jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Mengyang Shen | C. NIU | Xuchao Wang | Jia-Bo Huang | Zhen Zhao | Shao‐Fei Ni | Zi‐Qiang Rong
Source: JACS Au (article, 2024-06-11)
Field: Chemistry — Inorganic Chemistry

Regio- and Enantioselective Hydromethylation of 3-Pyrrolines and Glycals Enabled by Cobalt Catalysis Enantioenriched 3-methylpyrrolidine, with its unique chiral nitrogen-containing core skeleton, exists widely in various functional molecules, including natural products, bioactive compounds, and pharmaceuticals. Traditional methods for synthesizing these valuable methyl-substituted heterocycles often involve enzymatic processes or complex procedures with chiral auxiliaries, limiting the substrate scope and efficiency. Efficient catalytic methylation, especially in an enantioselective manner, has been a long-standing challenge in chemical synthesis. Herein, we present a novel approach for the remote and stereoselective installation of a methyl group onto N-heterocycles, leveraging a CoH-catalyzed asymmetric hydromethylation strategy. By effectively combining a commercial cobalt precursor with a modified bisoxazoline (BOX) ligand, a variety of easily accessible 3-pyrrolines can be converted to valuable enantiopure 3-(isotopic labeling)methylpyrrolidine compounds with outstanding enantioselectivity. This efficient protocol streamlines the two-step synthesis of enantioenriched 3-methylpyrrolidine, which previously required up to five or six steps under harsh conditions or expensive starting materials. Enantiopure drug ; Enantioselective synthesis ; Chemistry ; Combinatorial chemistry ; Catalysis ; Ligand (biochemistry) ; Kinetic resolution ; Stereoselectivity ; Chirality (physics) ; Cobalt ; Organic chemistry Asymmetric Hydrogenation and Catalysis ; Chemical Reactions and Isotopes ; Catalytic C–H Functionalization Methods
Authors: Ida Svanedal | Alireza Eivazi | Magnus Norgren | Håkan Edlund
Source: Current Opinion in Colloid & Interface Science (review, 2024-07-16)
Field: Chemistry — Organic Chemistry

Exploring the versatility of chelating surfactants: A review Chelating surfactants are amphiphilic molecules capable of forming coordination complexes with metal ions and self-assembling into organized structures. These compounds have gained significant attention in recent years due to their multifaceted applications in environmental remediation, industrial processes, and material sciences. This review provides an overview of the characterization techniques and recent advancements in the applications of chelating surfactants over the past few years. The review begins by elucidating the characterization methods employed to understand the physicochemical properties of chelating surfactants and gain insight into their complex behavior and interactions in various systems. The applications of chelating surfactants in remediation of wastewater and soil, flotation of minerals, oil recovery processes, and corrosion inhibition in metallic structures are explored. Through examination of recent fundamental research activities, innovative approaches, mechanisms of action, and advancements in the different application domains are highlighted. Lastly, some recent progress in the related field of metallosurfactants is explored, even though not all metallosurfactants are chelating. Chelation ; Environmental remediation ; Nanotechnology ; Characterization (materials science) ; Amphiphile ; Chemistry ; Biochemical engineering ; Materials science ; Organic chemistry ; Polymer ; Engineering Surfactants and Colloidal Systems ; Analytical chemistry methods development ; Environmental Chemistry and Analysis
Authors: Ioana Oprea | Terry Smith
Source: ACS Chemical Biology (review, 2024-12-27)
Field: Chemistry — Organic Chemistry

Click Chemistry Methodology: The Novel Paintbrush of Drug Design Click chemistry is an immensely powerful technique for the synthesis of reliable and efficient covalent linkages. When undertaken in living cells, the concept is thereby coined bioorthogonal chemistry. Used in conjunction with the photo-cross-linking methodology, it serves as a sound strategy in the exploration of biological processes and beyond. Its broad scope has led to widespread use in many disciplines; however, this Review focuses on the use of click and bioorthogonal chemistry within medicinal chemistry, specifically with regards to drug development applications, namely, the use of DNA-encoded libraries as a novel technique for lead compound discovery, as well as the synthesis of antisense oligonucleotides and protein-drug conjugates. This Review aims to provide a critical perspective and a future outlook of this methodology, such as potential widespread use in cancer therapy and personalized medicine. Bioorthogonal chemistry ; Click chemistry ; Scope (computer science) ; Computer science ; Nanotechnology ; Drug discovery ; Chemistry ; Aptamer ; Combinatorial chemistry ; Biochemistry ; Biology ; Materials science Click Chemistry and Applications ; Advanced biosensing and bioanalysis techniques ; Monoclonal and Polyclonal Antibodies Research
Authors: Dillon R. L. Rickertsen | Joshua D. Crow | Tamal Das | Ion Ghiviriga | Jennifer S. Hirschi | Daniel Seidel
Source: ACS Catalysis (article, 2024-09-16)
Field: Chemistry — Organic Chemistry

