jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Wesley J. Wagner | Austin B. Moyle | Nicole D. Wagner | Don L. Rempel | Michael L. Gross
Source: Analytical Chemistry (article, 2024-05-30)
Field: Chemistry — Spectroscopy

Evaluating Chemical Footprinting-Induced Perturbation of Protein Higher Order Structure Specific amino acid footprinting mass spectrometry (MS) is an increasingly utilized method for elucidating protein higher order structure (HOS). It does this by adding to certain amino acid residues a mass tag, whose reaction extent depends on solvent accessibility and microenvironment of the protein. Unlike reactive free radicals and carbenes, these specific footprinters react slower than protein unfolding. Thus, their footprinting, under certain conditions, provokes structural changes to the protein, leading to labeling on non-native structures. It is critical to establish conditions (i.e., reagent concentrations, time of reaction) to ensure that the structure of the protein following footprinting remains native. Here, we compare the efficacy of five methods in assessing protein HOS following footprinting at the intact protein level and then further localize the perturbation at the peptide level. Three are MS-based methods that provide dose-response plot analysis, evaluation of Poisson distributions of precursor and products, and determination of the average number of modifications. These MS-based methods reliably and effectively indicate HOS perturbation at the intact protein level, whereas spectroscopic methods (circular dichroism (CD) and dynamic light scattering (DLS)) are less sensitive in monitoring subtle HOS perturbation caused by footprinting. Evaluation of HOS at the peptide level indicates regions that are sensitive to localized perturbations. Peptide-level analysis also provides higher resolution of the HOS perturbation, and we recommend using it for future footprinting studies. Overall, this work shows conclusive evidence for HOS perturbation caused by footprinting. Implementation of quality control workflows can identify conditions to avoid the perturbation, for footprinting, allowing accurate and reliable identification of protein structural changes that accompany, for example, ligand interactions, mutations, and changes in solution environment. Chemistry ; Footprinting ; Perturbation (astronomy) ; Biophysics ; Computational chemistry ; Biochemistry ; Transcription factor ; Gene Mass Spectrometry Techniques and Applications ; Protein Structure and Dynamics ; Chemical Synthesis and Analysis
Authors: Tamina Kirsch | Tyler J. Hannah | Saurabh S. Chitnis
Source: Chemistry - A European Journal (article, 2024-10-22)
Field: Chemistry — Organic Chemistry

Influence of Pnictogen and Ligand Framework on the Lewis Acidity and Steric Environment in Pnictogen Pincer Complexes Pnictogen pincer complexes are a fascinating class of compounds due to their dynamic molecular and electronic structures, and valuable stoichiometric or catalytic reactivity. As recognition of their unique chemistry has grown, so too has the library of pincer ligands employed and pnictogen centres engaged to prepare them. Here we computationally study how the choice of pincer ligand framework and pnictogen influence the electronic and steric outcomes within the complexes obtained. The most relevant electronic parameter is the pnictogen-centred electrophilicity, which has been quantified by fluoride ion affinities and LUMO energies, while the most relevant steric parameter is the crowding around the central pnictogen, which has been quantified by the %V<sub>bur</sub> values and visualized using steric maps. The resulting trends are analyzed with reference to binding pocket size, acceptor orbital type, electronic delocalization, π-donor strengths, and heteroatom incorporation. Thus, considering 16 ligand frameworks and 4 heavy pnictogen centres, this study provides a broad-spectrum view of stereo-electronic variation in pnictogen pincer complexes, which, together with a recent study on geometric variation in the same family, provides a substantial dataset to guide future molecular design and reactivity studies. Pnictogen ; Steric effects ; Ligand (biochemistry) ; Chemistry ; Reactivity (psychology) ; Pincer ligand ; Computational chemistry ; Nucleophile ; Pincer movement ; Stereochemistry ; Organic chemistry ; Physics ; Catalysis ; Condensed matter physics ; Superconductivity Organometallic Complex Synthesis and Catalysis ; Organoboron and organosilicon chemistry ; Synthesis and characterization of novel inorganic/organometallic compounds
Authors: Xiangrui Zheng | Micaela Chacón | Thorsten Allers | Neil Dixon | James Winterburn
Source: Biochemical Engineering Journal (article, 2024-09-16)
Field: Materials Science — Biomaterials

