jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Raquel C. R. Gonçalves | Mathilde L. Boland | Susana P. G. Costa | M. Manuela M. Raposo
Source:  (article, 2022-11-01)
Field: Materials Science — Materials Chemistry

A BODIPY Derivative for Selective Fluorescent Chemosensing of Iron (III) A BODIPY derivative functionalized with a phenyl group at the meso-position was synthesized and characterized through 1H NMR and UV&ndash;Vis absorption/emission spectroscopies. The compound showed an absorption band at 497 nm and a fluorescence band at 513 nm, with a &Phi;F = 0.68 in acetonitrile. The evaluation of the chemosensing ability of the BODIPY was investigated in the presence of several ions with environmental and biomedical relevance. A highly selective fluorimetric response was observed for Fe3+ through fluorescence quenching upon successive additions of this cation. BODIPY ; Fluorescence ; Derivative (finance) ; Acetonitrile ; Photochemistry ; Absorption (acoustics) ; Quenching (fluorescence) ; Ion ; Chemistry ; Materials science ; Organic chemistry ; Optics Luminescence and Fluorescent Materials ; Molecular Sensors and Ion Detection ; Porphyrin and Phthalocyanine Chemistry
Authors: Alyssa Miller | Sean Chia | Zenon Toprakcioglu | Tuuli A. Hakala | R. Schmid | Yaduo Feng | Tadas Kartanas | Ayaka Kamada | Michele Vendruscolo | Francesco Simone Ruggeri | Tuomas P. J. Knowles
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-07-25)
Field: Chemistry — Electrochemistry

Enhanced surface nano-analytics of transient biomolecular processes Abstract The study of the physical and chemical properties of biomolecules enables the characterisation of fundamental molecular processes and mechanisms in health and disease. Bulk and single-molecule analytical methods provide rich information on biomolecules, but often require high concentrations and sample preparation away from physiologically relevant conditions. Here, we present the development and application of a lab-on-a-chip approach which combines rapid sample preparation, mixing and deposition to integrate with a range of nano-analytical methods in chemistry and biology, providing enhanced sensitivity and single molecule resolution. We demonstrate that this method empowers multidimensional study of heterogenous biomolecular systems in physiological buffers and concentrations over multiple length scales by nanoscopy and vibrational spectroscopy. We illustrate the capabilities of this platform by capturing and analysing the structural conformations of transient oligomeric species formed at the early stages of the self-assembly of α-synuclein, which are associated with the onset of Parkinson’s disease. TEASER Maintaining the heterogeneity and structural integrity of monomers and oligomers enables their quantitative study. Biomolecule ; Nanotechnology ; Nano- ; Chemistry ; Molecule ; Biological system ; Materials science ; Chemical physics ; Computer science ; Biology Electrochemical Analysis and Applications ; Microfluidic and Capillary Electrophoresis Applications ; Biosensors and Analytical Detection
Authors: Eliott Le Du | Julien Borrel | Jérôme Waser
Source: ChemRxiv (preprint, 2022-07-29)
Field: Chemistry — Organic Chemistry

Copper-Catalyzed Alkynylation of Hydrazides: An Easy Access to Functionalized Azadipeptides We report a copper-catalyzed alkynylation of azadipeptides using ethynylbenziodoxolone (EBX) reagents. Non-symmetrical ynehydrazides could be obtained in 25-97% yield using azaglycine derivatives as nucleophiles. The transfor-mation is compatible with most functional groups naturally occurring on amino acid side-chains and allows the transfer of silyl-, alkyl- and aryl-substituted alkynes. The obtained α-alkynyl azaglycine products could be further functionalized by nucleophilic attack or cycloaddition on the triple bond. Nucleophile ; Alkynylation ; Chemistry ; Aryl ; Yield (engineering) ; Catalysis ; Cycloaddition ; Reagent ; Alkyl ; Triple bond ; Combinatorial chemistry ; Copper ; Electrophile ; Medicinal chemistry ; Organic chemistry ; Double bond ; Materials science Click Chemistry and Applications ; Chemical Synthesis and Analysis ; Catalytic Alkyne Reactions
Authors: Sida Wang | Phil Liebing | Felix Engelhardt | Liane Hilfert | Sabine Busse | R. Goldhahn | Frank T. Edelmann
Source: Zeitschrift für anorganische und allgemeine Chemie (article, 2022-09-28)
Field: Chemistry — Organic Chemistry

