jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Víctor Lechuga‐Islas | Melisa Trejo‐Maldonado | Ilya Anufriev | Ivo Nischang | İpek Terzioğlu | Jens Ulbrich | Ramiro Guerrero‐Santos | Luis Ernesto Elizalde-Herrera | Ulrich S. Schubert | Carlos Guerrero‐Sánchez
Source: Macromolecular Bioscience (article, 2022-10-19)
Field: Materials Science — Biomaterials

All‐Aqueous, Surfactant‐Free, and pH‐Driven Nanoformulation Methods of Dual‐Responsive Polymer Nanoparticles and their Potential use as Nanocarriers of pH‐Sensitive Drugs All-aqueous, surfactant-free, and pH-driven nanoformulation methods to generate pH- and temperature-responsive polymer nanoparticles (NPs) are described. Copolymers comprising a poly(methyl methacrylate) (PMMA) backbone with a few units of 2-(dimethylamino)ethyl methacrylate (DMAEMA) are solubilized in acidic buffer (pH 2.0) to produce pH-sensitive NPs. Copolymers of different molar mass (2.3-11.5 kg mol<sup>-1</sup> ) and DMAEMA composition (7.3-14.2 mol%) are evaluated using a "conventional" pH-driven nanoformulation method (i.e., adding an aqueous polymer solution (acidic buffer) into an aqueous non-solvent (basic buffer)) and a robotized method for pH adjustment of polymer dispersions. Dynamic light scattering, zeta-potential (ζ), and sedimentation-diffusion analyses suggest the formation of dual-responsive NPs of tunable size (from 20 to 110 nm) being stable for at least 28 days in the pH and temperature intervals from 2.0 to 6.0 and 25 to 50 °C, respectively. Ultraviolet-visible spectroscopic experiments show that these NPs can act as nanocarriers for the pH-sensitive dipyridamole drug, expanding its bioavailability and potential controlled release as a function of pH and temperature. These approaches offer alternative strategies to prepare stimuli-responsive NPs, avoiding the use of harmful solvents and complex purification steps, and improving the availability of biocompatible polymer nanoformulations for specific controlled release of pH-sensitive cargos. Nanocarriers ; Methacrylate ; Chemistry ; Aqueous solution ; Polymer ; Zeta potential ; Copolymer ; Dynamic light scattering ; Nanoparticle ; Molar mass ; Pulmonary surfactant ; Polymer chemistry ; Chemical engineering ; Drug delivery ; Organic chemistry Nanoparticle-Based Drug Delivery ; Advanced Drug Delivery Systems ; Antibiotics Pharmacokinetics and Efficacy
Authors: Junbo Chen | Chenhui Wang | Hao Li | Xin Xu | Jiangang Yang | Zhe Huo | Lixia Wang | Weifeng Zhang | Xudong Xiao | Yaping Ma
Source: Preprints.org (preprint, 2022-12-19)
Field: Materials Science — Materials Chemistry

Recent Advances in Surface Modifications of Elemental Two-Dimensional Materials: Structures, Properties, and Applications The advent of graphene opens up the research into two-dimensional (2D) material, which is considered as a revolutionary material in the future. Due to its unique geometric structure, graphene exhibits a series of exotic physical and chemical properties. Besides, single-element-based 2D materials (Xenes) have garnered tremendous interest. At present, 16 kinds of Xenes (silicene, borophene, germanene, phosphorene, tellurene, etc.) have been explored, mainly distributed in the third, fourth, fifth and sixth main groups. The current methods to prepare monolayer or few-layer 2D materials include epitaxy growth, mechanical exfoliation, and liquid phase exfoliation. Although two Xenes (aluminene and indiene) have not been synthesized due to the limitations of synthetic methods or stability of Xenes, other Xenes have been successfully realized by elaborately artificial design and synthesis. Focusing on elemental 2D materials, this review mainly summarizes the recently reported work about tuning the electronic, optical, mechanical, or chemical properties of Xenes via surface modifications achieved by controllable approaches (doping, adsorption, strain, intercalation, phase transition, etc.) to broaden the applications in various fields, including spintronics, electronics, optoelectronics, superconducting, photovoltaics, sensors, catalysis, and biomedicines. These advances in surface modification of Xenes have laid a theoretical and experimental foundation for the development of 2D materials and their practical applications in diverse fields. Germanene ; Nanotechnology ; Materials science ; Silicene ; Exfoliation joint ; Graphene ; Spintronics ; Phosphorene ; Monolayer ; Surface modification ; Ferromagnetism ; Chemistry ; Physics ; Physical chemistry Graphene research and applications ; 2D Materials and Applications ; Advanced Photocatalysis Techniques
Authors: Saulius Juodkazis | Soon Hock Ng
Source: Preprints.org (preprint, 2022-02-21)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Nanoscale Plasmonic Printing Nanoscale structuring/printing is of interest for range of applications in 3D subtractive and additive manufacturing (3D+/-). Basic principles of light field enhancement and control at the nanoscale are overviewed in this section/chapter for bulk, surface, and localised plasmons (1D, 2D, and 3D localisation, respectively). All these plasmons are resonant phenomena which have common Lorentzian spectral lineshape which relates refractive and absorption properties as well as defining the phase of transmitted and scattered light. Localisation of light at the nanoscale creates the possibility of modification with matching resolution. Harnessing this light enhancement can be demonstrated as a "nano-pen" for direct write nanolithography. Plasmon ; Nanoscopic scale ; Materials science ; Nanotechnology ; Nanolithography ; Subtractive color ; 3D printing ; Nanophotonics ; Surface plasmon ; Optoelectronics ; Optics ; Fabrication ; Physics Gold and Silver Nanoparticles Synthesis and Applications ; Nanofabrication and Lithography Techniques ; Photonic Crystals and Applications
Authors: Nazila Yaghini | Jaap den Doelder
Source: Polymer (article, 2022-12-07)
Field: Materials Science — Polymers and Plastics