Enhanced 4-hydroxybutyrate incorporation into the PHA terpolymer of Haloferax mediterranei by heterologous expression of 4-hydroxybutyrate-CoA transferases/synthetases The polyhydroxyalkanoate terpolymer, P[(3HB)- co -(3HV)- co -(4HB)], is a promising plastic alternative for specialized applications, notably in medical and pharmaceutical sectors. Haloferax mediterranei (Hfx), an extreme halophile archaeon, is a P[(3HB)- co -(3HV)- co -(4HB)] terpolymer production host, however the native molar proportion of 4HB incorporated into the terpolymer is low. To improve incorporation, four 4-hydroxybutyrate-CoA transferases/synthetases from Clostridum kluyveri (OrfZ), Clostridium aminobutyricum (AbfT), Nitrosopumilis maritimus ( Nm CAT), and Cupriavidus necator N-1 ( Cn CAT), were heterologously expressed in H. mediterranei , and evaluated for their ability to supply 4HB-CoA for PHA terpolymer production. Growth, PHA synthesis, and polymer composition were evaluated for the four heterologous strains in shake-flask, with Hfx_ Nm CAT demonstrating superior growth, terpolymer titre and 4HB molar ratio. Co-feeding with γ-butyrolactone was optimised, and Hfx_ Nm CAT was further evaluated under fed-batch fermentation where a maximum PHA titre of 0.7 g/L, containing 52 mol% 4HB, was achieved. This is an order of magnitude improvement in 4HB terpolymer incorporation by H. mediterranei . • Heterologous 4HB-CoA transferase/synthetase expression in H. mediterranei . • PHA terpolymer production from glucose and γ-butyrolactone co-feed. • P[(3HB)- co -(5 mol% 3HV)- co -(52 mol% 4HB)] production in fed-batch fermentation. Polyhydroxyalkanoates ; Biochemistry ; Chemistry ; Heterologous ; Heterologous expression ; Bacteria ; Biology ; Recombinant DNA ; Genetics ; Gene biodegradable polymer synthesis and properties ; Microbial Metabolic Engineering and Bioproduction ; Enzyme Catalysis and Immobilization
Authors: Mounir Bouras
Source: Progress In Electromagnetics Research Letters (article, 2024-01-01)
Field: Materials Science — Surfaces, Coatings and Films

High-performance Silicon Nitride Grating-coupled SPR Sensors for Gas Detection and Biosensing Surface Plasmon Resonance (SPR) serves as a crucial optical technique in the realm of chemical sensing. Under specific conditions, the reflectivity of a thin metal film exhibits an exceptional sensitivity to optical changes in the medium on one side. In this investigation, we propose and simulate a plasmonic sensor incorporating a silicon nitride grating with Ag layers for the detection of solution and gas at an optical communication wavelength of 1550 nm. In both cases of the surface diffraction-grating, there is a notable enhancement in angular sensitivity compared to conventional prism-coupled configurations. Simulations, employing rigorous coupled wave analysis (RCWA), highlight that the suggested sensor, optimized in design parameters, offers notably superior sensitivity, a lower detection limit, and a higher figure of merit (FOM) than existing grating-based SPR sensors. This implies the potential realization of refractive index sensors with a high figure of merit through such streamlined and compact configurations. Biosensor ; Grating ; Materials science ; Silicon nitride ; Nanotechnology ; Optoelectronics ; Silicon Optical Coatings and Gratings ; Analytical Chemistry and Sensors ; Photonic and Optical Devices
Authors: Krisztina Sárosi | Christopher Tuinenga | Gergely F. Samu | Károly Mogyorósi | Júlia Dudás | Bálint Tóth | Péter Jójárt | Barnabás Gilicze | Imre Seres | Zsolt Bengery | Csaba Janáky | Viktor Chikán
Source: The Journal of Physical Chemistry C (article, 2024-02-27)
Field: Materials Science — Materials Chemistry