Acridine/Lewis Acid Complexes as Powerful Photocatalysts: A Combined Experimental and Mechanistic Study A class of <i>in-situ</i> generated Lewis acid (LA) activated acridine complexes is reported, which act as potent photochemical catalysts for the oxidation of a variety of protected secondary amines. Acridine/LA complexes exhibit tunable excited state reduction potentials ranging from +2.07 to 2.38 V vs. SCE. The ytterbium triflate complex of 3,6-di-<i>t</i>-butyl-9-mesitylacridine catalyzes a photochemical Giese-type reaction of Boc-protected secondary amines with challenging conjugate acceptors such as acrylates, that are inaccessible to the analogous acridinium (<i>t</i>-Bu-Mes-Acr<sup>⊕</sup>) catalyzed reaction. The mechanism of this reaction was investigated using a suite of physical organic probes including intramolecular <sup>13</sup>C kinetic isotope effects (KIEs), variable time normalization analysis (VTNA) kinetics, determination of redox potentials, and computational studies. In the reaction catalyzed by <i>t</i>-Bu-Mes-Acr<sup>⊕</sup>, mechanistic studies are consistent with single-electron transfer (SET) from the ground-state reduced <i>t</i>-Bu-Mes-Acr<sup>•</sup> to the α-keto radical intermediate as the first irreversible step in the catalytic cycle. Intriguingly, we find that the reduced acridine/LA complexes are better ground state reductants (-0.72 to -0.74 V vs SCE) relative to <i>t</i>-Bu-Mes-Acr<sup>•</sup> (-0.59 V vs SCE) and predict that the increased substrate reactivity stems from a lower energy barrier for this key SET event. Acridine ; Catalysis ; Lewis acids and bases ; Chemistry ; Combinatorial chemistry ; Photochemistry ; Nanotechnology ; Computational chemistry ; Organic chemistry ; Materials science Radical Photochemical Reactions ; Catalytic C–H Functionalization Methods ; Sulfur-Based Synthesis Techniques
Authors: Peihua Lin | Bo Zhang | Hongli Yang | Shengfei Yang | Pengpeng Xue | Ying Chen | Shiyi Yu | Jichao Zhang | Yixiao Zhang | Liwei Chen | Chunhai Fan | Fangyuan Li | Daishun Ling
Source: Nature Communications (article, 2024-03-06)
Field: Materials Science — Materials Chemistry

An artificial protein modulator reprogramming neuronal protein functions Reversible protein phosphorylation, regulated by protein phosphatases, fine-tunes target protein function and plays a vital role in biological processes. Dysregulation of this process leads to aberrant post-translational modifications (PTMs) and contributes to disease development. Despite the widespread use of artificial catalysts as enzyme mimetics, their direct modulation of proteins remains largely unexplored. To address this gap and enable the reversal of aberrant PTMs for disease therapy, we present the development of artificial protein modulators (APROMs). Through atomic-level engineering of heterogeneous catalysts with asymmetric catalytic centers, these modulators bear structural similarities to protein phosphatases and exhibit remarkable ability to destabilize the bridging μ<sub>3</sub>-hydroxide. This activation of catalytic centers enables spontaneous hydrolysis of phospho-substrates, providing precise control over PTMs. Notably, APROMs, with protein phosphatase-like characteristics, catalytically reprogram the biological function of α-synuclein by directly hydrolyzing hyperphosphorylated α-synuclein. Consequently, synaptic function is reinforced in Parkinson's disease. Our findings offer a promising avenue for reprogramming protein function through de novo PTMs strategy. Reprogramming ; Phosphatase ; Phosphorylation ; Function (biology) ; Cell biology ; Chemistry ; Posttranslational modification ; Protein phosphatase 2 ; Biology ; Computational biology ; Biochemistry ; Enzyme ; Cell Advanced Nanomaterials in Catalysis ; Electrochemical sensors and biosensors ; Peptidase Inhibition and Analysis
Authors: Silvia Cattani | Neeraj Kumar Pandit | Michele Buccio | Davide Balestri | Lutz Ackermann | Gianpiero Cera
Source: Angewandte Chemie International Edition (article, 2024-05-24)
Field: Chemistry — Organic Chemistry

Iron‐Catalyzed C−H Alkylation/Ring Opening with Vinylbenzofurans Enabled by Triazoles We report an unprecedented iron-catalyzed C-H annulation using readily available 2-vinylbenzofurans as the reaction pattern. The redox-neutral strategy, based on cheap, non-toxic, and earth-abundant iron catalysts, exploits triazole assistance to promote a cascade C-H alkylation, benzofuran ring-opening and insertion into a Fe-N bond, to form highly functionalized isoquinolones. Detailed mechanistic studies supported by DFT calculations fully disclosed the manifold of the iron catalysis. Alkylation ; Ring (chemistry) ; Catalysis ; Chemistry ; Organic chemistry Catalytic C–H Functionalization Methods ; Asymmetric Hydrogenation and Catalysis ; Synthesis and Catalytic Reactions
Authors: Jun Zhang | Kai Wu | Xiaoqing Gao | M. Zhang | Xin Zhou | Florian Bertram | Chen Shen | Yunlong Zhou
Source: Science Advances (article, 2024-10-18)
Field: Materials Science — Biomaterials

