jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Mengjie Wang | Lanping Dang | Wan Xu | Zhiying Ma | Liuliu Shao | Guangxia Wang | Chunli Li | Hua Wang
Source: Beilstein Journal of Organic Chemistry (article, 2022-07-08)
Field: Chemistry — Organic Chemistry

Thiophene/selenophene-based S-shaped double helicenes: regioselective synthesis and structures 2,5-Di(trimethylsilanyl)dithieno[2,3-<i>b</i>:3',2'-<i>d</i>]thiophene ((TMS)<sub>2</sub>-<i>bb</i>-<b>DTT</b>), 2,5-di(trimethylsilanyl)diseleno[2,3-<i>b</i>:3',2'-<i>d</i>]thiophene ((TMS)<sub>2</sub>-<i>bb</i>-<b>DST</b>), and 2,5-di(trimethylsilanyl)diseleno[2,3-<i>b</i>:3',2'-<i>d</i>] selenophene ((TMS)<sub>2</sub>-<i>bb</i>-<b>DSS</b>) were used as starting materials to synthesize three S-shaped double helicenes (i.e., <b>DH</b>-<b>1</b>, <b>DH</b>-<b>2</b>, and <b>DH</b>-<b>3</b>) through monobromination, formylation, the Wittig reaction, and double oxidative photocyclization. The photocyclization was a highly regioselective process. The molecular structures of <b>DH</b>-<b>1</b> and <b>DH</b>-<b>2</b> were confirmed by X-ray single-crystal analysis. Multiple intermolecular interactions, such as C-S, C-Se, S-S, S-Se, and Se-Se, were observed in the crystal packing structures of these compounds. Spectroscopic results and our previous work showed that the combination of molecular structure change and heteroatom replacement from S to Se could precisely modulate molecular energy levels. Thiophene ; Chemistry ; Regioselectivity ; Formylation ; Heteroatom ; Wittig reaction ; Double bond ; Crystal structure ; Stereochemistry ; Intermolecular force ; Ring (chemistry) ; Crystallography ; Molecule ; Organic chemistry ; Catalysis Synthesis and Properties of Aromatic Compounds ; Porphyrin and Phthalocyanine Chemistry ; Photochromic and Fluorescence Chemistry
Authors: Kristina Wicht | Mathijs Baert | Norwin von Doehren | Gert Desmet | André de Villiers | Frédéric Lynen
Source: Journal of Chromatography A (article, 2022-10-20)
Field: Chemistry — Spectroscopy

Speeding up temperature-responsive × reversed-phase comprehensive liquid chromatography through the combined exploitation of temperature and flow rate gradients Chemistry ; Volumetric flow rate ; Chromatography ; Analyte ; Temperature gradient ; Aqueous solution ; Analytical Chemistry (journal) ; Flow (mathematics) ; Polymer ; Phase (matter) ; Mechanics Analytical Chemistry and Chromatography ; Microfluidic and Capillary Electrophoresis Applications ; Chromatography in Natural Products
Authors: Nzar Rauf Abdullah | Botan Jawdat Abdullah | Chi‐Shung Tang | Viðar Guðmundsson
Source: arXiv (Cornell University) (preprint, 2022-01-01)
Field: Materials Science — Materials Chemistry

Enhanced ultraviolet absorption in BN monolayers caused by tunable buckling The optical properties of a hexagonal Boron Nitride (BN) monolayer across the UV spectrum are studied by tuning its planar buckling. The strong $\sigma\text{-}\sigma$ bond through sp$^2$ hybridization of a flat BN monolayer can be changed to a stronger $\sigma\text{-}\pi$ bond through sp$^3$ hybridization by increasing the planar buckling. This gives rise to the $s$- and $p$-orbital contributions to form a density of states around the Fermi energy, and these states dislocate to a lower energy in the presence of an increased planar buckling. Consequently, the wide band gap of a flat BN monolayer is reduced to a smaller band gap in a buckled BN monolayer enhancing its optical activity in the Deep-UV region. The optical properties such as the dielectric function, the reflectivity, the absorption, and the optical conductivity spectra are investigated. It is shown that the absorption rate can be enhanced by $(12\text{-}15)\%$ for intermediate values of planar buckling in the Deep-UV region, and $(15\text{-}20)\%$ at higher values of planar buckling in the near-UV region. Furthermore, the optical conductivity is enhanced by increased planar buckling in both the visible and the Deep-UV regions depending on the direction of the polarization of the incoming light. Our results may be useful for optoelectronic BN monolayer devices in the UV range including UV spectroscopy, deep-UV communications, and UV photodetectors. Monolayer ; Materials science ; Band gap ; Fermi level ; Planar ; Ultraviolet ; Buckling ; Absorption spectroscopy ; Optical conductivity ; Absorption (acoustics) ; Optoelectronics ; Conductivity ; Molecular physics ; Optics ; Chemistry ; Condensed matter physics ; Nanotechnology ; Electron ; Physics ; Composite material 2D Materials and Applications ; Boron and Carbon Nanomaterials Research ; Graphene research and applications
Authors: Gaurav Jhaa | Pattath D. Pancharatna | Musiri M. Balakrishnarajan
Source: ChemRxiv (preprint, 2022-12-20)
Field: Materials Science — Materials Chemistry