Temperature Dependent Carrier Dynamics in Ga-Alloyed CdSe/ZnS Core–Shell Quantum Dots In this work, temperature dependent transient absorption spectroscopy measurements are presented on gallium-alloyed CdSe/ZnS core–shell nanoparticles between 30 and 130 °C. To our knowledge, temperature dependent measurements in these systems have been reported only in a few papers, although all processes related to carrier recombination are affected by temperature. For these experiments, gallium-alloyed CdSe/ZnS QD samples were used with nominal doping percentages of 2.5%, 7.5%, 15%. The experimental results show that the transient absorption decay is faster for the pristine CdSe/ZnS samples than in the gallium-alloyed samples at all temperatures. It is assumed that Ga-alloying promotes the formation of trions in the samples by introducing occupied impurity levels within the bandgap of CdSe. The resulting Coulomb blockade will, in turn, prolong the hot-electron relaxation process. By variation of the temperature, the distribution of charge carriers in the different recombination channels can be altered to accelerate recombination in the Ga-alloyed samples at higher temperatures. These measurements demonstrated their usefulness for observing the redistribution of charge carriers among different relaxation pathways. Gallium ; Materials science ; Quantum dot ; Charge carrier ; Band gap ; Recombination ; Doping ; Cadmium selenide ; Impurity ; Relaxation (psychology) ; Carrier lifetime ; Nanoparticle ; Chemical physics ; Analytical Chemistry (journal) ; Molecular physics ; Optoelectronics ; Chemistry ; Nanotechnology ; Silicon Quantum Dots Synthesis And Properties ; Chalcogenide Semiconductor Thin Films ; Semiconductor Quantum Structures and Devices
Authors: B. Campbell | J. V. Riffle | A. de la Torre | Qiaochu Wang | K. W. Plumb | Shawna Hollen
Source: Physical Review Materials (article, 2024-03-06)
Field: Materials Science — Materials Chemistry

Nanoscale electronic inhomogeneities in <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mn>1</mml:mn><mml:mi>T</mml:mi><mml:msub><mml:mtext>-TaS</mml:mtext><mml:mn>2</mml:mn></mml:msub></mml:mrow></mml:math> In 1T-TaS2, native defects create electronic inhomogeneities spanning 5-10 nanometers that coexist with a well-formed commensurate charge density wave with a 1.3 nm period. Over these inhomogeneities, the band center shifts by up to 60meV and the gap varies by more than 100 meV. Surprisingly, the charge density wave order is unperturbed. These results reopen questions of how disorder affects charge density wave phases in correlated systems and emphasize the importance of real-space measurements in resolving the structural and electronic properties of quantum materials. Materials science ; Charge (physics) ; Condensed matter physics ; Algorithm ; Physics ; Computer science ; Quantum mechanics 2D Materials and Applications ; Electronic and Structural Properties of Oxides ; Surface and Thin Film Phenomena
Authors: Magali Batteau | Élodie Bouju | Adriana Ramírez-Romero | Sylvie Nuccio | René de Vaumas | Florian Delrue | Karine Faure
Source: Analytical Methods (article, 2024-01-01)
Field: Chemistry — Spectroscopy

