jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Salila Pengthaisong | Beatriz Piniello | G.J. Davies | Carme Rovira | James R. Ketudat Cairns
Source: ACS Catalysis (article, 2023-04-14)
Field: Chemistry — Organic Chemistry

Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation Retaining glycoside hydrolases use acid/base catalysis with an enzymatic acid/base protonating the glycosidic bond oxygen to facilitate leaving-group departure alongside attack by a catalytic nucleophile to form a covalent intermediate. Generally, this acid/base protonates the oxygen laterally with respect to the sugar ring, which places the catalytic acid/base and nucleophile carboxylates within about 4.5-6.5 Å of each other. However, in glycoside hydrolase (GH) family 116, including disease-related human acid β-glucosidase 2 (GBA2), the distance between the catalytic acid/base and the nucleophile is around 8 Å (PDB: 5BVU) and the catalytic acid/base appears to be above the plane of the pyranose ring, rather than being lateral to that plane, which could have catalytic consequences. However, no structure of an enzyme-substrate complex is available for this GH family. Here, we report the structures of <i>Thermoanaerobacterium xylanolyticum</i> β-glucosidase (<i>Tx</i>GH116) D593N acid/base mutant in complexes with cellobiose and laminaribiose and its catalytic mechanism. We confirm that the amide hydrogen bonding to the glycosidic oxygen is in a perpendicular rather than lateral orientation. Quantum mechanics/molecular mechanics (QM/MM) simulations of the glycosylation half-reaction in wild-type <i>Tx</i>GH116 indicate that the substrate binds with the nonreducing glucose residue in an unusual relaxed <sup>4</sup><i>C</i><sub>1</sub> chair at the <i>-1</i> subsite. Nevertheless, the reaction can still proceed through a <sup>4</sup><i>H</i><sub>3</sub> half-chair transition state, as in classical retaining β-glucosidases, as the catalytic acid D593 protonates the perpendicular electron pair. The glucose C6OH is locked in a <i>gauche</i>, <i>trans</i> orientation with respect to the C5-O5 and C4-C5 bonds to facilitate perpendicular protonation. These data imply a unique protonation trajectory in Clan-O glycoside hydrolases, which has strong implications for the design of inhibitors specific to either lateral protonators, such as human GBA1, or perpendicular protonators, such as human GBA2. Chemistry ; Glycosidic bond ; Stereochemistry ; Nucleophile ; Protonation ; Hydrogen bond ; Oxocarbenium ; Pyranose ; Dihedral angle ; Glycoside hydrolase ; Hydrolase ; QM/MM ; Catalysis ; Organic chemistry ; Enzyme ; Molecule Carbohydrate Chemistry and Synthesis ; Enzyme Production and Characterization ; Enzyme Catalysis and Immobilization
Authors: Hong Su | Jiangping Liu | Yanan Hu | Tianhao Ai | Chenhao Gong | Jichang Lu | Yongming Luo
Source: Nanomaterials (article, 2023-02-19)
Field: Materials Science — Materials Chemistry

