jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Emily Hruska | Quansong Zhu | Somnath Biswas | Matthew T. Fortunato | Dustin Broderick | Christina Morales | John M. Herbert | Claudia Turró | L. Robert Baker
Source: ChemRxiv (preprint, 2023-10-17)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Water-Mediated Charge Transfer and Electron Localization in a Co3Fe2 Cyanide-Bridged Trigonal Bipyramidal Complex The effects of temperature and chemical environment on a pentanuclear cyanide-bridged, trigonal bipyramidal molecular magnet has been investigated. Using element and oxidation state specific near-ambient pressure XPS (NAP-XPS) to probe charge transfer and second order, non- linear vibrational spectroscopy, which is sensitive to symmetry changes based on charge (de)localization coupled with DFT a detailed picture of environmental effects on charge-transfer induced spin transitions is presented. The molecular cluster, Co3Fe2(tmphen)6(μ-CN)6(t-CN)6, abbrev. Co3Fe2, shows changes in electronic behavior depending on chemical environment. NAP-XPS shows that temperature changes induce a metal-to-metal charge transfer (MMCT) in Co3Fe2 between a Co and Fe center, while cycling between ultrahigh vacuum and 2 mbar water at constant temperature, causes oxidation state changes not fully captured by the MMCT picture. Sum frequency generation vibrational spectroscopy (SFG-VS) probes the role of the cyanide ligand, which controls the electron (de)localization via the superexchange coupling. Spectral shifts and intensity changes indicate a change from a charge delocalized, Robin-Day Class II/III high spin state to a charge localized, Class I low spin state consistent with DFT. In the presence of a H-bonding solvent the complex adopts a localized electronic structure, while removal of the solvent delocalizes the charges and drives a MMCT. This change in Robin-Day classification of the complex as a function of chemical environment results in reversible switching of the dipole moment, analogous to molecular multiferroics. These results illustrate the important role of chemical environment and solvation on underlying charge and spin transitions in this and related complexes. Chemistry ; X-ray photoelectron spectroscopy ; Trigonal bipyramidal molecular geometry ; Chemical shift ; Chemical physics ; Crystallography ; Photochemistry ; Physical chemistry ; Nuclear magnetic resonance ; Crystal structure ; Physics Magnetism in coordination complexes ; Organic and Molecular Conductors Research ; Molecular Junctions and Nanostructures
Authors: Kang Du | Ivan J. Dmochowski
Source: The Journal of Physical Chemistry C (article, 2023-07-10)
Field: Chemistry — Inorganic Chemistry

Thermally Tunable Adsorption of Xenon in Crystalline Molecular Sorbent The thermostability of encapsulated xenon is investigated in a series of isostructural crystalline sorbents. These sorbents consist of metal-organic capsules, with the general formula of [Co<sub>n</sub>Fe<sub>4-n</sub>L<sub>6</sub>]<sup>4-</sup> (n = 1, 2, 3 and 4), where L<sup>2-</sup> is an organic linker with two sulfonate groups. In the crystalline sorbent, guanidinium cations form H-bond networks with the peripheral sulfonate groups in the solid state and trap xenon in the molecular cavities, which are at least 2.7 times the volume of xenon. When heated, the sorbent retains xenon up to 561 K, i.e., 396 K higher than the boiling point of xenon. Furthermore, the thermostability of trapped xenon can be modulated by varying the ratio of Co:Fe in the crystalline sorbent. Elemental analysis on a single crystal by energy dispersive X-ray spectroscopy confirms the homogeneous distribution of Co and Fe in the sorbent. Structural analyses reveal that the expansion of capsule cavity is proportional to the Co:Fe ratio, with increases of 0.049(1) Å and 6.4(8) Å<sup>3</sup> in metal-metal distance and cavity volume, per substitution of Fe by Co center. Steric repulsion between peripheral sulfonate groups is found to render a hypothetical face-centered cubic structure of (C(NH<sub>2</sub>)<sub>3</sub>)<sub>4</sub>[Fe<sub>4</sub>L<sub>6</sub>] not accessible, which would have trapped xenon with exceptional thermostability. The stable and tunable trapping of xenon in crystalline sorbents by over-sized molecular cavities suggests a new strategy for separation and storage of xenon, through introduction of kinetic barriers, such as H-bond networks. Xenon ; Sorbent ; Chemistry ; Materials science ; Crystallography ; Adsorption ; Thermostability ; Analytical Chemistry (journal) ; Physical chemistry ; Organic chemistry Metal-Organic Frameworks: Synthesis and Applications ; Covalent Organic Framework Applications ; Supramolecular Chemistry and Complexes
Authors: Angelika Becht | Justyna Frączyk | Joanna Waśko | Elżbieta Menaszek | Jakub Kajdanek | Katarzyna Miłowska | Beata Kolesińska
Source: Journal of Peptide Science (article, 2023-08-22)
Field: Materials Science — Biomaterials