Synthesis and Complexation Study of New Aminoalkynyl−amidinate Ligands Abstract The current library of amidinate ligands has been extended by the synthesis of two novel dimethylamino‐substituted alkynylamidinate anions of the composition [Me 2 N−CH 2 −C≡C−C(NR) 2 ] − (R = i Pr, cyclohexyl (Cy)). The unsolvated lithium derivatives Li[Me 2 N−CH 2 −C≡C−C(NR) 2 ] ( 1 : R = i Pr, 2 : R = Cy) were obtained in good yields by treatment of in situ‐ prepared Me 2 N−CH 2 −C≡C−Li with the respective carbodiimides, R−N=C=N−R. Recrystallization of 1 and 2 from THF afforded the crystalline THF adducts Li[Me 2 N−CH 2 −C≡C−C(NR) 2 ] ⋅ n THF ( 1 a : R = i Pr, n =1; 2 a : R = Cy, n =1.5). Precursor 2 was subsequently used to study initial complexation reactions with selected di‐ and trivalent transition metals. The dark red homoleptic vanadium(III) tris(alkynylamidinate) complex V[Me 2 N−CH 2 −C≡C−C(NCy) 2 ] 3 ( 3 ) was prepared by reaction of VCl 3 (THF) 3 with 3 equiv. of 2 (75 % yield). A salt‐metathesis reaction of 2 with anhydrous FeCl 2 in a molar ratio of 2 : 1 afforded the dinuclear homoleptic iron(II) alkynylamidinate complex Fe 2 [Me 2 N−CH 2 −C≡C−C(NCy) 2 ] 4 ( 4 ) in 69 % isolated yield. Similarly, treatment of Mo 2 (OAc) 4 with 3 or 4 equiv. of 2 provided the dinuclear, heteroleptic molybdenum(II) amidinate complex Mo 2 (OAc)[Me 2 N−CH 2 −C≡C−C(NCy) 2 ] 3 ( 5 ; yellow crystals, 50 % isolated yield). The cyclohexyl‐substituted title compounds 2 a , 4 , and 5 were structurally characterized through single‐crystal X‐ray diffraction studies. Homoleptic ; Chemistry ; Adduct ; Molybdenum ; Yield (engineering) ; Medicinal chemistry ; Molar ratio ; Vanadium ; Metathesis ; Lithium (medication) ; Stereochemistry ; Metal ; Inorganic chemistry ; Polymerization ; Catalysis ; Organic chemistry Organometallic Complex Synthesis and Catalysis ; Ferrocene Chemistry and Applications ; Coordination Chemistry and Organometallics
Authors: Ruibin Liang | Amirhossein Bakhtiiari
Source: ChemRxiv (preprint, 2022-01-25)
Field: Materials Science — Materials Chemistry

Effects of enzyme-ligand interactions on the photoisomerization of a light-regulated chemotherapeutic drug Molecular photoswitches permit using light to control protein activity with high spatiotemporal resolutions, thereby alleviating the side effects of conventional chemotherapy. However, due to the challenges in probing ultrafast photoisomerization reactions in biological environments, it remains elusive how the protein influences the photochemistry of the photoswitches, which hampers the rational design of light-regulated therapeutics. To overcome this challenge, we employed first-principles non-adiabatic dynamics simulations to characterize the photodynamics of the phototrexate (PTX), a recently developed photoswitchable anticancer chemotherapeutic that reversibly inhibits its target enzyme dihydrofolate reductase (DHFR). Our simulations show that the protein environment impedes the trans to cis photoisomerization of the PTX. The confinement in the ligand-binding cavity slows down the isomerization kinetics and quantum yield of the photoswitch by reshaping its conical intersection, increasing its excited-state free energy barrier, and quenching its local density fluctuations. Therefore, we predict that the PTX’s trans to cis photoisomerization in solution precedes its binding with the protein, despite the favorable binding energy of the trans isomer. Our findings highlight the importance of the protein environment on the photochemical reactions of the molecular photoswitches. As such, our work represents an important step towards the rational design of light-regulated drugs in photopharmacology. Photoisomerization ; Photoswitch ; Chemistry ; Conical intersection ; Ligand (biochemistry) ; Molecular dynamics ; Biophysics ; Isomerization ; Dihydrofolate reductase ; Photochemistry ; Enzyme ; Computational chemistry ; Molecule ; Biochemistry ; Biology ; Receptor Photochromic and Fluorescence Chemistry ; Photoreceptor and optogenetics research ; Click Chemistry and Applications
Authors: Thomas G. Molley | Shouyuan Jiang | Chantal Kopecky | Chavinya D. Ranaweera | Gagan K. Jalandhra | Jelena Rnjak‐Kovacina | K. Kilian
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-09-04)
Field: Materials Science — Materials Chemistry