Simulations mapping the influence of oxygen, extruder residence time, and mechanical shear on low-density polyethylene structure during recycling We present a computational study of the development of structural properties for recycled low-density polyethylene (LDPE). First, we apply the population balance method together with the method of moments to study the mutual influences of scission and crosslinking reactions. Then, we study the combined effects of extruder residence time and oxygen concentration as the initiator of thermo-mechanical degradation in the recycling process of LDPE in a twin-screw extruder. Further, we extend the models to study the influence of mechanical scission. We explore various case study scenarios to incorporate the effect of extruder residence time and mechanical shear. It is concluded that the competition between random scission and crosslinking, as well as the presence of oxygen, play important roles in the degradation of LDPE during recycling. Random scission is a key factor in terms of altering molecular weight distribution (MWD) during a recycling extrusion process. The various explored scenarios with mechanical scission demonstrate the sensitivity of molecular structure to the combination of competing mechanisms during recycling. Low-density polyethylene ; Plastics extrusion ; Extrusion ; Polyethylene ; Materials science ; Residence time (fluid dynamics) ; Composite material ; Residence time distribution ; Shear (geology) ; Chemical engineering ; Polymer chemistry ; Chemistry ; Mineralogy ; Engineering Polymer crystallization and properties ; Microplastics and Plastic Pollution ; Asphalt Pavement Performance Evaluation
Authors: Aleksandar Kondinski | Abhishek Banerjee | Sib Sankar Mal
Source: Preprints.org (preprint, 2022-07-04)
Field: Materials Science — Materials Chemistry

Hervé and Krebs Type Magnetic Polyoxometalate Dimers Lacunary polyoxometalates (POMs) are negatively charged metal−oxo clusters, formally obtained from plenary topologies via fragment removal. Owing to the fragment removal, the lacunary POMs archetypes are rich in nucleophilic terminal oxo ligands, making them suitable for post-synthetic coordination with various heterometals. Trilacunary heteropolytungstates (het-ero-POTs) based on bowl-shaped {W9O30} framework incorporating a central lone-pair containing {XO3} hetergroup (X = AsIII, SbIII, and BiIII) function as all-inorganic scaffolds that in the presence of d-block metal cations typically construct sandwich-like dimers of Hervé and/or Krebs. Herein we review the preparative approaches, compositional and magnetic versatility of the constructing Hervé and Krebs type dimers and discuss prospective use as POMtronics. Polyoxometalate ; Lacunary function ; Chemistry ; Crystallography ; Antiparallel (mathematics) ; Nucleophile ; Lone pair ; Metal ; Stereochemistry ; Nanotechnology ; Materials science ; Molecule ; Physics ; Organic chemistry ; Catalysis ; Mathematics ; Magnetic field ; Pure mathematics Polyoxometalates: Synthesis and Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Chemical Synthesis and Reactions
Authors: Jinfeng Chen | Lei Zhang | Zhao Sun | Hongyi Li | Jingyi Li | Xinli Xue | Qingqing Zhu | Bowen Dong | Yuanyuan Wang | Yang Yang | Yongqiang Dong | Guangyu Guo | Hongqiang Jiang | An Zhang | Guoqing Zhang | Zhichao Hou | Xiangnan Li | Jing-Hua Yang
Source: Oxidative Medicine and Cellular Longevity (article, 2022-01-01)
Field: Chemistry — Spectroscopy