Topological Impact of Delocalization on the Stability and Bandgap of Partially Oxidized Graphene Strategic perturbations on graphene framework to inflict a tunable energy bandgap promises intelligent electronics that are smaller, faster, flexible, and much more efficient than silicon. Despite different chemical schemes, a clear scalable strategy for micromanaging the bandgap is lagging. Since conductivity arises from the delocalized π-electrons, chemical intuition suggests that selective saturation of some sp2 carbons will allow strategic control over the bandgap. However, the logical cognition of different 2D π-delocalization topologies is complex. Their impact on the thermodynamic stability and bandgap remains unknown. Using partially oxidized graphene with its facile and reversible epoxides, we show that delocalization overwhelmingly influences the nature of the frontier bands. Organic electronic effects like hyperconjugation, conjugation, aromaticity, etc., can be used effectively to understand the impact of delocalization. By keeping a constant C4O stoichiometry, the relative stability of various π-delocalization topologies is directly assessed without resorting to resonance energy concepts. Our results demonstrate that >C=C< and aromatic sextets are the two fundamental blocks resulting in a large bandgap in isolation. Extending the delocalization across these units will increase the stability at the expense of the band gap. The bandgap is directly related to the extent of bond alternation within the π-framework, with forced single/double bonds causing the large gap. Furthermore, it also establishes the ground rules for the thermodynamic stability associated with the π-delocalization in 2D systems. We anticipate our findings will provide the heuristic guidance for designing partially saturated graphene with desired bandgap and stability using chemical intuition. Delocalized electron ; Band gap ; Graphene ; Chemical physics ; Materials science ; Topology (electrical circuits) ; Aromaticity ; Computational chemistry ; Nanotechnology ; Chemistry ; Optoelectronics ; Molecule ; Organic chemistry ; Mathematics Graphene research and applications ; Molecular Junctions and Nanostructures ; Fullerene Chemistry and Applications
Authors: Kaylee D. Hakkel | Don M. J. van Elst | Maurangelo Petruzzella | Martin Ebermann | Francesco Pagliano | Anne van Klinken | Andrea Fiore
Source: Electronics Letters (article, 2022-10-03)
Field: Chemistry — Spectroscopy

High‐performance integrated mid‐infrared filter arrays Abstract A static filter array is developed based on Fabry–Perot cavities operating in the mid‐infrared range from 2 to 4.5 µm, matching the absorption region of several gases relevant for air quality monitoring. The filters include two distributed Bragg reflectors and a high‐index tuning element with varying thickness in between. The filters display high peak transmittance () and controllable peak width. The robustness, ease of fabrication and the possibility to tune the optical response to a specific application make the integrated filter arrays suitable for compact sensing systems. Infrared ; Filter (signal processing) ; Materials science ; Electronic engineering ; Optoelectronics ; Remote sensing ; Computer science ; Optics ; Engineering ; Electrical engineering ; Physics ; Geology Spectroscopy and Laser Applications ; Photonic Crystal and Fiber Optics ; Semiconductor Lasers and Optical Devices
Authors: Sarbast M. Ahmed | Faiq H. S. Hussain | Marco Leusciatti | Barbara Mannucci | Mariella Mella | Paolo Quadrelli
Source: ARKIVOC (article, 2022-06-02)
Field: Chemistry — Organic Chemistry

