trypanosoma brucei ; Chemistry ; Biochemistry ; Drug discovery ; Docking (animal) ; Stereochemistry ; Computational biology ; Combinatorial chemistry ; Enzyme ; Biology Synthesis and Biological Evaluation ; Synthesis and biological activity
Authors: Ina Poehner | Antonio Quotadamo | Joanna Panecka-Hofman | Rosaria Luciani | Matteo Santucci | Pasquale Linciano | Giacomo Landi | F. Di Pisa | Lucia Dello Iacono | Cecilia Pozzi | Stefano Mangani | Sheraz Gul | Gesa Witt | Bernhard Ellinger | Maria Kuzikov | Nuno Santarém | Anabela Cordeiro‐da‐Silva | Maria Paola Costi | Alberto Venturelli | Rebecca C. Wade
Source: ChemRxiv (preprint, 2020-10-01)
Field: Chemistry — Organic Chemistry

Multitarget, Selective Compound Design Yields Picomolar Inhibitors of a Kinetoplastid Pteridine Reductase 1 The optimization of compounds with multiple targets in the drug discovery cycle is a difficult multidimensional problem. Here, we present a systematic, multidisciplinary approach to the development of selective anti-parasitic compounds. Efficient microwave-assisted synthesis of pteridines along with iterations of crystallographic structure determination were used to validate computational docking predictions and support derivation of a structure-activity relationship for multitarget inhibition. This approach yielded compounds showing picomolar inhibition of T. brucei pteridine reductase 1 (PTR1), nanomolar inhibition of L. major PTR1, along with selective submicromolar inhibition of parasitic dihydrofolate reductase (DHFR). Moreover, by combining design for polypharmacology with a property-based on-parasite optimization, we found three compounds that exhibited micromolar EC50 values against T. brucei brucei, whilst retaining their target inhibition. Our results provide a basis for the further development of pteridine-based compounds and we expect our multitarget approach to be generally applicable to the design and optimization of anti-infective agents. Pteridine ; Dihydrofolate reductase ; Trypanosoma brucei ; Chemistry ; Docking (animal) ; Drug discovery ; Biochemistry ; Stereochemistry ; Combinatorial chemistry ; Enzyme ; Computational biology ; Biology Synthesis and biological activity ; Synthesis and Biological Evaluation ; Cancer therapeutics and mechanisms
Authors: Vijendra Kumar | Abhishek Barnwal | R. K. Shukla | Jyoti Shakya
Source: arXiv (Cornell University) (preprint, 2020-06-01)
Field: Materials Science — Materials Chemistry

Enhancement of Thermal Conductivity in Polymer Composites by Maximizing Surface-Contact Area of Polymer-Filler Interface In this article we discuss in detail the effective approaches to enhance the thermal conductivity in polymer composites. It is shown from numerical simulations that maximizing interfacial area between filler and polymer enhances very significantly the effective thermal conductivity in composites. Our study outlines two main facts. (a) Although the nature of the filler's geometry plays an important role in the effective thermal conductivity, we show that among the different geometries thermal conductivity is high for those geometries for which the ratio of surface-area to volume is high. Thus non-spherical shaped fillers show high thermal conductivity compared to the spherical fillers. (b) For fillers of a particular geometry, by maximizing its surface area without changing the volume fraction of the metallic filler, the effective thermal conductivity increases. Thus, the interfacial area between filler and polymer plays an important role in the enhancement of thermal conductivity. Maximizing interfaces facilitates more routes for heat conduction through the metallic filler. Thus filler material can be transformed to result into more surface such that more interfaces between the filer polymer can be obtained. It is also observed that as this interfacial area increases, increase in effective thermal conductivity follows from linear to the logarithmic growth. It should be noted that to inherit the polymer properties there is a restriction on the upper bound of volume fraction of the fillers. The current study bring out an important step in this direction. Our results are technologically very important in designing composite polymers for better heat conduction, and are very cost-effective. This study also provides a connection between the bulk and the surface area in effectively determination of the thermal conductivity. Thermal conductivity ; Materials science ; Composite material ; Volume fraction ; Thermal conduction ; Filler (materials) ; Polymer ; Thermal contact conductance ; Composite number ; Contact area ; Conductivity ; Thermal grease ; Thermal ; Thermal resistance ; Chemistry ; Thermodynamics Thermal properties of materials ; Graphene research and applications ; High voltage insulation and dielectric phenomena
Authors: Antoine Juneau | Taylor O. Hope | Jason H. Malenfant | Mihai Mesko | Jacob A. Mcneill | Mathieu Frenette
Source: ChemRxiv (preprint, 2020-10-07)
Field: Chemistry — Organic Chemistry