Resolving phytosterols in microalgae using offline two-dimensional reversed phase liquid chromatography-supercritical fluid chromatography coupled with quadrupole time-of-flight mass spectrometry Sterols are unsaponifiable lipids resulting from plant metabolism that exhibit interesting bioactive properties. Microalgae are a major source of specific phytosterols, most of which are still not fully characterized. The similarity in sterol structures and the existence of positional isomers make the separation of phytosterols challenging. A method was developed based on an offline two-dimensional (2D) system, reversed-phase liquid chromatography (RPLC)-supercritical fluid chromatography (SFC)/quadrupole time-of-flight (Q-ToF) mass spectrometry, for the identification of sterols in microalgae. Subsequent positive-mode MS/MS was used to confirm the identified phytosterols. The 2D chromatogram exhibited a pattern related to the positions of the double bonds, which were confirmed by standard injection, enabling structural elucidation. The analysis of the unsaponifiable fraction of two algae, namely <i>Scenedesmus obliquus</i>, a freshwater microalgae, and <i>Padina pavonica</i>, a marine macroalgae, highlighted the ability of the method to distinguish a large number of sterol isomers. Unsaponifiable ; Chromatography ; Supercritical fluid chromatography ; Chemistry ; Sterol ; Mass spectrometry ; Phytosterol ; Supercritical fluid ; Quadrupole time of flight ; High-performance liquid chromatography ; Tandem mass spectrometry ; Organic chemistry ; Cholesterol ; Biochemistry Analytical Chemistry and Chromatography ; Metabolomics and Mass Spectrometry Studies ; Algal biology and biofuel production
Authors: Leelakrishna Reddy
Source: Heliyon (review, 2024-07-11)
Field: Materials Science — Materials Chemistry

Exploring Gd3+-activated calcium-based host materials for phototherapy lamps: A comprehensive review Apart from the use of sun therapy for the cure of many skin diseases and disorders of bygone days, nowadays artificial light sources of a narrowband (NB) ultraviolet-B (UV-B) have effectively revolutionized the treatment of such skin diseases. The crucial role of gadolinium (Gd<sup>3+</sup>) ions in calcium-based hosts lies in their narrowband emission spectrum, specifically at 311-315 nm, attributed to the <sup>6</sup>P<sub>7/2</sub> to <sup>8</sup>S<sub>7/2</sub> transition. Calcium-based materials, known for their chemical stability, facilitate Gd<sup>3+</sup> embedding, enabling UV activation and express emission in the narrowband range. This emission spectrum is well-suited for skin treatments, aligning with the action spectrum of various skin diseases. Gd<sup>3+</sup> activated host materials in fluorescent lamps are considered prime sources of NB-UVB emissions. Calcium-based host materials are proving to be popular environments for embedding of dopants for such emissions. Calcium-based phosphor materials are leading the research in phototherapy applications due to their strong UV-B emissions, especially when activated by Gd<sup>3+</sup> ions. Applications of phosphor host materials of this nature are generally chemically and thermally stable, have a low synthesis temperature and which produce enhanced NB-UVB emissions specifically suited for phototherapy lamps. This paper is a review of calcium -based phosphor host materials in Gd<sup>3+</sup> activated materials or through energy transfers from sensitized dopant ions for enhanced NB-UVB emissions that is pertinent for treatments of many skin diseases such as psoriasis, vitiligo, eczema, and many other skin conditions. Calcium ; Host (biology) ; Medicine ; Nanotechnology ; Materials science ; Biology ; Internal medicine ; Genetics Luminescence Properties of Advanced Materials ; Nanoplatforms for cancer theranostics ; Luminescence and Fluorescent Materials
Authors: Kakaraparthi Kranthiraja | Waner He | Hao‐Wei Yu | Feng Zhen | Naoya Nozaki | Hidetoshi Matsumoto | Ming‐Hsuan Yu | Yong Li | Sergei Manzhos | Mats R. Andersson | Chu‐Chen Chueh | Tsuyoshi Michinobu | Prashant Sonar
Source: Solar RRL (article, 2024-05-18)
Field: Materials Science — Polymers and Plastics

