jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Shuai Yang | Lanlu Lu | Ji Li | Qingqing Cheng | Bingbao Mei | Xuewen Li | Jianing Mao | Panzhe Qiao | Fanfei Sun | Jingyuan Ma | Qing Xu | Zheng Jiang
Source: SusMat (article, 2023-04-27)
Field: Materials Science — Materials Chemistry

Boosting hydrogen peroxide production via establishment and reconstruction of single‐metal sites in covalent organic frameworks Abstract Covalent organic frameworks (COFs) have been well developed in electrocatalytic systems owing to their controllable skeletons, porosities, and functions. However, the catalytic process in COFs remains underexplored, hindering an in‐depth understanding of the catalytic mechanism. In this work, uniform Pt–N 1 O 1 Cl 4 sites chelated via C–N and C=O bonds along the one‐dimensional and open channels of TP–TTA–COF were established. Different from conventional single‐metal sites constructed for the near‐free platinum for hydrogen evolution, the as‐constructed PtCl–COF showed 2e − oxygen reduction for H 2 O 2 production. We tracked the dynamic evolution process of atomic Pt sites in which Pt–N 1 O 1 Cl 4 was transformed into Pt–N 1 O 1 (OH) 2 using in situ X‐ray adsorption. The theoretical calculations revealed that the strong Pt–support interaction in Pt–N 1 O 1 (OH) 2 facilitated *OOH formation and thus led to higher selectivity and activity for the oxygen reduction reaction in the 2e − pathway. This work can expand the applications of COFs through the regulation of their local electronic states for the manipulation of the metal center. Catalysis ; Hydrogen peroxide ; Covalent bond ; Platinum ; Adsorption ; Chemistry ; Selectivity ; Metal-organic framework ; Metal ; Hydrogen ; Boosting (machine learning) ; Hydrogen bond ; Materials science ; Photochemistry ; Nanotechnology ; Physical chemistry ; Molecule ; Organic chemistry ; Computer science Covalent Organic Framework Applications ; Advanced Photocatalysis Techniques ; Metal-Organic Frameworks: Synthesis and Applications
Authors: Wei‐Chun Chou | Zhoumeng Lin
Source: Current Opinion in Biotechnology (review, 2023-12-15)
Field: Materials Science — Biomaterials

Impact of protein coronas on nanoparticle interactions with tissues and targeted delivery Drug delivery ; Nanotechnology ; Nanoparticle ; Targeted drug delivery ; Chemistry ; Delivery system ; Biophysics ; Materials science ; Biology ; Pharmacology Nanoparticle-Based Drug Delivery ; Polymer Surface Interaction Studies ; Protein Interaction Studies and Fluorescence Analysis
Authors: Md. Mohosin Ali | Tajmul Hasan | Javed Masood Khan | Dileep Kumar | Anis Ahmad | Shahed Rana | Mohammad Majibur Rahman | Md. Anamul Hoque | Shariff E. Kabir
Source: RSC Advances (article, 2023-01-01)
Field: Chemistry — Organic Chemistry