Comparative Study of α- and β-MnO2 on Methyl Mercaptan Decomposition: The Role of Oxygen Vacancies As a representative sulfur-containing volatile organic compounds (S-VOCs), CH<sub>3</sub>SH has attracted widespread attention due to its adverse environmental and health risks. The performance of Mn-based catalysts and the effect of their crystal structure on the CH<sub>3</sub>SH catalytic reaction have yet to be systematically investigated. In this paper, two different crystalline phases of tunneled MnO<sub>2</sub> (α-MnO<sub>2</sub> and β-MnO<sub>2</sub>) with the similar nanorod morphology were used to remove CH<sub>3</sub>SH, and their physicochemical properties were comprehensively studied using high-resolution transmission electron microscope (HRTEM) and electron paramagnetic resonance (EPR), H<sub>2</sub>-TPR, O<sub>2</sub>-TPD, Raman, and X-ray photoelectron spectroscopy (XPS) analysis. For the first time, we report that the specific reaction rate for α-MnO<sub>2</sub> (0.029 mol g<sup>-1</sup> h<sup>-1</sup>) was approximately 4.1 times higher than that of β-MnO<sub>2</sub> (0.007 mol g<sup>-1</sup> h<sup>-1</sup>). The as-synthesized α-MnO<sub>2</sub> exhibited higher CH<sub>3</sub>SH catalytic activity towards CH<sub>3</sub>SH than that of β-MnO<sub>2</sub>, which can be ascribed to the additional oxygen vacancies, stronger surface oxygen migration ability, and better redox properties from α-MnO<sub>2</sub>. The oxygen vacancies on the catalyst surface provided the main active sites for the chemisorption of CH<sub>3</sub>SH, and the subsequent electron transfer led to the decomposition of CH<sub>3</sub>SH. The lattice oxygen on catalysts could be released during the reaction and thus participated in the further oxidation of sulfur-containing species. CH<sub>3</sub>SSCH<sub>3</sub>, S<sup>0</sup>, SO<sub>3</sub><sup>2-</sup>, and SO<sub>4</sub><sup>2-</sup> were identified as the main products of CH<sub>3</sub>SH conversion. This work offers a new understanding of the interface interaction mechanism between Mn-based catalysts and S-VOCs. Catalysis ; X-ray photoelectron spectroscopy ; High-resolution transmission electron microscopy ; Oxygen ; Electron paramagnetic resonance ; Chemistry ; Nanorod ; Chemisorption ; Raman spectroscopy ; Sulfur ; Redox ; Crystal structure ; Sulfidation ; Inorganic chemistry ; Photochemistry ; Transmission electron microscopy ; Materials science ; Crystallography ; Chemical engineering ; Nanotechnology ; Organic chemistry ; Nuclear magnetic resonance Catalytic Processes in Materials Science ; Electrocatalysts for Energy Conversion ; Catalysis and Hydrodesulfurization Studies
Authors: Madagonda M. Vadiyar | Ji‐Young Kim | Jee‐Hwan Bae | Kyung‐Wan Nam
Source: Carbon Energy (article, 2023-03-10)
Field: Materials Science — Materials Chemistry

Imidazole linker‐induced covalent triazine framework–ZIF hybrids for confined hollow carbon super‐heterostructures toward a long‐life supercapacitor Abstract Carbon super‐heterostructures with high nitrogen contents from the covalent hybrid precursors of covalent triazine frameworks (CTFs) and zeolitic imidazolic frameworks (ZIFs) are scarcely explored because of CTF's ordered structure and toxic superacid that dissolves or destabilizes the metal nodes. To solve this problem, herein, we report a straightforward two‐step pathway for the covalent hybridization of disordered CTF (d–CTF)–ZIF composites via preincorporation of an imidazole (IM) linker into ordered CTFs, followed by the imidazole‐site‐specific covalent growth of ZIFs. Direct carbonization of these synthesized d–CTF−IM−ZIF hybrids results in unique hollow carbon super‐heterostructures with ultrahigh nitrogen content (&gt;18.6%), high specific surface area (1663 m 2 g −1 ), and beneficial trace metal (Co/Zn NPs) contents for promoting the redox pseudocapacitance. As proof of concept, the obtained carbon super‐heterostructure (Co–Zn–NC SNH –800) is used as a positive electrode in an asymmetric supercapacitor, demonstrating a remarkable energy density of 61 Wh kg −1 and extraordinary cyclic stability of 97% retention after 30,000 cycles at the cell level. Our presynthetic modifications of CTF and their covalent hybridization with ZIF crystals pave the way toward new design strategies for synthesizing functional porous carbon materials for promising energy applications. Covalent bond ; Pseudocapacitance ; Supercapacitor ; Materials science ; Carbonization ; Heterojunction ; Carbon fibers ; Imidazole ; Linker ; Nanotechnology ; Chemical engineering ; Polymer chemistry ; Chemistry ; Organic chemistry ; Composite number ; Electrode ; Electrochemistry ; Physical chemistry ; Optoelectronics ; Composite material Covalent Organic Framework Applications ; Supercapacitor Materials and Fabrication ; Advanced Photocatalysis Techniques
Authors: Fabio Carniato | Marco Ricci | Lorenzo Tei | Francesca Garello | Chiara Furlan | Enzo Terreno | Enrico Ravera | Giacomo Parigi | Claudio Luchinat | Mauro Botta
Source: Small (article, 2023-06-22)
Field: Materials Science — Materials Chemistry