Phosphorylation of 10-bromoanthracen-9-yl-cyclopenta[d]isoxazol-6-ols: chemistry suitable for antivirals Regioisomeric nor-nucleoside analogues, brominated at the anthracene ring, have been prepared and phosphorylated according to different protocols affording a variety of phosphate and phosphonate derivatives. Chiral phosphorus derivatives were also obtained as inseparable mixtures of diastereisomers. The synthetic methods are described and found to be reliable and robust, affording nor-nucleosides and nornucleotides, available in large amounts for in vitro antiviral evaluation. Chemistry ; Medicinal chemistry ; Combinatorial chemistry ; Computational chemistry ; Organic chemistry Organophosphorus compounds synthesis ; Synthesis and Reactivity of Sulfur-Containing Compounds ; Synthesis and Reactions of Organic Compounds
Authors: Philip Rainsford | Fredrik G. Rylandsholm | Martin Jakubec | Eric Juskewitz | Mitchell A. Silk | Richard A. Engh | Johan Isaksson
Source: ChemRxiv (preprint, 2022-11-11)
Field: Chemistry — Physical and Theoretical Chemistry

Label-free measurement of antimicrobial peptide interactions with lipid vesicles and nanodiscs using microscale thermophoresis Antimicrobial peptides (AMPs) are a promising source of inspiration for new antibiotic discovery, in part because they believed to not trigger rapid resistance. AMPs can target many features of the cell surface, and effective resistance development may require multiple mutations in parallel that have large fitness costs. Although they have diverse modes of action, AMPs will often begin by binding to the membrane; cell-penetrating peptides will subsequently need to cross it. Characterization of AMP activity can thus be inferred by the determination of KD (dissociation constant for binding affinity) and KP (partitioning constant). Here we demonstrate that microscale thermophoresis (MST) can be used for reliable label-free measurement of KD and KP utilising the intrinsic tryptophan fluorescence - removing the need for chromophore labelling. The MST results of binding to small unilamellar vesicles (SUVs) and styrene maleic acid (SMA) based nanodiscs are compared to the corresponding surface plasmon resonance (SPR) measurements. SMA-QA nanodiscs are shown to be best suited for accurate measurements, while vesicles are a viable alternative. Unmodified SMA-nanodiscs proved unsuitable due to interactions between the cationic AMPs and the anionic polymer belt. Significant reduction of KD was observed when 5% anionic lipids were included in the lipid composition of the membrane models. This highlights the preference of the tested AMPs for anionic bacterial membranes, and the measured KD and KP values correlate well with their activity towards S. aureus and E. coli. We conclude that MST is a promising method for fast and efficient detection of peptide-lipid interactions, and the relative strength of the interactions can be reliably ranked within a library of screened compounds. Microscale thermophoresis ; Peptide ; Dissociation constant ; Vesicle ; Lipid bilayer ; Chemistry ; Biophysics ; Microscale chemistry ; Surface plasmon resonance ; Antimicrobial peptides ; Membrane ; Biochemistry ; Nanotechnology ; Materials science ; Nanoparticle ; Biology thermodynamics and calorimetric analyses ; Field-Flow Fractionation Techniques ; Lipid Membrane Structure and Behavior
Authors: Sarkar M. A. Kawsar | Mebarka Ouassaf | Samir Chtita | Aishi Barua Jui | Salah Belaıdı
Source: Macedonian Journal of Chemistry and Chemical Engineering (article, 2022-06-30)
Field: Chemistry — Organic Chemistry

PASS prediction, molecular docking and pharmacokinetic studies of acyl substituted bioactive galactopyranoside esters as antibacterial agents Currently, methyl-β-D-galactopyranoside (MDG) esters have become a focus of attention due to their promising biological and pharmacokinetic properties and could be a good choice in unraveling the global issue of pathogenic multidrug resistance. Structural modification of MDG can improve its mode of biological activity. In line with these efforts, a series of previously synthesized MDG esters were designed and evaluated by Prediction of Activity Spectra for Substances (PASS), molecular docking simulation, and pharmacokinetic depiction. Encouraging PASS activity was observed for several aliphatic and aromatic MDG esters, and antibacterial efficacy was more promising than other features. In support, molecular docking studies were performed against the macrolide phosphotransferase enzyme MPH to identify a potential allosteric binding site for these esters. Molecular docking indicated that the shape of the MDG esters and their ability to form multiple electrostatic and hydrogen bonds with the active site corresponds to the binding modes of other minor-groove binders. Pharmacokinetic predictions were also performed to evaluate the absorption, metabolism, and toxic properties of MDG esters. These findings demonstrate that MDG esters are promising for use as biocompatible antibacterial agents in the future. Docking (animal) ; Chemistry ; Active site ; Combinatorial chemistry ; Molecular model ; Pharmacokinetics ; Antibacterial activity ; Allosteric regulation ; Stereochemistry ; Enzyme ; Biochemistry ; Pharmacology ; Bacteria ; Biology Carbohydrate Chemistry and Synthesis ; Synthesis and biological activity ; Metal complexes synthesis and properties
Authors: M. Corasaniti | Run Yang | Yu Liu | C. Petrović | L. Degiorgi
Source: New Journal of Physics (article, 2022-12-01)
Field: Materials Science — Materials Chemistry