Association behavior and physico-chemical parameters of a cetylpyridinium bromide and levofloxacin hemihydrate mixture in aqueous and additive media The investigation of the micellization of a mixture of cetylpyridinium bromide (CPB) and levofloxacin hemihydrate (LFH) was carried out by a conductivity technique in aqueous and aq. additive mixtures, including NaCl, NaOAc, NaBenz, 4-ABA, and urea. The aggregation behavior of the CPB + LFH mixture was studied considering the variation in additive contents and the change in experimental temperature. The micelle formation of the CPB + LFH mixture was examined from the breakpoint observed in the specific conductivity <i>versus</i> surfactant concentration plots. Different micellar characteristics, such as the critical micelle concentration (CMC) and the extent of counter ion bound (<i>β</i>), were evaluated for the CPB + LFH mixture. The CMC and <i>β</i> were found to undergo a change with the types of solvents, composition of solvents, and working temperatures. The Δ<i>G</i><sup>0</sup><sub>m</sub> values of the CPB + LFH system in aqueous and aq. additive solutions were found to be negative, which denotes a spontaneous aggregation phenomenon of the CPB + LFH system. The changes in Δ<i>H</i><sup>0</sup><sub>m</sub> and Δ<i>S</i><sup>0</sup><sub>m</sub> for the CPB + LFH mixture were also detected with the alteration in the solvent nature and solution temperature. The Δ<i>H</i><sup>0</sup><sub>m</sub> and Δ<i>S</i><sup>0</sup><sub>m</sub> values obtained for the association of the CPB + LFH mixture reveal that the characteristic interaction forces may possibly be ion-dipole, dipole-dipole, and hydrophobic between CPB and LFH. The thermodynamics of transfer and Δ<i>H</i><sup>0</sup><sub>m</sub>-Δ<i>S</i><sup>0</sup><sub>m</sub> compensation variables were also determined. All the parameters computed in the present investigation are illustrated with proper logic. Bromide ; Chemistry ; Aqueous solution ; Levofloxacin ; Aqueous medium ; Association (psychology) ; Inorganic chemistry ; Organic chemistry ; Biochemistry ; Psychology Surfactants and Colloidal Systems ; Analytical Chemistry and Chromatography ; Protein Interaction Studies and Fluorescence Analysis
Authors: Victoria R. Mingione | YiTing Paung | Ian R Outhwaite | Markus A. Seeliger
Source: Biochemical Society Transactions (review, 2023-02-16)
Field: Chemistry — Organic Chemistry

Allosteric regulation and inhibition of protein kinases The human genome encodes more than 500 different protein kinases: signaling enzymes with tightly regulated activity. Enzymatic activity within the conserved kinase domain is influenced by numerous regulatory inputs including the binding of regulatory domains, substrates, and the effect of post-translational modifications such as autophosphorylation. Integration of these diverse inputs occurs via allosteric sites that relate signals via networks of amino acid residues to the active site and ensures controlled phosphorylation of kinase substrates. Here, we review mechanisms of allosteric regulation of protein kinases and recent advances in the field. Allosteric regulation ; Autophosphorylation ; Kinase ; Phosphorylation ; Allosteric enzyme ; Biochemistry ; Enzyme ; Protein kinase A ; Cell biology ; Biology ; Chemistry Synthesis and Biological Evaluation ; Fungal Plant Pathogen Control ; Enzyme function and inhibition
Authors: Valdemaras Petrosius | Pedro Aragon-Fernandez | Tabiwang N. Arrey | Nil Üresin | Benjamin Furtwängler | Hamish Stewart | Eduard Denisov | J. Petzoldt | Amelia C. Peterson | Christian Hock | Eugen Damoc | Alexander Makarov | Vlad Zabrouskov | Bo Porse | Erwin M. Schoof
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-06-08)
Field: Chemistry — Spectroscopy

Evaluating the capabilities of the Astral mass analyzer for single-cell proteomics Abstract The complexity of human physiology arises from well-orchestrated interactions between trillions of single cells in the body. While single-cell RNA sequencing (scRNA-seq) has enhanced our understanding of cell diversity, gene expression alone does not fully characterize cell phenotypes. Additional molecular dimensions, such as proteins, are needed to define cellular states accurately. Mass spectrometry (MS)-based proteomics has emerged as a powerful tool for comprehensive protein analysis, including single-cell applications. However, challenges remain in terms of throughput and proteomic depth, in order to maximize the biological impact of single-cell proteomics by Mass Spectrometry (scp-MS) workflows. This study leverages a novel high-resolution, accurate mass (HRAM) instrument platform, consisting of both an Orbitrap and an innovative HRAM Asymmetric Track Lossless (Astral) analyzer. The Astral analyzer offers high sensitivity and resolution through lossless ion transfer and a unique flight track design. We evaluate the performance of the Thermo Scientific Orbitrap Astral MS using Data-Independent Acquisition (DIA) and assess proteome depth and quantitative precision for ultra-low input samples. Optimal DIA method parameters for single-cell proteomics are identified, and we demonstrate the ability of the instrument to study cell cycle dynamics in Human Embryonic Kidney (HEK293) cells, and cancer cell heterogeneity in a primary Acute Myeloid Leukemia (AML) culture model. Proteomics ; Orbitrap ; Computational biology ; Mass spectrometry ; Proteome ; Quantitative proteomics ; Chemistry ; Single-cell analysis ; Computer science ; Cell ; Nanotechnology ; Biology ; Biochemistry ; Chromatography ; Gene ; Materials science Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Single-cell and spatial transcriptomics
Authors: Qiu‐Shui Mu | Xiang Gao | Zheng Cui | Yue‐Jian Lin | Guo‐Xin Jin
Source: Science China Chemistry (article, 2023-09-07)
Field: Chemistry — Organic Chemistry