Method to Predict Reagents in Iridium-Based Photoredox Catalysis Visible-light photoredox catalysts with oxidizing excited states have been broadly applied in organic synthesis. Following photon absorption by the photocatalyst, electron transfer from an organic reagent is the most common mechanistic outcome for this class of reaction. Reduction potentials for organic reagents are therefore useful to predict reactivity and DFT proved to be useful as a predictive tool in this regard. Due to the complex mechanisms that follow electron transfer, kinetics play a crucial role in the success of photoredox reactions. We extend the predictive tools of DFT to estimate the electron transfer &lt;i&gt;rates&lt;/i&gt; between an excited photocatalyst and various organic substrates. To calibrate our model, 49 electron transfer rate constants were experimentally measured in acetonitrile for the catalyst Ir[dF(CF&lt;sub&gt;3&lt;/sub&gt;)ppy]&lt;sub&gt;2&lt;/sub&gt;(dtbpy)&lt;sup&gt;+&lt;/sup&gt;. The rate constants, k&lt;i&gt;&lt;sub&gt;q&lt;/sub&gt;&lt;/i&gt;, gave a clear predictive trend when compared to calculated ionization energies in “frozen solvent”, which was a better predictor than standard reduction potentials in our case. The calculated k&lt;i&gt;&lt;sub&gt;q&lt;/sub&gt;&lt;/i&gt; gave an average error of 17% for log(k&lt;sub&gt;q&lt;/sub&gt;) values between 4 and 11. This simple method can predict the reactivity of hundreds of reagents &lt;i&gt;in silico&lt;/i&gt;. Notably, the calculations offered unexpected insight that we could translate into success for the C-H activation of acetylacetone as a proof-of-concept. Chemistry ; Reagent ; Reactivity (psychology) ; Electron transfer ; Reaction rate constant ; Catalysis ; Oxidizing agent ; Excited state ; Photocatalysis ; Acetonitrile ; Photochemistry ; Kinetics ; Physical chemistry ; Organic chemistry ; Physics Radical Photochemical Reactions ; Advanced Photocatalysis Techniques ; CO2 Reduction Techniques and Catalysts
Authors: Kevin C. Slep | Amy E. Howard | Jaime C. Fox
Source: UNC Libraries (article, 2020-11-09)
Field: Chemistry — Organic Chemistry