Diketopyrrolopyrrole‐Dioxo‐Benzodithiophene‐Based Multifunctional Conjugated Polymers for Organic Field‐Effect Transistors and Perovskite Solar Cells While dual‐acceptor‐type conjugated polymers have witnessed a great success in organic field‐effect transistors (OFETs), their potential multifunctionality in other optoelectronic devices has been overlooked. Herein, three conjugated polymers (DPPF‐BDD, DPPT‐BDD, and DPPSe‐BDD) comprising furan/thiophene/selenophene‐flanked diketopyrrolopyrrole (DPP) and dioxo‐benzodithiophene (BDD) as repeating units are designed, synthesized, and characterized. Modulating the chalcogen on DPP flank shows an impact on dual‐acceptor polymer optoelectronic properties. Subsequently, the potential of these polymers in both OFETs and perovskite solar cells (PSCs) either as semiconductors or as passivation materials, respectively, is investigated. Interestingly, DPPF‐BDD, DPPT‐BDD, and DPPSe‐BDD show ambipolar behavior in vacuum with hole ( μ h ) and electron ( μ e ) mobilities of 0.0263/0.0223, 0.0187/0.0123, and 0.0070/0.0051 cm 2 V −1 s −1 , respectively. Upon doping tetrabutylammonium iodide into DPPF‐BDD, DPPT‐BDD, and DPPSe‐BDD polymers, the respective OFETs show relatively higher μ h and μ e (0.0389/0.0503; 0.0289/0.0259; 0.0058/0.0156 cm 2 V −1 s −1 ) than the undoped polymer OFETs. Furthermore, DPPF‐BDD‐, DPPT‐BDD‐, and DPPSe‐BDD‐incorporated (in the antisolvent treatment and PCBM electron transport layer) PSCs display maximum power conversion efficiency of 23.48%, 22.85%, and 23.35%, respectively, surpassing the control device (22.83%), which is benefited from the perovskite surface passivation and the charge extraction improvement. Overall, a new class of multifunctional DPP‐based dual‐acceptor‐type polymers that are highly compatible with OFETs and high‐performance PSCs is presented. Conjugated system ; Perovskite (structure) ; Materials science ; Polymer ; Organic solar cell ; Optoelectronics ; Chemistry ; Organic chemistry ; Composite material Conducting polymers and applications ; Perovskite Materials and Applications ; Organic Electronics and Photovoltaics
Authors: Alyona A. Starikova | Maxim G. Chegerev | А. Г. Стариков | Владимир И. Минкин
Source: Chemistry (article, 2024-08-23)
Field: Materials Science — Electronic, Optical and Magnetic Materials

The Magnetic Properties of Fluorenyl and tert-Butyl-nitroxyl Acene-Based Derivatives: A Quantum Chemical Insight Acenes, as a class of polycyclic aromatic hydrocarbons, attract considerable attention due to their remarkable nonlinear optical and magnetic properties. The aim of this work was the elucidation of the capability of radical-substituted acene derivatives to undergo spin-state-switching rearrangements. For this purpose, a series of acene-based (anthracene, pentacene, heptacene) molecules bearing fluorenyl and tert-butyl-nitroxyl radicals were investigated through comprehensive quantum chemical modeling of their electronic structures, isomerization and magnetic properties. A possible mechanism of the transformation of the closed-shell folded isomer into the biradical twisted structure of the bis-fluorenyl anthracene has been ascertained by applying the procedure of searching for the Minimum Energy Crossing Point. The conditions favoring the occurrence of spin-state-switching in such classes of polycyclic aromatic hydrocarbon derivatives have been formulated. By varying the size of an acene core and the type of radical substituent, the compounds capable of changing their magnetic properties have been revealed. Considering the unique features of radical-bearing acene-based derivatives, the proposed molecules can be used as functional materials in photonics and electronics. Acene ; Nitroxyl ; Quantum chemical ; Chemistry ; Photochemistry ; Organic chemistry ; Molecule Magnetism in coordination complexes ; Electron Spin Resonance Studies ; Organic Chemistry Cycloaddition Reactions
Authors: Zahra Noori | Ibério de P. R. Moreira | Josep María Bofill | Jordi Poater
Source: ChemistryOpen (article, 2024-03-05)
Field: Materials Science — Materials Chemistry