Selective construction of molecular Solomon links and figure-eight knots by fine-tuning unsymmetrical ligands Steric effects ; Ligand (biochemistry) ; Chemistry ; Denticity ; Molecule ; Hydrogen bond ; Selectivity ; Crystallography ; Single crystal ; Crystal structure ; Stereochemistry ; Topology (electrical circuits) ; Catalysis ; Organic chemistry Organometallic Complex Synthesis and Catalysis ; Supramolecular Chemistry and Complexes ; Crystallography and molecular interactions
Authors: Dipankar Saha | Johnson Dalmieda | Vinay Patel
Source: ACS Applied Electronic Materials (article, 2023-06-07)
Field: Materials Science — Materials Chemistry

Surface-Modified MXenes: Simulation to Potential Applications MXenes are promising two-dimensional materials with good electrical conductivity, layered structure, biocompatibility, hydrophilicity, chemical inertness, and high surface area. Since the discovery of MXenes, they have been used for multiple applications, including energy storage, sensors, electronics, and optical devices. Theoretically, various MXenes are predicted by multiple studies, but few have been synthesized experimentally. The synthesized MXenes can possess various terminating groups that provide a great avenue to modify the surface of MXenes to fine-tune their chemical and physical properties. Notably, the terminating group of MXenes can be adjusted using diverse modification strategies, including covalent and noncovalent approaches. To advance future applications, it is necessary to have a deeper understanding of both theoretical and experimental approaches of MXenes. Although there have been some reviews on MXenes, less attention has been paid to the essential principle involved in surface modification using covalent and noncovalent chemistry and the controllable design of various MXenes compositions based on the theoretical calculations. This review focuses on a detailed understanding of the synthesis process of MXenes, as well as theoretical and experimental approaches toward the determination of their physical and chemical properties. In effect, both synthetic methods and postsynthesis functionalization will be complemented by density functional theory calculations. Furthermore, various functionalization strategies of MXenes have been discussed. Finally, we have provided an overview of current trends of modified MXenes in energy storage devices, electrocatalysts, and sensors applications with a brief comparison of the current state-of-the-art methods. This review will help researchers understand the feasibility of MXenes at the fundamental level for potential use in large-scale practical applications. MXenes ; Surface modification ; Nanotechnology ; Materials science ; Computer science ; Chemistry ; Physical chemistry MXene and MAX Phase Materials ; 2D Materials and Applications ; Advanced Memory and Neural Computing
Authors: Fraz Saeed Butt | Allana Lewis | Riccardo Rea | Nurul A. Mazlan | Ting Chen | Norbert Radacsi | Enzo Mangano | Xianfeng Fan | Yaohao Yang | Shuiqing Yang | Yi Huang
Source: ACS Applied Materials & Interfaces (article, 2023-06-22)
Field: Chemistry — Inorganic Chemistry