Open Search‐Based Proteomics Reveals Widespread Tryptophan Modifications Associated with Hypoxia in Lung Cancer The tryptophan residue has a large hydrophobic surface that plays a unique role in the folded protein conformation and functions. Tryptophan modifications are presumably to be readily detected in proteins due to the vulnerability of the indole structure to electrophilic attacks. In this study, we report a systematic identification of sequence variations at tryptophan, termed tryptophan variants, from the proteome of patients with nonsmall cell lung cancer (NSCLC). Using shotgun proteomics and a modified open search algorithm, 25 tryptophan variants on 2481 sites in over 858 proteins were identified. Among these, 6 tryptophan variants are previously identified, 15 are newly annotated, and 4 are still unknown, most of which are involved in the cascade of oxidation in the blood microparticle. Remarkably, Trp313 of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was up-oxidized whereas Trp16 and Trp38 of hemoglobin (HBB) were down-oxidized in NCSLC tissues. The results were further supported by an independent cohort of 103 lung adenocarcinoma samples, reflecting a negative feedback and potential detoxification mechanism against tumor glycolysis and hypoxia. Overall, the study reports a quick approach to explore tryptophan variants at the proteomic scale. Our findings highlight the predominant role of tryptophan oxidation in regulating the redox balance of cancer cells and its potential role as prognostic biomarker for patients with NSCLC. Tryptophan ; Proteome ; Biology ; Proteomics ; Biochemistry ; Amino acid ; Gene Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Cancer, Hypoxia, and Metabolism
Authors: Caroline Delehedde | Marcel Culcasi | Emilie Ricquebourg | Mathieu Cassien | Didier Siri | B Blaive | Sylvia Pietri | Sophie Laurent
Source: Molecules (article, 2022-07-14)
Field: Chemistry — Organic Chemistry

Novel Sterically Crowded and Conformationally Constrained α-Aminophosphonates with a Near-Neutral pKa as Highly Accurate 31P NMR pH Probes. Application to Subtle pH Gradients Determination in Dictyostelium discoideum Cells In order to discover new 31P NMR markers for probing subtle pH changes (<0.2 pH unit) in biological environments, fifteen new conformationally constrained or sterically hindered α-aminophosphonates derived from diethyl(2-methylpyrrolidin-2-yl)phosphonate were synthesized and tested for their pH reporting and cytotoxic properties in vitro. All compounds showed near-neutral pKas (ranging 6.28−6.97), chemical shifts not overlapping those of phosphorus metabolites, and spectroscopic sensitivities (i.e., chemical shifts variation Δδab between the acidic and basic forms) ranging from 9.2−10.7 ppm, being fourfold larger than conventional endogenous markers such as inorganic phosphate. X-ray crystallographic studies combined with predictive empirical relationships and ab initio calculations addressed the inductive and stereochemical effects of substituents linked to the protonated amine function. Satisfactory correlations were established between pKas and both the 2D structure and pyramidalization at phosphorus, showing that steric crowding around the phosphorus is crucial for modulating Δδab. Finally, the hit 31P NMR pH probe 1b bearing an unsubstituted 1,3,2-dioxaphosphorinane ring, which is moderately lipophilic, nontoxic on A549 and NHLF cells, and showing pKa = 6.45 with Δδab = 10.64 ppm, allowed the first clear-cut evidence of trans-sarcolemmal pH gradients in normoxic Dictyostelium discoideum cells with an accuracy of <0.05 pH units. Chemistry ; Steric effects ; Protonation ; Phosphonate ; Amine gas treating ; Dictyostelium discoideum ; Chemical shift ; Stereochemistry ; Nuclear magnetic resonance spectroscopy ; Ab initio ; Acid dissociation constant ; Organic chemistry ; Aqueous solution ; Ion ; Biochemistry ; Physical chemistry Organophosphorus compounds synthesis ; Electron Spin Resonance Studies ; Advanced NMR Techniques and Applications
Authors: Martin Lämmle | Benedikt Bagemihl | Djawed Nauroozi | Lydia Petermann | Andrea Pannwitz | Sven Rau
Source: ChemPhotoChem (article, 2022-04-13)
Field: Chemistry — Organic Chemistry