Selection of collagen IV fragments forming the outer sphere of the native protein: Assessment of biological activity for regenerative medicine The aim of this research was to select the fragments that make up the outer layer of the collagen IV (COL4A6) protein and to assess their potential usefulness for regenerative medicine. It was expected that because protein-protein interactions take place via contact between external domains, the set of peptides forming the outer sphere of collagen IV will determine its interaction with other proteins. Cellulose-immobilized protein fragment libraries treated with polyclonal anti-collagen IV antibodies were used to select the peptides forming the outer sphere of collagen IV. In the first test, 33 peptides that strongly interacted with the polyclonal anti-collagen IV antibodies were selected from a library of non-overlapping fragments of collagen IV. The selected fragments of collagen IV (cleaved from the cellulose matrix) were tested for their cytotoxicity, their effects on cell viability and proliferation, and their impact on the formation of reactive oxygen species (ROS). The studies used RAW 264.7 mouse macrophage cells and Hs 680.Tr human fibroblasts. PrestoBlue, ToxiLight™, and ToxiLight 100% Lysis Control assays were conducted. The viability of fibroblasts cultured with the addition of increasing concentrations of the peptide mix did not show statistically significant differences from the control. Fragments 161-170, 221-230, 721-730, 1331-1340, 1521-1530, and 1661-1670 of COL4A6 were examined for cytotoxicity against BJ normal human foreskin fibroblasts. None of the collagen fragments were found to be cytotoxic. Further research is underway on the potential uses of collagen IV fragments in regenerative medicine. Chemistry ; Polyclonal antibodies ; Cytotoxicity ; Fibroblast ; Peptide ; Regenerative medicine ; Molecular biology ; Biochemistry ; Antibody ; Cell ; In vitro ; Immunology ; Biology Collagen: Extraction and Characterization ; Cell Adhesion Molecules Research ; Silk-based biomaterials and applications
Authors: Souria Benallou | Souhail Besbes | Abdelatif Bouyacoub | Éric Grelet
Source: Liquid Crystals (article, 2023-04-24)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Synthesis of achiral rod-shaped triazolic molecules and investigation of their striped texture and propeller-patterned nematic droplets In this study, novel achiral mesogens containing 4,4'-biphenyl central core connected on both sides through an ester function to 1-(4-(alkyloxy)phenyl)-1H-[1,2,3]-triazolyl group have been synthesized and characterized. Different mesophases have been identified, with the appearance of both a periodic striped pattern and propeller-patterned droplets close to the transition between the nematic and the smectic-C phases. This periodic texture has been found to be independent of the geometry of the sample cell. These observations suggest a spontaneous symmetry breaking which can result either from an intrinsic enantioselective self-sorting process with a chirality synchronization mechanism, or from an extrinsic surface mechanism at the interface between the two phases. Liquid crystal ; Materials science ; Texture (cosmology) ; Chirality (physics) ; Propeller ; Molecule ; Symmetry breaking ; Crystallography ; Biphenyl ; Chemical physics ; Chiral symmetry breaking ; Condensed matter physics ; Organic chemistry ; Physics ; Image (mathematics) ; Chemistry ; Optoelectronics Liquid Crystal Research Advancements ; Photochromic and Fluorescence Chemistry ; Molecular spectroscopy and chirality
Authors: Matthew Parry | Kenneth B. Crozier | Andrey A. Sukhorukov | Dragomir N. Neshev
Source: arXiv (Cornell University) (preprint, 2023-09-05)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Optimization of metasurfaces for lasing with symmetry constraints on the modes The development of active metasurface systems, such as lasing metasurfaces, requires the optimization of multiple modes at the absorption and lasing wavelength bands, including their quality factor, mode profile and angular dispersion. Often, these requirements are contradictory and impossible to obtain with conventional design techniques. Importantly, the properties of the eigenmodes of a metasurface are directly linked to their symmetry, which offers an opportunity to explore mode symmetry as an objective in optimization routines for active metasurface design. Here, we propose and numerically demonstrate a novel multi-objective optimization technique based on symmetry projection operators to quantify the symmetry of the metasurface eigenmodes. We present, as an example, the optimization of a lasing metasurface based on up-converting nano-particles. Our technique allows us to optimize the absorption mode dispersion, as well as the directionality of the lasing emission and therefore offers advantages for novel lasing systems with high directionality and low lasing threshold. Lasing threshold ; Symmetry (geometry) ; Dispersion (optics) ; Optics ; Absorption (acoustics) ; Physics ; Laser ; Optoelectronics ; Mathematics Metamaterials and Metasurfaces Applications ; Millimeter-Wave Propagation and Modeling ; Radio Wave Propagation Studies
Authors: R. S. Yaro | Musa Abdullahi | Y.Y. Deeni | Danjuma Dausayi Sulaiman
Source: FUDMA Journal of Sciences (article, 2023-07-07)
Field: Materials Science — Biomaterials