Novel Nanogels Loaded with Mn(II) Chelates as Effective and Biologically Stable MRI Probes Here it is described nanogels (NG) based on a chitosan matrix, which are covalently stabilized by a bisamide derivative of Mn-t-CDTA (t-CDTA = trans-1,2-diaminocyclohexane-N,N,N',N'-tetraacetic acid). the Mn(II) complex acts both as a contrast medium and as a cross-linking agent. These nanogels are proposed as an alternative to the less stable paramagnetic nanogels obtained by electrostatic interactions between the polymeric matrix and paramagnetic Gd(III) chelates. The present novel nanogels show: i) relaxivity values seven times higher than that of typical monohydrated Mn(II) chelates at the clinical fields, thanks to the combination of a restricted mobility of the complex with a fast exchange of the metal-bound water molecule; ii) high stability of the formulation over time at pH 5 and under physiological conditions, thus excluding metal leaking or particles aggregation; iii) good extravasation and accumulation, with a maximum contrast achieved at 24 h post-injection in mice bearing subcutaneous breast cancer tumor; iv) high T<sub>1</sub> contrast (1 T) in the tumor 24 h post-injection. These improved properties pave the way for the use of these paramagnetic nanogels as promising magnetic resonance imaging (MRI) probes for in vitro and in vivo preclinical applications. Chelation ; Chitosan ; Paramagnetism ; Covalent bond ; Nanogel ; MRI contrast agent ; Materials science ; In vivo ; Magnetic resonance imaging ; Metal ; Nuclear magnetic resonance ; Chemistry ; Nuclear chemistry ; Nanotechnology ; Drug delivery ; Nanoparticle ; Organic chemistry Lanthanide and Transition Metal Complexes ; Nanoparticle-Based Drug Delivery ; Advanced MRI Techniques and Applications
Authors: Qianqian Wu | Yang Lü | Ling Zou | Yang Wang | Qingshan Liu | Anwei Zhang | Jiang Cao | Guangyou Shi | Jian He | Xiaochao Yang
Source: Advanced Healthcare Materials (article, 2023-05-11)
Field: Materials Science — Materials Chemistry

Small Ceria Nanoclusters with High ROS Scavenging Activity and Favorable Pharmacokinetic Parameters for the Amelioration of Chronic Kidney Disease The over production of reactive oxygen species (ROS) plays a critical role in the progression of chronic kidney disease (CKD). Organic ROS scavengers currently used for CKD treatment do not satisfy low dosage and high efficiency requirements. Ceria nanomaterials featured with renewable ROS scavenging activity are potential candidates for CKD treatment. Herein, a method for the synthesis of ceria nanoclusters (NCs) featured with small size of ≈1.2 nm is reported. The synthesized NCs are modified by three hydrophilic ligands with different molecular weights, including succinic acid (SA), polyethylene glycol diacid 600 (PEG600), and polyethylene glycol diacid 2000 (PEG2000). The surface modified NCs exhibit excellent ROS scavenging activity due to the high Ce<sup>3+</sup> /Ce<sup>4+</sup> ratio in their crystal structures. Compared with bigger-sized ceria nanoparticles (NPs) (≈45 nm), NCs demonstrate smoother blood concentration-time curve, lower organ accumulation, and faster metabolic rate superiorities. The administration of NCs to CKD mice, especially PEG600 and PEG2000 modified NCs, can effectively inhibit oxidative stress, inflammation, renal fibrosis, and apoptosis in their kidneys. Due to these benefits, the constructed NCs can ameliorate the progression of CKD. These findings suggest that NCs is a potential redox nanomedicine for future clinical treatment of CKD. Reactive oxygen species ; Polyethylene glycol ; Oxidative stress ; Nanoclusters ; Materials science ; Kidney disease ; Nanomaterials ; PEG ratio ; Apoptosis ; Cancer research ; Pharmacology ; Chemistry ; Nanotechnology ; Biochemistry ; Medicine ; Internal medicine Advanced Nanomaterials in Catalysis ; Nanocluster Synthesis and Applications ; Neurological Complications and Syndromes
Authors: Jiaming Ding | Amos B. Smith
Source: Journal of the American Chemical Society (article, 2023-08-10)
Field: Chemistry — Organic Chemistry