Optical fingerprints of the electronic band reconstruction in van der Waals magnetic materials Abstract We report a broadband study of the charge dynamics in the van der Waals magnetic materials 2H- M x TaS 2 ( M = Mn and Co), which span the onset of both long-range antiferromagnetic (AFM) and ferromagnetic (FM) order, depending on the intercalation M and its concentration x . We discover a spectral weight ( SW ) shift from high to low energy scales for FM compositions, while reversely SW is removed from low towards high spectral energies for AFM compounds. This maps the related reconstruction of the electronic band structure along the crossover from the FM to AFM order, which restores an occupation balance in the density of states between spin majority and minority bands of the intercalated 3 d elements. van der Waals force ; Physics ; Antiferromagnetism ; Ferromagnetism ; Condensed matter physics ; Spin (aerodynamics) ; Broadband ; Heterojunction ; Atomic physics ; Optics ; Molecule 2D Materials and Applications ; Organic and Molecular Conductors Research ; Physics of Superconductivity and Magnetism
Authors: Olivier Languin–Cattoën | Fabio Sterpone | Guillaume Stirnemann
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-11-16)
Field: Materials Science — Materials Chemistry

Binding site plasticity regulation of the FimH catch-bond mechanism Abstract The bacterial fimbrial adhesin FimH is a remarkable and well-studied catch-bond protein found at the tip of E. coli type 1 pili, which allows pathogenic strains involved in urinary tract infections to bind high-mannose glycans exposed on human epithelia. The catch-bond behavior of FimH, where the strength of the interaction increases when a force is applied to separate the two partners, enables the bacteria to resist clearance when they are subjected to shear forces induced by urine flow. Two decades of experimental studies performed at the single-molecule level, as well as X-ray crystallography and modeling studies, have led to a consensus picture whereby force separates the binding domain from an inhibitor domain, effectively triggering an allosteric conformational change in the former. This force-induced allostery is thought to be responsible for an increased binding affinity at the core of the catch-bond mechanism. However, some important questions remain, the most challenging one being that the crystal structures corresponding to these two allosteric states show almost superimposable binding-site geometries, which questions the molecular origin for the large difference in affinity. Using molecular dynamics with a combination of enhanced-sampling techniques, we demonstrate that the static picture provided by the crystal structures conceals a variety of binding-site conformations that have a key impact on the apparent affinity. Crucially, the respective populations in each of these conformations are very different between the two allosteric states of the binding domain, which can then be related to experimental affinity measurements. We also evidence a previously unappreciated but important effect: in addition to the well-established role of the force as an allosteric regulator via domain separation, application of force tends to directly favor the high-affinity binding-site conformations. We hypothesize that this additional local catch-bond effect could delay unbinding between the bacteria and the host cell before the global allosteric transition occurs, as well as stabilizing the complex even more once in the high-affinity allosteric state. Allosteric regulation ; Biophysics ; Chemistry ; Pilus ; Binding site ; Molecular dynamics ; Mechanism (biology) ; Plasma protein binding ; Crystallography ; Stereochemistry ; Biology ; Biochemistry ; Computational chemistry ; Escherichia coli ; Receptor ; Physics Enzyme Structure and Function ; Escherichia coli research studies ; Protein Structure and Dynamics
Authors: Katriann Arja | Robert Selegård | Markéta Paloncýová | Mathieu Linares | Mikaël Lindgren | Patrick Norman | Daniel Aili | K. Peter R. Nilsson
Source: ChemPlusChem (article, 2022-09-02)
Field: Materials Science — Biomaterials