ANTIBACTERIAL ACTIVITIES OF LEAF METHANOLIC EXTRACTS OF Leptadenia hastata AGAINST Escherichia coli CLINICAL ISOLATE The research aims at potential activities of leaf methanolic extracts of Leptadenia hastata against clinical Escherichia coli and extraction, phytochemicals and biochemical tests to the plant and organism. Escherichia coli is Gram negative, non-capsulated, bacillus, clinically important bacteria mostly isolated clinically and capable to cause gastro enteritis, urinary tract infections, diarrhea among others. L. hastata is a climbing shrub that produces flexible latex which become woody at the base. Potential activities of L. hastata leaf methanolic extracts against clinical Escherichia coli were observed. L. hastata leaf were sampled, Phyto-chemically screened using methanol and processed using Di-MethylSulfurOxide (DMSO). Clinical Bacterial Isolates were collected from Murtala Muhammed Specialist Hospital Kano, Kano State, Nigeria, investigated and screened for E. coli using Gram’s staining technique and some biochemical tests procedure for confirmation. L. hastata leaf methanolic extracts were processed against the isolates. Four (4) E. coli were found and tested against leaf methanolic extracts of L. hastata at different concentrations of 125, 250, 500 and 1000 mg/mL respectively. Activity was observed directly proportional to the concentrations, where the Minimum inhibitory concentration (MIC) and Minimum bactericidal concentration (MBC) were at 500 and 1000 mg/mL accordingly. The research may lead to effective drug development against the clinical E. coli to address its pathogenicity, for the Public Health benefit. It is recommended that further research should be carried out to determine bioactive components of L. hastata leaf, toxicity level tests and Molecular characterization to the isolate (E. coli). Escherichia coli ; Minimum inhibitory concentration ; Biology ; Minimum bactericidal concentration ; Bacteria ; Traditional medicine ; Microbiology ; Antimicrobial ; Medicine ; Biochemistry Phytochemistry and Bioactive Compounds ; Essential Oils and Antimicrobial Activity ; Fungal Biology and Applications
Authors: Jessica Bowles | Sascha Jähnigen | Federica Agostini | Rodolphe Vuilleumier | Anne Zehnacker | F. Calvo | Carine Clavaguéra
Source: ChemRxiv (preprint, 2023-12-21)
Field: Chemistry — Spectroscopy

Vibrational circular dichroism spectroscopy with a classical polarizable force field: alanine in the gas and condensed phases Polarizable force fields are an essential component for the chemically accurate modeling of complex molecular systems with a significant degree of fluxionality, beyond harmonic or perturbative approximations. In this contribution we examine the performance of such an approach for the vibrational spectroscopy of the alanine amino acid, in the gas and condensed phases, from the Fourier transform of appropriate time correlation functions generated along molecular dynamics (MD) trajectories. While the infrared (IR) spectrum only requires the electric dipole moment, the vibrational circular dichroism (VCD) spectrum further requires knowledge of the magnetic dipole moment, for which we provide relevant expressions to be used under polarizable force fields. The AMOEBA force field was employed here to model alanine in the neutral and zwitterionic isolated forms, solvated by water or nitrogen, and as a crystal. Within this framework, comparison of the electric and magnetic dipole moments to those obtained with nuclear velocity perturbation theory based on density-functional theory for the same MD trajectories are found to agree well with one another. The statistical convergence of both the IR and VCD spectra is examined and found to be more demanding in the latter case. Polarizability ; Dipole ; Chemistry ; Force field (fiction) ; Vibrational circular dichroism ; Molecular physics ; Molecular dynamics ; Electric dipole moment ; Density functional theory ; Infrared spectroscopy ; Spectroscopy ; Circular dichroism ; Computational chemistry ; Physics ; Molecule ; Crystallography ; Quantum mechanics Molecular spectroscopy and chirality ; Spectroscopy and Quantum Chemical Studies ; Protein Structure and Dynamics
Authors: Jiaqi Guo | Weiyi Tan | Hongjian He | Bing Xu
Source: Angewandte Chemie (article, 2023-07-20)
Field: Materials Science — Biomaterials