Highly-Controlled Soft-Templating Synthesis of Hollow ZIF-8 Nanospheres for Selective CO<sub>2</sub> Separation and Storage Global warming is an ever-rising environmental concern, and carbon dioxide (CO<sub>2</sub>) is among its major causes. Different technologies, including adsorption, cryogenic separation, and sequestration, have been developed for CO<sub>2</sub> separation and storage/utilization. Among these, carbon capture using nano-adsorbents has the advantages of excellent CO<sub>2</sub> separation and storage performance as well as superior heat- and mass-transfer characteristics due to their large surface area and pore volume. In this work, an environmentally friendly, facile, bottom-up synthesis of ZIF-8 hollow nanospheres (with reduced chemical consumption) was developed for selective CO<sub>2</sub> separation and storage. During this soft-templating synthesis, a combined effect of ultra-sonication and low-temperature hydrothermal synthesis showed better control over an oil-in-water microemulsion formation and the subsequent growth of large-surface-area hollow ZIF-8 nanospheres having excellent particle size distribution. Systematic studies on the synthesis parameters were also performed to achieve fine-tuning of the ZIF-8 crystallinity, hollow structures, and sphere size. The optimized hollow ZIF-8 nanosphere sample having uniform size distribution exhibited remarkable CO<sub>2</sub> adsorption capability (∼2.24 mmol g<sup>-1</sup> at 0 °C and 1.75 bar), a CO<sub>2</sub>/N<sub>2</sub> separation selectivity of 12.15, a good CO<sub>2</sub> storage capacity (1.5-1.75 wt %), and an excellent cyclic adsorption/desorption performance (up to four CO<sub>2</sub> adsorption/desorption cycles) at 25 °C. In addition, the samples showed exceptional structural stability with only ∼15% of overall weight loss up to 600 °C under a nitrogen environment. Therefore, the hollow ZIF-8 nanospheres as well as their highly controlled soft-templating synthesis method reported in this work are useful in the course of the development of nanomaterials with optimized properties for future CO<sub>2</sub> capture technologies. Materials science ; Nanotechnology ; Chemical engineering ; Separation (statistics) Metal-Organic Frameworks: Synthesis and Applications ; Covalent Organic Framework Applications ; Membrane Separation and Gas Transport
Authors: Shengjun Du | Baolin Huang | Zhu Lin | Ying Wu | Jiawu Huang | Zhong Li | Hao Yu | Jing Xiao
Source: Carbon (article, 2023-09-12)
Field: Chemistry — Inorganic Chemistry

Optimizing gas transport for C3H6/C3H8 size sieving separation via fine pore engineering of carbon microspheres Propane ; Diffusion ; Chemical engineering ; Gaseous diffusion ; Mass transfer ; Kinetic energy ; Chemistry ; Materials science ; Activation energy ; Kinetics ; Nanotechnology ; Physical chemistry ; Thermodynamics ; Organic chemistry ; Chromatography Metal-Organic Frameworks: Synthesis and Applications ; Membrane Separation and Gas Transport ; Catalytic Processes in Materials Science
Authors: Yin Fang | Xiaozhuan Liang | Ningyu Zhang | Kangwei Liu | Rui Huang | Zhuo Chen | Xiaohui Fan | Huajun Chen
Source: arXiv (Cornell University) (preprint, 2023-06-13)
Field: Materials Science — Materials Chemistry

Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models Large Language Models (LLMs), with their remarkable task-handling capabilities and innovative outputs, have catalyzed significant advancements across a spectrum of fields. However, their proficiency within specialized domains such as biomolecular studies remains limited. To address this challenge, we introduce Mol-Instructions, a comprehensive instruction dataset designed for the biomolecular domain. Mol-Instructions encompasses three key components: molecule-oriented instructions, protein-oriented instructions, and biomolecular text instructions. Each component aims to improve the understanding and prediction capabilities of LLMs concerning biomolecular features and behaviors. Through extensive instruction tuning experiments on LLMs, we demonstrate the effectiveness of Mol-Instructions in enhancing large models' performance in the intricate realm of biomolecular studies, thus fostering progress in the biomolecular research community. Mol-Instructions is publicly available for ongoing research and will undergo regular updates to enhance its applicability. Computer science ; Realm ; Key (lock) ; Task (project management) ; Component (thermodynamics) ; Scale (ratio) ; Domain (mathematical analysis) ; Data science ; Systems engineering Machine Learning in Materials Science ; Machine Learning in Bioinformatics ; Protein Structure and Dynamics
Authors: Juner Zhang | Ailiena O. Maggiolo | Edwin Alfonzo | Runze Mao | Nicholas J. Porter | Nayla M. Abney | Frances H. Arnold
Source: Nature Catalysis (article, 2023-01-19)
Field: Chemistry — Organic Chemistry