Gas modulating microcapsules for spatiotemporal control of hypoxia Abstract Oxygen is a vital molecule involved in regulating development, homeostasis, and disease. The oxygen levels in tissue vary from 1 to 8% with deviations having major biological consequences. In this work, we developed an approach to encapsulate enzymes and nanozymes, at an unprecedented loading capacity, which precisely controls the oxygen content in cell culture. Here, a single microcapsule is able to locally perturb the oxygen balance, and varying the concentration and distribution of matrix embedded microcapsules provides spatiotemporal control. We demonstrate attenuation of hypoxia signaling in populations of stem cells, cancer cells, endothelial cells, and cancer spheroids. Capsule containing hydrogel films applied to chick chorioallantoic membranes encourage neovascularization, providing scope for topical treatments or hydrogel wound dressings. We further demonstrate versatility by loading capsules with ceria nanorods as “nanozymes” to modulate active oxygen species with potential as a cytoprotective treatment. The approach can be used in multiple formats, including deposition in hydrogels, as granular solids for 3D bioprinting, and as injectable biomaterials. Overall, this platform’s simplicity and flexibility will prove useful for fundamental studies of oxygen-mediated processes in virtually any in vitro or in vivo format, with scope for inclusion in biomedical materials where controlling hypoxia may be clinically advantageous. Self-healing hydrogels ; In vivo ; Chemistry ; Hypoxia (environmental) ; Nanotechnology ; Cell biology ; Biomedical engineering ; Biophysics ; Materials science ; Oxygen ; Biology ; Medicine Advanced Nanomaterials in Catalysis ; Nanoplatforms for cancer theranostics ; Extracellular vesicles in disease
Authors: Xiaoshen Ma | Yuan Jiang
Source: ChemRxiv (preprint, 2022-11-01)
Field: Chemistry — Organic Chemistry

Synthesis of gem-diboromethyl substituted bicyclo[1.1.1]pentanes and their application in palladium-catalysed cross couplings We describe a general transition-metal free synthesis of gem-diboromethyl substituted bicyclo[1.1.1]pentane (BCP) and other related C(sp3)-rich carbocyclic benzene bioisosteres from their corresponding p-tosylhydrazones. These novel functionalized benzene bioisosteres demonstrated unique reactivities towards palladium-catalyzed C(sp2)-C(sp3) cross couplings. The overall transformation can be applied to relatively complex substrates with potential utility in drug discovery. Palladium ; Bicyclic molecule ; Benzene ; Pentane ; Chemistry ; Catalysis ; Combinatorial chemistry ; Stereochemistry ; Medicinal chemistry ; Organic chemistry Catalytic C–H Functionalization Methods ; Catalytic Cross-Coupling Reactions ; Radical Photochemical Reactions
Authors: Estitxu Echenique‐Errandonea | Ricardo F. Mendes | Flávio Figueira | Paula Barbosa | Sara Rojas | Duane Choquesillo‐Lazarte | Javier Cepeda | Duarte Ananias | Filipe M. Figueiredo | Filipe A. Almeida Paz | Antonio Rodrı́guez-Diéguez | José M. Seco
Source: Nanomaterials (article, 2022-12-08)
Field: Chemistry — Inorganic Chemistry

Easy Handling and Cost-Efficient Processing of a Tb3+-MOF: The Emissive Capacity of the Membrane-Immobilized Material, Water Vapour Adsorption and Proton Conductivity The development of convenient, non-complicated, and cost-efficient processing techniques for packing low-density MOF powders for industry implementation is essential nowadays. To increase MOFs' availability in industrial settings, we propose the synthesis of a novel 3D Tb-MOF (<b>1</b>) and a simple and non-expensive method for its immobilization in the form of pellets and membranes in polymethacrylate (PMMA) and polysulphone (PSF). The photoluminescent properties of the processed materials were investigated. To simulate industrial conditions, stability towards temperature and humidity have been explored in the pelletized material. Water-adsorption studies have been carried out in bulk and processed materials, and because of the considerable capacity to adsorb water, proton-conduction studies have been investigated for <b>1</b>. Adsorption ; Materials science ; Pellets ; Membrane ; Chemical engineering ; Water vapor ; Humidity ; Conductivity ; Nanotechnology ; Composite material ; Organic chemistry ; Chemistry Metal-Organic Frameworks: Synthesis and Applications ; Gas Sensing Nanomaterials and Sensors ; Covalent Organic Framework Applications
Authors: Kednerlin Dornevil
Source: Digital Archive @ GSU (article, 2022-04-12)
Field: Chemistry — Inorganic Chemistry