Drosophila melanogaster Mini Spindles TOG3 Utilizes Unique Structural Elements to Promote Domain Stability and Maintain a TOG1- and TOG2-like Tubulin-binding Surface Microtubule-associated proteins regulate microtubule (MT) dynamics spatially and temporally, which is essential for proper formation of the bipolar mitotic spindle. The XMAP215 family is comprised of conserved microtubule-associated proteins that use an array of tubulin-binding tumor overexpressed gene (TOG) domains, consisting of six (A–F) Huntingtin, elongation factor 3, protein phosphatase 2A, target of rapamycin (HEAT) repeats, to robustly increase MT plus-end polymerization rates. Recent work showed that TOG domains have differentially conserved architectures across the array, with implications for position-dependent TOG domain tubulin binding activities and function within the XMAP215 MT polymerization mechanism. Although TOG domains 1, 2, and 4 are well described, structural and mechanistic information characterizing TOG domains 3 and 5 is outstanding. Here, we present the structure and characterization of Drosophila melanogaster Mini spindles (Msps) TOG3. Msps TOG3 has two unique features as follows: the first is a C-terminal tail that stabilizes the ultimate four HEAT repeats (HRs), and the second is a unique architecture in HR B. Structural alignments of TOG3 with other TOG domain structures show that the architecture of TOG3 is most similar to TOG domains 1 and 2 and diverges from TOG4. Docking TOG3 onto recently solved Stu2 TOG1· and TOG2·tubulin complex structures suggests that TOG3 uses similarly conserved tubulin-binding intra-HEAT loop residues to engage α- and β-tubulin. This indicates that TOG3 has maintained a TOG1- and TOG2-like TOG-tubulin binding mode despite structural divergence. The similarity of TOG domains 1–3 and the divergence of TOG4 suggest that a TOG domain array with polarized structural diversity may play a key mechanistic role in XMAP215-dependent MT polymerization activity. Drosophila melanogaster ; Tubulin ; Cell biology ; Drosophila (subgenus) ; Domain (mathematical analysis) ; Biology ; Microtubule ; Neuroscience ; Genetics ; Mathematics Synthetic Organic Chemistry Methods ; 14-3-3 protein interactions
Authors: Gwladys Nizou | Enikő Molnár | Nadège Hamon | Ferenc K. Kalman | Olivier Fougère | Olivier Rousseaux | David Esteban‐Gómez | Carlos Platas‐Iglesias | Maryline Beyler | Gyula Tircsó | Raphaël Tripier
Source: ChemRxiv (preprint, 2020-11-09)
Field: Materials Science — Materials Chemistry

Pyclen-Based Ligands Bearing Pendant Picolinate Arms for Gadolinium Complexation We report the synthesis of two pyclen-based regioisomer ligands (pyclen = 3,6,9,15-tetraazabicyclo[9.3.1]pentadeca1(15),11,13-triene) functionalized with picolinic acid pendant arms either at positions 3,9-pc2pa (L5) or 3,6-pc2pa (L6) of the macrocyclic fragment. The ligands were prepared by regiospecific protection of one of the amine nitrogen atom of the macrocycle using Boc and Alloc protecting groups, respectively. The X-ray structure of the Gd(III) complex of L5 contains trinuclear [(GdL5)3(H2O)3] 3+ entities in which the monomeric units are joined by 2- 1 : 1 carboxylate groups. However, the 1H and 89Y NMR spectra of its Y(III) analogue support the formation of monomeric complexes in solution. The Tb(III) complexes are highly luminescent, with emission quantum yields of up to 50% for [TbL5] + . The luminescence lifetimes recorded in H2O and D2O solutions indicate the presence of a water molecule coordinated to the metal ion, as also evidenced by the 1H relaxivities measured for the Gd(III) analogues. The Gd(III) complexes present very different exchange rates of the coordinated water molecule (kex 298 = 87.1 and 1.06 106 s -1 for [GdL5] + and [GdL6] + , respectively). The very high water exchange rate of [GdL5] + is associated to the steric hindrance originated by the coordination of the ligand around the water binding site, which favors a dissociatively activated water exchange process. The Gd(III) complexes present rather high thermodynamic stabilities (logKGdL = 20.47 and 19.77 for [GdL5] + and [GdL6] + , respectively). Furthermore, these complexes are remarkably inert with respect to their acid-assisted dissociation, in particular the complex of L5. Chemistry ; Steric effects ; Ligand (biochemistry) ; Carboxylate ; Monomer ; Molecule ; Crystallography ; Luminescence ; Denticity ; Picolinic acid ; Stereochemistry ; Crystal structure ; Organic chemistry ; Polymer Lanthanide and Transition Metal Complexes ; Radioactive element chemistry and processing ; DNA Repair Mechanisms
Authors: Carlos E. Rodríguez López | Benke Hong | Christian Paetz | Yoko Nakamura | Κωνσταντίνος Κουδούνας | Valentina Passeri | Luciana Baldoni | Fiammetta Alagna | Ornella Calderini | Sarah E. O’Connor
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2020-08-28)
Field: Chemistry — Organic Chemistry