Chemodivergent C(sp3)–H and C(sp2)–H cyanomethylation using engineered carbene transferases Carbene ; Chemistry ; Substrate (aquarium) ; Chemoselectivity ; Stereochemistry ; Alkylation ; Molecule ; Enzyme ; Combinatorial chemistry ; Catalysis ; Surface modification ; Organic chemistry ; Biology Cyclopropane Reaction Mechanisms ; Catalytic C–H Functionalization Methods ; Synthesis and Catalytic Reactions
Authors: Muhammad Khalid | Mashal Khan | Iqra Shafiq | Khalid Mahmood | Muhammad Nadeem Akhtar | Javed Iqbal | Wajid Zaman | Ataualpa Albert Carmo Braga
Source: Heliyon (article, 2023-01-17)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Role of donors in triggering second order non-linear optical properties of non-fullerene FCO-2FR1 based derivatives: A theoretical perspective The organic compounds are known as an emerging class in the field of nonlinear optical (NLO) materials. In this paper, D-π-A configured oxygen containing organic chromophores (<b>FD2-FD6</b>) were designed by incorporating various donors in the chemical structure of <b>FCO-2FR1</b>. This work is also inspired by the feasibility of <b>FCO-2FR1</b> as an efficient solar cell. Theoretical approach involving DFT functional <i>i.e</i>., B3LYP/6-311G(d,p) was utilized to achieve useful information regarding their electronic, structural, chemical and photonic properties. The structural modifications revealed significant electronic contribution in designing HOMOs and LUMOs for the derivatives with lowered energy gaps. The lowest HOMO-LUMO band gap obtained was 1.223 eV for <b>FD2</b> compound in comparison to the reference molecule (<b>FCO-2FR1</b>) <i>i.e.,</i> 2.053 eV. Moreover, the DFT findings revealed that the end-capped substituents play a key role in enhancing the NLO response of these push-pull chromophores. The UV-Vis spectra of tailored molecules revealed larger <i>λ</i> <sub>max</sub> values than the reference compound. Furthermore, strong intramolecular interactions showed the highest stabilization energy (28.40 kcal mol<sup>-1</sup>) for <b>FD2</b> in the natural bond orbitals (NBOs) transitions, combined with the least binding energy (-0.432 eV). Successfully, the NLO results were favorable for the same chromophore (<b>FD2</b>) which showed the highest value for dipole moment (<i>μ</i> <sub>tot</sub> = 20.049 <i>D</i>) and first hyper-polarizability (<i>β</i> <sub>tot</sub> = 11.22 × 10<sup>-27</sup> <i>esu</i>). Similarly, the largest value for linear polarizability ⟨<i>α</i>⟩ was obtained as 2.936 × 10<sup>-22</sup> <i>esu</i> for <b>FD3</b> compound. Overall, the designed compounds were calculated with greater NLO values as compared to <b>FCO-2FR1</b>. The current study may provoke the researchers towards designing of highly efficient NLO materials <i>via</i> using the suitable organic linking species. Polarizability ; Intramolecular force ; Chromophore ; Molecule ; HOMO/LUMO ; Band gap ; Computational chemistry ; Antiaromaticity ; Density functional theory ; Materials science ; Electronic structure ; Dipole ; Chemistry ; Photochemistry ; Stereochemistry ; Aromaticity ; Organic chemistry ; Optoelectronics Nonlinear Optical Materials Research ; Porphyrin and Phthalocyanine Chemistry ; Nonlinear Optical Materials Studies
Authors: Chunling Qin | Shuang Chen | Hassanien Gomaa | Mohamed A. Shenashen | Sherif A. El‐Safty | Qian Liu | Cuihua An | Xijun Liu | Qibo Deng | Ning Hu
Source: Acta Physico-Chimica Sinica (article, 2023-10-16)
Field: Materials Science — Surfaces, Coatings and Films