Heme Iron Catalysis: Contrast to Non-Heme Iron Enzymes Metalloenzymes catalyze a wide range of chemical transformations. Their remarkable versatility is imparted to them by their metal centers that are redox active or function as Lewis acids. They utilize transition metals such as iron that has accessibility to a variety of redox states, allowing them to efficiently activate and insert molecular oxygen into a wide range of unactivated organic substrates. The work described in this dissertation is the structural and mechanistic characterization of both heme and non-heme iron-dependent metalloenzymes. Precisely, the focus is placed on three enzymes, a cytochrome P450, CYP121, a tyrosine hydroxylase, LmbB2, and an extradiol dioxygenase, 3-hydroxyanthranilate 3,4-dioxygenase (HAO). The first two enzymes expand the repertoire of activities performed by hemoproteins. CYP121 catalyzes an unusual C-C crosslinking reaction that is distinct from traditional oxygenase chemistry performed by this family. LmbB2 is one of the first enzymes that mediate aromatic amino acid hydroxylation without using a pterin cofactor. Finally, HAO serves as the prototype for type III extradiol dioxygenase chemistry. A broad spectrum of biochemical and spectroscopic techniques was used to investigate the oxygen activation techniques by both LmbB2 and CYP121 and the role of second sphere ligands in the HAO active site. Specifically, rapid-kinetic methods, EPR spectroscopy, and X-ray crystallography allowed the elucidation of enzyme structure and function properties. In CYP121, using peracetic acid as an oxidant, similarities with canonical P450 enzymes through the use of a catalytic shunt pathway were demonstrated. We also identify the first intermediate in this pathway, an alkyperoxo species with an unusual 5/2 spin signal observed by EPR spectroscopy. In the LmbB2 study, a compound ES-like species was observed by UV-Vis and EPR spectroscopy. This intermediate was shown to be catalytically competent and able to react specifically to the substrate L-tyrosine. Finally, the role of a second sphere Pro97 residue in the active site of HAO was investigated using enzymatic assays. Long-range remote structural influences were observed using protein crystallography techniques between the active site and the conformation of the surface residues. Heme ; Chemistry ; Biochemistry ; Enzyme ; Catalysis Metal-Catalyzed Oxygenation Mechanisms ; Porphyrin Metabolism and Disorders ; Metalloenzymes and iron-sulfur proteins
Authors: Aja Ana Pavlič
Source: SPIRE - Sciences Po Institutional REpository (preprint, 2022-05-25)
Field: Chemistry — Electrochemistry