Total Synthesis of the Reported Structure of Neaumycin B The stereoselective total synthesis of structure <b>1</b> assigned to the macrolide natural product neaumycin B is reported in a 2.3% overall yield on 90 mg scale. The synthesis features a gram-scale nickel-catalyzed reductive cross-coupling/spiroketalization tactic to construct the spiroketal core of neaumycin B. The stereostructures of the C3-C6, C8-C14, and C20-C41 segments of synthetic neaumycin B were unambiguously verified by X-ray crystallography. Chemistry ; Total synthesis ; Stereochemistry Synthetic Organic Chemistry Methods ; Microbial Natural Products and Biosynthesis ; Chemical Synthesis and Analysis
Authors: Behnam Ahmadikia | Orestis Paraskevas | William Van Hyning | Jonathan M. Hestroffer | Irene J. Beyerlein | Christos Thrampoulidis
Source: Acta Materialia (article, 2023-12-07)
Field: Materials Science — Materials Chemistry

Data-driven texture design for reducing elastic and plastic anisotropy in titanium alloys Anisotropy ; Materials science ; Titanium alloy ; Plasticity ; Texture (cosmology) ; Stiffness ; Elastic modulus ; Microstructure ; Condensed matter physics ; Composite material ; Alloy ; Computer science ; Artificial intelligence ; Optics ; Physics Titanium Alloys Microstructure and Properties ; Microstructure and mechanical properties ; Metallurgy and Material Forming
Authors: Linh Chi T. Cao | Meng‐Huan Zhou | Pakorn Opaprakasit | Paiboon Sreearunothai | Yuki Nagao | Sakoolkan Boonruang | Hoorieh Fallah | Shih‐Feng Tseng | Shu‐Han Hsu
Source: Advanced Materials Interfaces (article, 2023-04-18)
Field: Materials Science — Materials Chemistry

Facile Fabrication of Oxygen‐Enriched MXene‐Based Sensor and Their Ammonia Gas‐Sensing Enhancement Abstract Various sensing materials have been demonstrated to increase the precision of sensing technology. Nevertheless, this complicates the fabrication process for materials integration to obtain devices that can simultaneously accommodate various gas detectors, like electronic nose. The study here focuses on exploring the sensing response of different functionalization of specific sensing materials to provide an alternative way to achieve selective response to multiple gases. Triethoxysilylpropyl succinic anhydride silane (TESPSA) was introduced on 2D material MXene‐Ti 3 C 2 T x to form carboxylic acid terminated MXene (COOH‐Ti 3 C 2 T x ) and alternately coated with polyaniline (COOH‐Ti 3 C 2 T x /PANI). This modification doubled up the gas binding sites and improved the binding strength of the Ti 3 C 2 T x surface to NH 3 gas molecules. The 5CC‐COOH‐Ti 3 C 2 T x /PANI sensor prepared from five coating cycles showed the highest sensitivity (214.70 %) with fast gas response rate at 80 ppm NH 3 (1.75 % s ‐1 ). Therefore, the different signal responses from specific functionalization of the same sensing material functionalization will allow the possible sensor array fabrication to achieve fingerprint‐like sensing map recognition in the presence of mixed gases. Surface modification ; Materials science ; Fabrication ; Ammonia gas ; Ammonia ; Nanotechnology ; Molecule ; Polyaniline ; Chemical engineering ; Organic chemistry ; Chemistry ; Composite material ; Polymer MXene and MAX Phase Materials ; Gas Sensing Nanomaterials and Sensors
Authors: Neeta Deshpande | Santosh Kumar Sharma | P. William | A. B. Pawar
Source: Journal of Nano- and Electronic Physics (article, 2023-01-01)
Field: Chemistry — Inorganic Chemistry