Adjusting UV‐Vis Spectrum of Alizarin by Insertion of Auxochromes First synthesized in 1868, alizarin became one of the first synthetic dyes and was widely used as a red dye in the textile industry, making it more affordable and readily available than the traditional red dyes derived from natural sources. Despite extensive both experimental and computational analyses on the electronic effects of substituents on the shape of the visible spectrum of alizarin and alizarin Red S, no previous systematic work has been undertaken with the aim to fine tune the dominant absorption region defining its color by introducing other electron-withdrawing or electron-donor groups. For such, we have performed a comprehensive study of electronic effects of substituents in position C<sub>3</sub> of alizarin by means of a time dependent DFT approach. These auxochromes attached to the chromophore are proven to alter both the wavelength and intensity of absorption. It is shown that the introduction of an electron-donor group in alizarin causes the transition bands to be significantly red-shifted whereas electron-withdrawing groups cause a minor blue-shifting. Alizarin ; Spectrum (functional analysis) ; ALIZARIN RED ; Photochemistry ; Chemistry ; Nuclear chemistry ; Physics ; Medicine Photochromic and Fluorescence Chemistry ; Synthesis of Organic Compounds ; Dyeing and Modifying Textile Fibers
Authors: Jessica Ettedgui | Kazutoshi Yamamoto | Burchelle Blackman | Norikazu Koyasu | Natarajan Raju | Olga Vasalatiy | Hellmut Merkle | Eduard Y. Chekmenev | Boyd M. Goodson | Murali C. Krishna | Rolf E. Swenson
Source: Angewandte Chemie International Edition (article, 2024-06-03)
Field: Chemistry — Spectroscopy

In vivo Metabolic Sensing of Hyperpolarized [1‐<sup>13</sup>C]Pyruvate in Mice Using a Recyclable Perfluorinated Iridium Signal Amplification by Reversible Exchange Catalyst Real-time visualization of metabolic processes in vivo provides crucial insights into conditions like cancer and metabolic disorders. Metabolic magnetic resonance imaging (MRI), by amplifying the signal of pyruvate molecules through hyperpolarization, enables non-invasive monitoring of metabolic fluxes, aiding in understanding disease progression and treatment response. Signal Amplification By Reversible Exchange (SABRE) presents a simpler, cost-effective alternative to dissolution dynamic nuclear polarization, eliminating the need for expensive equipment and complex procedures. We present the first in vivo demonstration of metabolic sensing in a human pancreatic cancer xenograft model compared to healthy mice. A novel perfluorinated Iridium SABRE catalyst in a fluorinated solvent and methanol blend facilitated this breakthrough with a 1.2-fold increase in [1-<sup>13</sup>C]pyruvate SABRE hyperpolarization. The perfluorinated moiety allowed easy separation of the heavy-metal-containing catalyst from the hyperpolarized [1-<sup>13</sup>C]pyruvate target. The perfluorinated catalyst exhibited recyclability, maintaining SABRE-SHEATH activity through subsequent hyperpolarization cycles with minimal activity loss after the initial two cycles. Remarkably, the catalyst retained activity for at least 10 cycles, with a 3.3-fold decrease in hyperpolarization potency. This proof-of-concept study encourages wider adoption of SABRE hyperpolarized [1-<sup>13</sup>C]pyruvate MR for studying in vivo metabolism, aiding in diagnosing stages and monitoring treatment responses in cancer and other diseases. Hyperpolarization (physics) ; In vivo ; Chemistry ; Iridium ; Catalysis ; Biophysics ; Biochemistry ; Nuclear magnetic resonance spectroscopy ; Organic chemistry ; Biology Advanced NMR Techniques and Applications ; Electron Spin Resonance Studies ; Magnetism in coordination complexes