Autohydrolysis of Diglycine‐Activated Succinic Esters Boosts Cellular Uptake Abstract Rapid cellular uptake of synthetic molecules remains a challenge, and the motif frequently employed to generate prodrugs, succinic ester, unfortunately lowers the efficacy of the desired drugs due to their slow ester hydrolysis and low cell entry. Here we show that succinic ester‐containing diglycine drastically boosts the cellular uptake of supramolecular assemblies or prodrugs. Specifically, autohydrolysis of the diglycine‐activated succinic esters turns the nanofibers of the conjugates of succinic ester and self‐assembling motif into nanoparticles for fast cellular uptake. The autohydrolysis of diglycine‐activated succinic esters and drug conjugates also restores the efficacy of the drugs. 2D nuclear magnetic resonance (NMR) suggests that a “U‐turn” of diglycine favors intramolecular hydrolysis of diglycine‐activated succinic esters to promote autohydrolysis. As an example of rapid autohydrolysis of diglycine‐activated succinic esters for instant cellular uptake, this work illustrates a nonenzymatic bond cleavage approach to develop effective therapeutics for intracellular targeting. Chemistry ; Succinic anhydride ; Succinic acid ; Prodrug ; Hydrolysis ; Combinatorial chemistry ; Organic chemistry ; Biochemistry Supramolecular Self-Assembly in Materials ; RNA Interference and Gene Delivery ; Chemical Synthesis and Analysis
Authors: Takahiro Iwamoto | Mika Suzuki | Hibiki Hasegawa | Hinako Abeta | Yusuke Matsuo | Takayuki Tanaka | Nobuhiro Yasuda | Youichi Ishii
Source: Chemistry - An Asian Journal (article, 2023-08-23)
Field: Chemistry — Organic Chemistry

One‐pot Syntheses of Benzo‐ and Benzofuran‐fused Iridaoxabenzenes via CH Bond Activations of Alkyl‐bridged Diphenol Derivatives One-pot syntheses of new π-extended metallaaromatic compounds have been developed by utilizing Ir-mediated CH bond activation of ethylene- or ethylidene-bridged diphenol derivatives. Depending on the bridging alkyl groups, two types of iridaoxabenzenes, both of which are doubly fused with benzo and benzofuran units, have been obtained. Studies on their structures and electronic characters indicate that both complexes have an aromatic character on the iridaoxacycles, and their π-conjugated systems are fully delocalized over the whole molecular skeletons. These novel metallaaromatic complexes exhibited some reactivities which are distinct from those reported for the non-fused metallaaromatic compounds. Benzofuran ; Chemistry ; Alkyl ; Delocalized electron ; Conjugated system ; Ethylene ; Electron delocalization ; Stereochemistry ; Organic chemistry ; Polymer Catalytic C–H Functionalization Methods ; Catalytic Cross-Coupling Reactions ; Cyclopropane Reaction Mechanisms
Authors: Elizabeth Abi Aad
Source: SPIRE - Sciences Po Institutional REpository (preprint, 2023-04-19)
Field: Chemistry — Analytical Chemistry