Empirical Analysis of the Emerging Trends in the Photovoltaic Technologies of Condensed Matter Physics Journal of Nano- and Electronic Physics. Scientific journal. ISSN: 2077-6772. Journal abbreviation: J. Nano- Electron. Phys. No page charges. All articles are freely available on-line. Issued 4 times per year. Publisher: Sumy State University. (Sumy, Ukraine) Nanotechnology ; Field (mathematics) ; Subject matter ; Engineering physics ; Variety (cybernetics) ; Characterization (materials science) ; Materials science ; Physics ; Computer science ; Political science Metal-Organic Frameworks: Synthesis and Applications ; Machine Learning in Materials Science ; Polyoxometalates: Synthesis and Applications
Authors: Xiangyu Wang | Tong Wei | XU Ying-qiu | Li-Wei Wu | Yingdong Han | Jiao Cui
Source: Journal of Advanced Ceramics (article, 2023-04-27)
Field: Materials Science — Polymers and Plastics

High-entropy perovskite oxides: An emergent type of photochromic oxides with fast response for handwriting display Stimulus-responsive materials are fundamental to the broad and ever-growing field of intelligence research, which bridge intelligent systems with the Internet of Things (IoT) in future lifestyles. Among these materials, writable materials have received great interest; however, carbonization and irreversible writing processes are generally inevitable for extensively investigated organic compounds. Photochromism is a potential mode of composing information. Nevertheless, inorganic materials usually exhibit weak photochromic effects. Here, a novel strategy of designing high-entropy perovskite (HEP) oxides is put forward to develop a new inorganic photochromic system with satisfying performance. A series of HEP oxides are synthesized for the first time. Benefiting from excellent photochromic features, real-time information encoding was achieved. The mechanism-related photochromism is also discussed. Distinct from the previous works, it is believed that the present photochromic-based HEP oxides provide a new and manyfold research space for the future development of conventional writable materials and the disclosing of unprecedented properties and phenomena. Photochromism ; Materials science ; Nanotechnology ; Computer science ; Perovskite (structure) ; Chemistry ; Organic chemistry Transition Metal Oxide Nanomaterials ; Advanced Photocatalysis Techniques ; TiO2 Photocatalysis and Solar Cells
Authors: Ростислав Е. Трифонов | В. А. Островский
Source: International Journal of Molecular Sciences (article, 2023-12-06)
Field: Chemistry — Organic Chemistry

Tetrazoles and Related Heterocycles as Promising Synthetic Antidiabetic Agents Tetrazole heterocycle is a promising scaffold in drug design, and it is incorporated into active pharmaceutical ingredients of medications of various actions: hypotensives, diuretics, antihistamines, antibiotics, analgesics, and others. This heterocyclic system is metabolically stable and easily participates in various intermolecular interactions with different biological targets through hydrogen bonding, conjugation, or van der Waals forces. In the present review, a systematic analysis of the activity of tetrazole derivatives against type 2 diabetes mellitus (T2DM) has been performed. As it was shown, the tetrazolyl moiety is a key fragment of many antidiabetic agents with different activities, including the following: peroxisome proliferator-activated receptors (PPARs) agonists, protein tyrosine phosphatase 1B (PTP1B) inhibitors, aldose reductase (AR) inhibitors, dipeptidyl peptidase-4 (DPP-4) inhibitors and glucagon-like peptide 1 (GLP-1) agonists, G protein-coupled receptor (GPCRs) agonists, glycogen phosphorylases (GP) Inhibitors, α-glycosidase (AG) Inhibitors, sodium glucose co-transporter (SGLT) inhibitors, fructose-1,6-bisphosphatase (FBPase) inhibitors, IkB kinase ε (IKKε) and TANK binding kinase 1 (TBK1) inhibitors, and 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1). In many cases, the tetrazole-containing leader compounds markedly exceed the activity of medications already known and used in T2DM therapy, and some of them are undergoing clinical trials. In addition, tetrazole derivatives are very often used to act on diabetes-related targets or to treat post-diabetic disorders. Chemistry ; Tetrazole ; Pharmacology ; Biochemistry ; Stereochemistry ; Medicine Synthesis of Tetrazole Derivatives ; Biochemical and Molecular Research ; Quinazolinone synthesis and applications
Authors: Heng Chen | Xiaoting Liu | Yongfeng Huang | Guangliang Li | Feng Yu | Feng Xiong | Mengqi Zhang | Luzhao Sun | Qian Yang | Kaicheng Jia | Ruqiang Zou | Huanxin Li | Sheng Meng | Li Lin | Jincan Zhang | Hailin Peng | Zhongfan Liu
Source: Advanced Materials (article, 2023-04-02)
Field: Materials Science — Materials Chemistry