Monosubstitution of 1<i>H</i>‐Imidazo[4,5‐<i>f</i>][1,10]phenanthroline Ligands Yields Maximum Luminescence Quantum Yield in Ruthenium Polypyridyl Complexes Abstract Six different monoarylated N‐aryl‐1 H ‐imidazo[4,5‐ f ][1,10]phenanthroline (Rip) ligands and their corresponding ruthenium complexes [(tbbpy) 2 Ru(Rip)] 2+ Ru(Rip) have been synthesized bearing different aryl substituents on the imidazole unit including electron donating and accepting groups. N,N’‐disubstitution on the imidazole unit yielded five new 1‐aryl‐3‐benzyl‐1 H ‐imidazo[4,5‐ f ][1,10]phenanthrolinium bromide (RR'ip) + ligands and the corresponding ruthenium complexes [(tbbpy) 2 Ru(RR'ip)] 3+ Ru(RR'ip). All complexes were characterized in terms of their structural, photophysical, photochemical and electrochemical properties. The photophysical data revealed a high luminescence quantum yield (21.6–22.8 %) for monoarylated Ru(Rip) complexes compared to [Ru(bpy) 3 ] 2+ (9.5 %) under inert conditions. Generating the imidazolium unit, yielding Ru(RR'ip)‐complexes lead to notable loss of quantum yields. Furthermore, we observed an enhanced photostability of Ru(RR'ip) complexes in the case of ortho substituted aryl groups. Ruthenium ; Aryl ; Chemistry ; Imidazole ; Phenanthroline ; Luminescence ; Quantum yield ; Bromide ; Medicinal chemistry ; Electrochemistry ; Yield (engineering) ; Fluorescence ; Photochemistry ; Stereochemistry ; Crystallography ; Catalysis ; Inorganic chemistry ; Organic chemistry ; Materials science ; Physical chemistry ; Alkyl ; Physics N-Heterocyclic Carbenes in Organic and Inorganic Chemistry ; Catalytic Cross-Coupling Reactions ; Catalytic C–H Functionalization Methods
Authors: Antony D. St‐Jacques | Joshua M. Rodriguez | Matthew G. Eason | Scott M. Foster | Safwat T. Khan | Adam M. Damry | Natalie K. Goto | Michael C. Thompson | Roberto A. Chica
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-09-17)
Field: Materials Science — Materials Chemistry

Computational remodeling of an enzyme conformational landscape for altered substrate selectivity Abstract Structural plasticity of enzymes dictates their function. Yet, our ability to rationally remodel enzyme conformational landscapes to tailor catalytic properties remains limited. Here, we report a computational procedure for tuning conformational landscapes that is based on multistate design. Using this method, we redesigned the conformational landscape of a natural aminotransferase to preferentially stabilize a less populated but reactive conformation, and thereby increase catalytic efficiency with a non-native substrate to alter substrate selectivity. Steady-state kinetics of designed variants revealed selectivity switches of up to 1900-fold, and structural analyses by room-temperature X-ray crystallography and multitemperature nuclear magnetic resonance spectroscopy confirmed that conformational equilibria favoured the target conformation. Our computational approach opens the door to the fine-tuning of enzyme conformational landscapes to create designer biocatalysts with tailored functionality. Substrate (aquarium) ; Selectivity ; Chemistry ; Conformational change ; Enzyme ; Kinetics ; Biophysics ; Structural plasticity ; Substrate specificity ; Molecular dynamics ; Conformational ensembles ; Catalysis ; Stereochemistry ; Computational chemistry ; Biochemistry ; Biology ; Physics Enzyme Structure and Function ; Protein Structure and Dynamics ; Glycosylation and Glycoproteins Research
Authors: Srikanth Nayak | Raju R. Kumal | Ahmet Uysal
Source: ChemRxiv (preprint, 2022-03-17)
Field: Chemistry — Physical and Theoretical Chemistry