Regulating HER and OER Performances of 2D Materials by the External Physical Fields Computer science ; Materials science Electron and X-Ray Spectroscopy Techniques ; Semiconductor materials and devices
Authors: Sebastian Schäfer | Sebastian Kaufmann | Esther S. Rösch | Peter W. Roesky
Source: Chemical Society Reviews (review, 2023-01-01)
Field: Chemistry — Organic Chemistry

Divalent metallocenes of the lanthanides – a guideline to properties and reactivity Since the discovery in the early 1980s, the soluble divalent metallocenes of lanthanides have become a steadily growing field in organometallic chemistry. The predominant part of the investigation has been performed with samarium, europium, and ytterbium, whereas only a few reports dealing with other rare earth elements were disclosed. Reactions of these metallocenes can be divided into two major categories: (1) formation of Lewis acid-base complexes, in which the oxidation state remains +II; and (2) single electron transfer (SET) reductions with the ultimate formation of Ln(III) complexes. Due to the increasing reducing character from Eu(II) over Yb(II) to Sm(II), the plethora of literature concerning redox reactions revolves around the metallocenes of Sm and Yb. In addition, a few reactivity studies on Nd(II), Dy(II) and mainly Tm(II) metallocenes were published. These compounds are even stronger reducing agents but significantly more difficult to handle. In most cases, the metals are ligated by the versatile pentamethylcyclopentadienyl ligand: (C<sub>5</sub>Me<sub>5</sub>). Other cyclopentadienyl ligands are fully covered but only discussed in detail, if the ligand causes differences in synthesis or reactivity. Thus, the focus lays on three compounds: [(C<sub>5</sub>Me<sub>5</sub>)<sub>2</sub>Sm], [(C<sub>5</sub>Me<sub>5</sub>)<sub>2</sub>Eu] and [(C<sub>5</sub>Me<sub>5</sub>)<sub>2</sub>Yb] and their solvates. We discuss the synthesis and physical properties of divalent lanthanide metallocenes first, followed by an overview of the reactivity rendering the full potential of these versatile reactants. Lanthanide ; Divalent ; Chemistry ; Reactivity (psychology) ; Guideline ; Inorganic chemistry ; Combinatorial chemistry ; Organic chemistry ; Medicine ; Ion Organometallic Complex Synthesis and Catalysis ; Lanthanide and Transition Metal Complexes ; Magnetism in coordination complexes
Authors: Mizuki Tenjimbayashi | Timothée Mouterde | Pritam Kumar Roy | Koichiro Uto
Source: Nanoscale (review, 2023-01-01)
Field: Materials Science — Materials Chemistry

Liquid marbles: review of recent progress in physical properties, formation techniques, and lab-in-a-marble applications in microreactors and biosensors Liquid marbles (LMs) are nonsticking droplets whose surfaces are covered with low-wettability particles. Owing to their high mobility, shape reconfigurability, and widely accessible liquid/particle possibilities, the research on LMs has flourished since 2001. Their physical properties, fabrication mechanisms, and functionalisation capabilities indicate their potential for various applications. This review summarises the fundamental properties of LMs, the recent advances (mainly works published in 2020-2023) in the concept of LMs, physical properties, formation methods, LM-templated material design, and biochemical applications. Finally, the potential development and variations of LMs are discussed. Microreactor ; Reconfigurability ; Nanotechnology ; Materials science ; Wetting ; Computer science ; Chemistry ; Composite material Pickering emulsions and particle stabilization ; Archaeological and Geological Studies