Oxidization‐Temperature‐Triggered Rapid Preparation of Large‐Area Single‐Crystal Cu(111) Foil The controlled preparation of single-crystal Cu(111) is intensively investigated owing to the superior properties of Cu(111) and its advantages in synthesizing high-quality 2D materials, especially graphene. However, the accessibility of large-area single-crystal Cu(111) is still hindered by time-consuming, complicated, and high-cost preparation methods. Here, the oxidization-temperature-triggered rapid preparation of large-area single-crystal Cu(111) in which an area up to 320 cm<sup>2</sup> is prepared within 60 min, and where low-temperature oxidization of polycrystalline Cu foil surface plays a vital role, is reported. A mechanism is proposed, by which the thin Cu<sub>x</sub> O layer transforms to a Cu(111) seed layer on the surface of Cu to induce the formation of a large-area Cu(111) foil, which is supported by both experimental data and molecular dynamics simulation results. In addition, a large-size high-quality graphene film is synthesized on the single-crystal Cu(111) foil surface and the graphene/Cu(111) composites exhibit enhanced thermal conductivity and ductility compared to their polycrystalline counterpart. This work, therefore, not only provides a new avenue toward the monocrystallinity of Cu with specific planes but also contributes to improving the mass production of high-quality 2D materials. Materials science ; FOIL method ; Crystallite ; Graphene ; Single crystal ; Crystal (programming language) ; Layer (electronics) ; Chemical engineering ; Nanotechnology ; Composite material ; Crystallography ; Metallurgy Graphene research and applications ; Nanomaterials for catalytic reactions ; Copper-based nanomaterials and applications
Authors: Haofan Zhang | Fengming He | Gui‐Ping Gao | Sheng Lu | Qiaochu Wei | Hongyu Hu | Zhenhua Wu | Meijuan Fang | Xiumin Wang
Source: Molecules (review, 2023-01-17)
Field: Chemistry — Organic Chemistry

Approved Small-Molecule ATP-Competitive Kinases Drugs Containing Indole/Azaindole/Oxindole Scaffolds: R&amp;D and Binding Patterns Profiling Kinases are among the most important families of biomolecules and play an essential role in the regulation of cell proliferation, apoptosis, metabolism, and other critical physiological processes. The dysregulation and gene mutation of kinases are linked to the occurrence and development of various human diseases, especially cancer. As a result, a growing number of small-molecule drugs based on kinase targets are being successfully developed and approved for the treatment of many diseases. The indole/azaindole/oxindole moieties are important key pharmacophores of many bioactive compounds and are generally used as excellent scaffolds for drug discovery in medicinal chemistry. To date, 30 ATP-competitive kinase inhibitors bearing the indole/azaindole/oxindole scaffold have been approved for the treatment of diseases. Herein, we summarize their research and development (R&D) process and describe their binding models to the ATP-binding sites of the target kinases. Moreover, we discuss the significant role of the indole/azaindole/oxindole skeletons in the interaction of their parent drug and target kinases, providing new medicinal chemistry inspiration and ideas for the subsequent development and optimization of kinase inhibitors. Oxindole ; Indole test ; Kinase ; Chemistry ; Small molecule ; Profiling (computer programming) ; Combinatorial chemistry ; Molecule ; Pharmacology ; Stereochemistry ; Biochemistry ; Computational biology ; Biology ; Organic chemistry ; Computer science ; Catalysis Click Chemistry and Applications ; HER2/EGFR in Cancer Research ; Cancer Mechanisms and Therapy