Spontaneous and Ion-Specific Formation of Inverted Bilayers at Air/Aqueous Interface Developing better separation technologies for rare earth metals, an important aspect of a sustainable materials economy, is challenging due to their chemical similarities. Identifying molecular scale interactions that amplify the subtle differences between the rare earths can be useful in developing new separation technologies. Here, we describe ion-dependent monolayer to inverted bilayer transformation of extractant molecules at the air/aqueous interface. The inverted bilayers form with Lu3+ ions but not with Nd3+. By introducing Lu3+ ions to preformed monolayers, we extract kinetic parameters corresponding to the monolayer to inverted bilayer conversion. Temperature-dependent studies show Arrhenius behavior with an energy barrier of 40 kcal/mol. The kinetics of monolayer to inverted bilayer conversion is also affected by the character of the background anion, although anions are expected to be repelled from the interface. Our results show the outsized importance of ion-specific effects on interfacial structure and kinetics, pointing to their role in chemical separation methods. Monolayer ; Bilayer ; Chemical physics ; Ion ; Aqueous solution ; Chemistry ; Kinetics ; Arrhenius equation ; Molecule ; Materials science ; Nanotechnology ; Physical chemistry ; Activation energy ; Membrane ; Organic chemistry Electrostatics and Colloid Interactions ; Micro and Nano Robotics ; Pickering emulsions and particle stabilization
Authors: Illia Ruzhylo | Alix Sournia‐Saquet | Alain Moreau | Tom Delord | Éric Manoury | Rinaldo Poli | Agnès Labande
Source: European Journal of Inorganic Chemistry (article, 2022-03-15)
Field: Chemistry — Organic Chemistry

Heteroleptic Dirhodium(II) Complexes with Redox‐Active Ferrocenyl Ligands: Synthesis, Electrochemical Properties, and Redox‐Responsive Chemoselectivity in Carbene C−H Insertion Abstract A series of original heteroleptic dirhodium(II) complexes ( 4 a–j ) of formula [Rh 2 (OAc) 3 (L)], where L is a redox‐active ferrocenecarboxylate ligand, has been prepared. These dirhodium(II) complexes have been characterised by NMR, mass spectrometry and cyclic voltammetry. All complexes show a quasi‐reversible redox behaviour for the ferrocenyl unit. The latter can be selectively oxidised by [N(4‐C 6 H 4 Br) 3 ] + BF 4 − . Four selected heteroleptic complexes 4 a, 4 b , 4 f and 4 i , have been evaluated as catalysts for the intramolecular decomposition of a diazo compound 5 . The ratio between the aromatic substitution product 6 and the aliphatic C−H insertion product 7 increases (up to 19 % increase) when using the in situ generated oxidised form of the dirhodium(II) complexes ( 4 a + BF 4 − to 4 i + BF 4 − ). This shows that the oxidation of the ferrocenecarboxylate ligand has an effect on the chemoselectivity of the dirhodium‐catalysed diazo decomposition, and thus that the electronic properties of a complex can be tuned without exchanging ligands. Chemistry ; Chemoselectivity ; Redox ; Ligand (biochemistry) ; Carbene ; Cyclic voltammetry ; Medicinal chemistry ; Diazo ; Electrochemistry ; Intramolecular force ; Stereochemistry ; Combinatorial chemistry ; Catalysis ; Organic chemistry Cyclopropane Reaction Mechanisms ; Catalytic C–H Functionalization Methods ; Catalytic Cross-Coupling Reactions
Authors: Wei Zhang | Zhao Shu | Linjie Lu | Zhimin Fan | Shixin Ye
Source: Molecular Medicine Reports (article, 2022-01-05)
Field: Materials Science — Materials Chemistry

Activation of neurotrophin signalling with light‑inducible receptor tyrosine kinases Optogenetics combined with protein engineering based on natural light‑sensitive dimerizing proteins has evolved as a powerful strategy to study cellular functions. The present study focused on tropomyosin kinase receptors (Trks) that have been engineered to be light‑sensitive. Trk belongs to the superfamily of receptor tyrosine kinases (RTKs), which are single‑pass transmembrane receptors that are activated by natural ligands and serve crucial roles in cellular growth, differentiation, metabolism and motility. However, functional variations exist among receptors fused with light‑sensitive proteins. The present study proposed a signal transduction model for light‑induced receptor activation. This model is based on analysis of previous light‑induced Trk receptors reported to date and comparisons to the activation mechanism of natural receptors. In this model, quantitative differences on the dimerization induced from either top‑to‑bottom or bottom‑to‑up may lead to the varying amplitude of intracellular signals. We hypothesize that the top‑to‑bottom propagation is more favourable for activation and yields better results compared with the bottom‑to‑top direction. The careful delineation of the dimerization mechanisms fine‑tuning activation will guide future design for an optimum cellular output with the precision of light. Trk receptor ; Cell biology ; Receptor tyrosine kinase ; Receptor ; Biology ; Signal transduction ; Tyrosine kinase ; Tropomyosin receptor kinase C ; Neurotrophin ; Platelet-derived growth factor receptor ; Biochemistry ; Growth factor Photochromic and Fluorescence Chemistry ; Photoreceptor and optogenetics research ; Receptor Mechanisms and Signaling