Self‐Assembly of Chiro‐Optical Materials from Nonchiral Oligothiophene‐Porphyrin Derivatives and Random Coil Synthetic Peptides Biomimetic chiral optoelectronic materials can be utilized in electronic devices, biosensors and artificial enzymes. Herein, this work reports the chiro-optical properties and architectural arrangement of optoelectronic materials generated from self-assembly of initially nonchiral oligothiophene-porphyrin derivatives and random coil synthetic peptides. The photo-physical- and structural properties of the materials were assessed by absorption-, fluorescence- and circular dichroism spectroscopy, as well as dynamic light scattering, scanning electron microscopy and theoretical calculations. The materials display a three-dimensional ordered helical structure and optical activity that are observed due to an induced chirality of the optoelectronic element upon interaction with the peptide. Both these properties are influenced by the chemical composition of the oligothiophene-porphyrin derivative, as well as the peptide sequence. We foresee that our findings will aid in developing self-assembled optoelectronic materials with dynamic architectonical accuracies, as well as offer the possibility to generate the next generation of materials for a variety of bioelectronic applications. Porphyrin ; Random coil ; Electromagnetic coil ; Materials science ; Combinatorial chemistry ; Nanotechnology ; Chemistry ; Photochemistry ; Circular dichroism ; Crystallography ; Physics Supramolecular Self-Assembly in Materials ; Porphyrin and Phthalocyanine Chemistry ; Photoreceptor and optogenetics research
Authors: Ting Wan | Luca Capaldo | Davide Ravelli | Walter Vitullo | Felix de Zwart | Bas de Bruin | Timothy Noël
Source: ChemRxiv (preprint, 2022-08-12)
Field: Chemistry — Organic Chemistry

Photoinduced Halogen-Atom Transfer (XAT) by N-heterocyclic carbene boryl radicals for C(sp3)−C(sp3) bond formation In the realm of radical chemistry, halogen-atom transfer (XAT) is emerging as a powerful activation strategy in synthetic endeavors to engage otherwise recalcitrant organic halides. Although toxic tin radicals have been in the spotlight as halo-gen abstractors for decades, the era of photocatalysis has brought to light more sustainable options. Herein, we present a comprehensive study on the use of ligated boryl radicals to enable C(sp3)−C(sp3) bond forming reactions via XAT from alkyl halides. Two strategies have been developed using either direct light activation with near UV or photoredox conditions with visible light; both pivoting on N-heterocyclic carbene (NHC) boryl radicals. The present XAT strategy is very mild and accommodates a broad scope of alkyl halides, including medicinally-relevant compounds and biologically-active molecules. The key role of NHC boryl radicals in the operative reaction mechanism has been elucidated through a combination of ex-perimental, spectroscopic and computational studies. Chemistry ; Radical ; Carbene ; Photoredox catalysis ; Photochemistry ; Halogen ; Alkyl ; Combinatorial chemistry ; Oxidative addition ; Photocatalysis ; Organic chemistry ; Catalysis Radical Photochemical Reactions ; Catalytic C–H Functionalization Methods ; Sulfur-Based Synthesis Techniques
Authors: Andreas Hoffmann | Matthias Uhl | Maximilian U. Ceblin | Joachim Bansmann | Timo Jacob | Alexander J. C. Kuehne
Source: Plasma Processes and Polymers (article, 2022-08-19)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Atmospheric pressure plasma‐jet treatment of polyacrylonitrile‐nonwovens: Activation leading to high surface area carbon electrodes Abstract Carbon nanofiber nonwovens (CFN) are powerful electrode materials with exceptional performance in energy storage devices, such as batteries and supercapacitors. Small fiber‐diameters together with hierarchical porosity endow CFN‐electrode materials with large surface areas and high electrical capacitance. Porosity of the fiber surface is often realized by corrosive activation methods such as wet‐etching or using oxidative gases at elevated temperatures. In this study, we present a chemical‐free, environmental‐friendly, and easily controllable surface activation method using an atmospheric pressure plasma‐jet. We investigate the best instant for activation along the process chain and show that the surface area of nanofiber nonwovens can be tailored by adjusting the plasma exposure‐dose. Plasma‐activated CFNs show an almost 20‐fold increase in capacitance ( C sp PJ = 10.1 F/g) in an electrochemical supercapacitor setup compared to nonactivated CFN ( C sp noPJ = 0.55 F/g). Polyacrylonitrile ; Materials science ; Supercapacitor ; Electrode ; Capacitance ; Nanofiber ; Atmospheric-pressure plasma ; Atmospheric pressure ; Specific surface area ; Porosity ; Composite material ; Fiber ; Chemical engineering ; Plasma ; Plasma etching ; Etching (microfabrication) ; Carbon fibers ; Nanotechnology ; Composite number ; Polymer ; Chemistry Supercapacitor Materials and Fabrication ; Electrospun Nanofibers in Biomedical Applications ; Advanced Sensor and Energy Harvesting Materials