Two bi-functional cytochrome P450 CYP72 enzymes from olive ( <i>Olea europaea</i> ) catalyze the oxidative C-C bond cleavage in the biosynthesis of secoxy-iridoids - flavor and quality determinants in olive oil Summary Olive ( Olea europaea ) is an important crop in Europe, with high cultural, economic, and nutritional significance. Olive oil flavor and quality depend on phenolic secoiridoids, but the biosynthetic pathway of these iridoids remains largely uncharacterized. We discovered two novel, bi-functional cytochrome P450 enzymes, catalysing the rare oxidative C-C bond cleavage of 7-epi-loganin to produce oleoside methyl ester (OeOMES) and secoxyloganin (OeSXS), both through a ketologanin intermediary. Although these enzymes are homologous to the previously reported Catharanthus roseus Secologanin Synthase (CrSLS), the substrate and product profiles differ. Biochemical assays provided mechanistic insights into the two-step OeOMES and CrSLS reactions. Model-guided mutations of OeOMES changed the product profile in a predictable manner, revealing insights into the molecular basis for this change in product specificity. Our results suggest that, in contrast to published hypotheses, in planta production of secoxy-iridoids is secologanin independent. Notably, sequence data of cultivated and wild olives, points to a relation between domestication and OeOMES expression. Thus, the discovery of this key biosynthetic gene suggests a link between domestication and secondary metabolism, and could potentially be used as a genetic marker to guide next-generation breeding programs. Olea ; Biochemistry ; Cytochrome P450 ; Biology ; Enzyme ; Botany Edible Oils Quality and Analysis ; Plant biochemistry and biosynthesis ; Essential Oils and Antimicrobial Activity
Authors: Kankan Qin | Rui F. P. Pereira | Thibaud Coradin | V. de Zea Bermudez | Francisco Manuel Braz Fernandes
Source: ChemRxiv (preprint, 2020-11-12)
Field: Materials Science — Biomaterials

Redesigned Silk: A New Macroporous Biomaterial Platform for Antimicrobial Dermal Patches with Unique Exudate Wicking Ability Silk is one of the most important materials in the history of medical practice. Owing to its excellent strength, biocompatibility and degradability, silk from Bombyx mori – which is structured as a concentric assembly of silk fibroin (SF) coated by a sheath of sericin (SS) – has long been used for wound treatment. Here, we recapitulate for the first time the topology of native silk fibers using a radically new materials design-oriented approach to achieve unprecedented porous dermal patches suitable for controlled drug delivery. The method implies four steps: (1) removing SS; (2) creating anisotropic macroporosity in SF via ice templating; (3) stabilizing the SF foam with a methanolic solution of Rifamycin (Rif) antibiotic; and (4) coating Rif-loaded redesigned SF foams with a SS sheath. The core-shell SS@SF foams exhibit water wicking properties accommodate up to ~20% lateral deformation. Moreover, monitoring of antibacterial activity against Staphylococcus aureus revealed that the SS@SF foams’ Rif release extended up to 9 days. We anticipate that reverse-engineering of silk foams opens exciting new avenues towards the fabrication of advanced drug eluting silk-based biomaterial platforms with improved performance. The present approach can be generalizable to re-build multicomponent biological materials with tunable porosity.&lt;br&gt; Fibroin ; SILK ; Materials science ; Biocompatibility ; Biomaterial ; Porosity ; Drug delivery ; Bombyx mori ; Coating ; Textile ; Composite material ; Nanotechnology ; Chemistry Silk-based biomaterials and applications ; Biochemical and Structural Characterization ; RNA Interference and Gene Delivery