Spectroscopie Raman renforcée par la pointe (TERS) dans des conditions électrochimiques : vers la caractérisation in situ de nanomatériaux fonctionnels The objective of this work has been to expand developments that were further performed in STM towards AFM ones to broaden the range of systems which can be studied such as nanoparticles, 2D materials on conductive or insulating substrates or low-conductivity (multi) layers, passive layers and semiconductor materials among others, as mentioned earlier. Also, the thesis objective is to expand previous TERS development under electrochemical conditions, which has been achieved in the LISE laboratory in 2018, in the STM mode using partially isolated TERS active STM probes, with the new development in the AFM mode. The latter could broaden the range of possible systems which can be studied in the air and liquid and under electrochemical conditions, using hand-made TERS active AFM probes, initiated in this work as well. The initial step in this thesis was the optimization of manufacturing procedure of hand-made AFM-TERS probes, which were further used as the main tool for AFM imaging performances and TERS mapping. The measurements were implemented in the air and in liquid environment, whereas the TERS implementation in liquid, using point spectra, has been demonstrated for the first time using bulk metal AFM probes. Additionally, TERS mapping performances on nano-objects in the air have been performed as well, where the TERS molecule signature and the topography of the nano-particle have been obtained simultaneously. The challenge and core of this work is dedicated to the characterization of developed electroactive system by EC-AFM-TERS. The focus is on the electrochemical reduction of 4-nitrobenzene mercaptan (4-NBM) self-assembled monolayer in acidic and alkaline medium in two different configurations; upright and inverted. Thanks to the new design proposed for the bottom-illumination of AFM-TERS setup, the reduction of a 4-NBM monolayers could be followed in situ. The new setup was used for the first time to evaluate the reactivity of an electroactive (Raman non-resonant) molecular layer obtained by self-assembled monolayer of 4-NBM on gold. Characterization (materials science) ; Raman spectroscopy ; In situ ; Nanomaterials ; Materials science ; Electrochemistry ; Nanotechnology ; Spectroscopy ; Chemistry ; Electrode ; Physics ; Optics ; Physical chemistry ; Organic chemistry Electrochemical Analysis and Applications
Authors: Yu‐Chen Wang | Gabriel Théberge-Julien | Jean‐Claude Tardif | Éric Rhéaume | Frédéric Lesage | Ashok Kakkar
Source: Materials Advances (article, 2022-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Multifaceted ligand design facilitates chemical- or peptide-mediated linking of hollow gold nanoshells with tuned interparticle distance, interference and cytotoxicities Rational design of tunable multi-tasking ligands offers a versatile platform to link hollow gold nanoshells, in which molecular weight of polyethylene glycol arms and length of the spacer play key roles in composition control and optical properties. Nanoshell ; Polyethylene glycol ; Rational design ; Nanotechnology ; Materials science ; Ligand (biochemistry) ; PEG ratio ; Chemistry ; Nanoparticle ; Organic chemistry Gold and Silver Nanoparticles Synthesis and Applications ; Nanocluster Synthesis and Applications ; Advanced biosensing and bioanalysis techniques
Authors: Zhengyao Xia | Yan Li | Cheng Ji | Yucheng Jiang | Chunlan Ma | Ju Gao | Jinlei Zhang
Source: Nanomaterials (article, 2022-02-21)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Slow-Relaxation Behavior of a Mononuclear Co(II) Complex Featuring Long Axial Co-O Bond Co(II) mononuclear complex with different coordination geometry would display various of field-induced single-ion magnet (SIM) behaviors. Here, we identify a field-induced single-ion magnet in a mononuclear complex Co(H<sub>2</sub>DPA)<sub>2</sub>·H<sub>2</sub>O (H<sub>2</sub>DPA = 2,6-pyridine-dicarboxylic acid) by the hydrothermal method. The long axial Co-O coordination bond (Co1‧‧‧O3) can be formed by Co1 and O3. Therefore, Co(II) ion is six-coordinated in a distorted elongated octahedron. AC magnetization susceptibilities show that the effective energy barrier is up to 43.28 K. This is much larger than most mononuclear Co(II). The distorted elongated octahedron caused by the axial Co-O coordination bond is responsible for the high effective energy barrier. The distribution of electron density in Co1 and O3 atoms in the long axial bond would influence the magnetic relaxation process in turn. Our work deepens the relationship between the effective energy barrier and the weak change of ligand field by long axial bonds, which would facilitate constructing SIM with high energy temperature. Octahedron ; Crystallography ; Ligand field theory ; Relaxation (psychology) ; Ligand (biochemistry) ; Ion ; Bond length ; Materials science ; Chemistry ; Crystal structure ; Receptor Magnetism in coordination complexes ; Lanthanide and Transition Metal Complexes ; Electron Spin Resonance Studies
Authors: Anastasia Permyakova | Alshaba Kakar | Jonathan Bachir | Effrosyni Gkaniatsou | Bernard Haye | Nicolas Menguy | Farid Nouar | Christian Serre | Nathalie Steunou | Thibaud Coradin | Francisco M. Fernandes | Clémence Sicard
Source: ChemRxiv (preprint, 2022-09-01)
Field: Chemistry — Inorganic Chemistry

In situ Synthesis of a Mesoporous MIL-100(Fe) Bacteria Exoskeleton The mesoporous iron polycarboxylate MIL-100(Fe) was synthesized in presence of Pseudomonas putida bacteria. The synthesis was performed under green conditions, i.e. pure aqueous media at 30°C that were compatible with the preservation of the cell membrane integrity. Interestingly, the resulting bio-hybrid exhibited a very different microstructure than a physical mixture of the two components, as it led to the formation of a novel living material featuring an exoskeleton encapsulating individual bacteria cell. Interestingly, TEM and STEM on cross-sections revealed that this shell was not directly in contact with the cell wall, suggesting the exo-polysaccharides network promotes strong interactions with the MOF precursors leading to high proximity between the two components. Pseudomonas putida ; Mesoporous material ; Exoskeleton ; Bacteria ; Microstructure ; Biofilm ; In situ ; Membrane ; Chemical engineering ; Chemistry ; Materials science ; Bacterial cell structure ; Inulin ; Aqueous solution ; Nanotechnology ; Biophysics ; Crystallography ; Organic chemistry ; Biochemistry ; Biology ; Ecology ; Catalysis Metal-Organic Frameworks: Synthesis and Applications ; Polyoxometalates: Synthesis and Applications ; Peptidase Inhibition and Analysis