Impact de la Détente Instantanée Contrôlée (DIC) sur l’extraction des molécules bioactives de rhizomes de Rheum ribes L. Rheum ribes L. (rhubarb) is one of the most important Mediterranean medicinal plants. Preparing its rhizomes’ aqueous decoctions has become common among patients suffering from various diseases. Instant Controlled Pressure Drop (DIC) is a High-Temperature Short-Time treatment (HTST) followed by an abrupt pressure drop towards the vacuum (approximately 5 kPa). This technology increases the expansion and reduces the tortuosity of the treated matrix to ensure better diffusivity of the extraction solvents and greater availability of the active molecules. On the one hand, our research aimed at the impact of DIC treatment on the rhizomes of a Lebanese species of R. ribes L. The evaluations were based on the contents of total phenolics (TPC) and flavonoids (TFC) as well as the antioxidant capacities of aqueous extracts of the treated rhizomes. The results showed a negative correlation between the saturated steam pressure applied and the values of TPC, TFC, and the antioxidant activities of the samples. However, DIC treatment time had no significant influence on the response variables. In addition to these two DIC operating factors (pressure and treatment time), the effect of the rhizomes water content (W) was also studied. The results showed that the increase of “W” does not lead to better yields of phenolic compounds. On the other hand, this study presents the impact of DIC treatment on the biological activities (antibacterial and antiproliferative effects) of rhizome extracts. The results revealed that the aqueous extracts of DIC-treated rhizomes show weak antibacterial powers on E. coli and S. aureus, with slightly superior results in inhibiting the growth of S. aureus. Regarding the viability test of melanoma cancer cells, the results showed that the DIC treatment positively impacts the antiproliferative power of the treated samples compared with the untreated point (aqueous MP). In particular, two samples among those tested recorded an antiproliferative power of 60%. The HPLC and UHPLC assays revealed the presence of three anthraquinones (emodin, chrysophanol, and physcion) in the rhizome extracts and about twenty compounds from the flavonoid family. However, the amounts of anthraquinones detected are not significantly higher in the extracts treated with DIC than in the untreated ones. Finally, it was found that the total phenolic content of an aqueous sample treated with the optimal DIC parameters is equal to that of an untreated hydroalcoholic sample. Further experiments will be necessary to validate this result. Rhizome ; Ribes ; Traditional medicine ; Rheum (plant) ; Extraction (chemistry) ; Chemistry ; Chromatography ; Botany ; Medicine ; Biology Chromatography in Natural Products ; Phytochemistry and biological activity of medicinal plants ; Innovative Microfluidic and Catalytic Techniques Innovation
Authors: Muaz Belviranlı | Nilsel Okudan
Source: Research Square (preprint, 2023-06-15)
Field: Chemistry — Inorganic Chemistry

Coconut oil ameliorates behavioral alterations in rat model of Alzheimer’s Disease via attenuating oxidative damage and cholinergic impairment and upregulating synaptic transmission Cholinergic ; Neuroscience ; Disease ; Oxidative damage ; Transmission (telecommunications) ; Oxidative stress ; Cholinergic system ; Cognitive impairment ; Neurotransmission ; Medicine ; Psychology ; Internal medicine ; Computer science ; Receptor ; Telecommunications Coconut Research and Applications ; Medicinal Plants and Neuroprotection ; Fatty Acid Research and Health
Authors: Tianli Zhu | Mengting Zhao | Rongcheng Wang | C. C. Dong | Xuemei Dong | Jie Sun | Lixin Sun | Chunchang Zhao
Source:  (preprint, 2023-07-04)
Field: Chemistry — Spectroscopy

Hantzsch ester modified asymmetric BODIPY probe with ultra-high sensitivity for ultra-fast detection of endogenous hypochlorite in living cells Hypochlorite (ClO) is an important reactive oxygen species produced by the immune system to fight off invading pathogens, but its over-expression can interfere with normal physiological process and induce serious diseases. Although a variety of molecular probes have been reported for detecting ClO, the development of advanced fluorescent tools with faster response and higher sensitivity to precisely monitor ClO remains a challenge. In this work, two Hantzsch ester (a derivative of 1,4-dihydropyridine) derived fluorescent probes MeDHP-BCl and MeDHP-PhBCl were constructed based on asymmetric BODIPY-matrix. These probes exhibit significant fluo-rescence turn-on in the ultra-sensitive (detection limit &lt; 1 nM) and ultra-fast response (≤ 5 s) to ClO, the reaction has determined to be a highly selective N-Chlorination of Hantzsch ester which cannot be activated by various common bioactive species, including nitric ox-ide (NO) that could oxidize Hantzsch ester under aerobic physiological conditions in most reports. MeDHP-PhBCl possess a relatively longer fluorescence emission wavelength and higher quantum yield after activation, while more notably, MeDHP-BCl displayed lower cytotoxicity and more remarkable fluorescence increasement in the response to ClO, enabling selective and precise visualization of endogenous ClO over-expression in living RAW264.7 cells. Hypochlorite ; Fluorescence ; Chemistry ; Cytotoxicity ; Endogeny ; BODIPY ; Quantum yield ; Reactive oxygen species ; Detection limit ; Hypochlorous acid ; Biophysics ; Photochemistry ; Biochemistry ; In vitro ; Organic chemistry ; Biology ; Chromatography Molecular Sensors and Ion Detection ; Sulfur Compounds in Biology ; Nitric Oxide and Endothelin Effects