Achiral and chiral ligands synergistically harness chiral self-assembly of inorganics Chiral structures and functions are essential natural components in biominerals and biological crystals. Chiral molecules direct inorganics through chiral growth of facets or screw dislocation of crystal clusters. As chirality promoters, they initiate an asymmetric hierarchical self-assembly in a quasi-thermodynamic steady state. However, achieving chiral assembly requires a delicate balance between intricate interactions. This complexity causes the roles of achiral-chiral and inorganic components in crystallization to remain ambiguous. Here, we elucidate a definitive mechanism using an achiral-chiral ligand strategy to assemble inorganics into hierarchical, self-organized superstructures. Achiral ligands cluster inorganic building blocks, while chiral ligands impart chiral rotation. Achiral and chiral ligands can flexibly modulate the chirality of superstructures by fully using their competition in coordination chemistry. This dual-ligand strategy offers a versatile framework for engineering chiroptical nanomaterials tailored to optical devices and metamaterials with optical activities across a broad wavelength range, with applications in imaging, detection, catalysis, and sensing. Chirality (physics) ; Nanotechnology ; Materials science ; Self-assembly ; Ligand (biochemistry) ; Enantioselective synthesis ; Optical rotation ; Nanomaterials ; Molecule ; Chemistry ; Combinatorial chemistry ; Chemical physics ; Catalysis ; Organic chemistry ; Chiral symmetry breaking ; Physics ; Symmetry breaking Supramolecular Self-Assembly in Materials ; Crystallography and molecular interactions ; Supramolecular Chemistry and Complexes
Authors: Raghu Solanki | Sunita Patel
Source: Journal of the Science of Food and Agriculture (review, 2024-05-31)
Field: Chemistry — Organic Chemistry

Evodiamine and its nano‐based approaches for enhanced cancer therapy: recent advances and challenges Evodiamine is a bioactive alkaloid extracted from the Evodia rutaecarpa plant. It has various pharmacological effects including anti-cancer, anti-bacterial, anti-obesity, anti-neurodegenerative, anti-depressant, and cardiac protective properties. Evodiamine demonstrates potent anti-cancer activity by inhibiting the proliferation of cancer cells in vitro and in vivo. Despite the health-promoting properties of evodiamine, its clinical use is hindered by low water solubility, poor bioavailability, and toxicity. Thus, there is a need to develop alternative drug delivery systems for evodiamine to enhance its solubility, permeability, and stability, as well as to facilitate targeted, prolonged, and controlled drug release. Nanocarriers can increase the therapeutic potential of evodiamine in cancer therapy while reducing adverse side effects. To date, numerous attempts have been made through the development of smart nanocarriers to overcome the drawbacks of evodiamine. This review focuses on the pharmacological applications, anti-cancer mechanisms, and limitations of evodiamine. Various nanocarriers, including lipid-based nanoparticles, polymeric nanoparticles, cyclodextrins, and so forth, have been discussed extensively for evodiamine delivery. Nano-drug delivery systems could increase the solubility, bioavailability, stability, and therapeutic efficacy of evodiamine. This review aims to present a comprehensive and critical evaluation of several nano-formulations of evodiamine for cancer therapy. © 2024 Society of Chemical Industry. Evodiamine ; Cancer therapy ; Cancer ; Nanotechnology ; Medicine ; Computer science ; Pharmacology ; Materials science ; Internal medicine Synthesis and Biological Evaluation ; Quinazolinone synthesis and applications ; Catalytic Cross-Coupling Reactions
Authors: Xiuli Wu | Xiangyu Song | Ying Xia
Source: Advanced Science (article, 2024-03-09)
Field: Chemistry — Organic Chemistry

High‐Valent Copper Catalysis Enables Regioselective Fluoroarylation of <i>Gem</i>‐Difluorinated Cyclopropanes Transition-metal (TM) catalyzed reaction of gem-difluorinated cyclopropanes (gem-DFCPs) has drawn much attention recently. The reaction generally occurs via the activation of the distal C─C bond in gem-DFCPs by a low-valent TM through oxidative addition, eventually producing mono-fluoro olefins as the coupling products. However, achieving regioselective activation of the proximal C─C bond in gem-DFCPs that overcomes the intrinsic reactivity via TM catalysis remains elusive. Here, a new reaction mode of gem-DFCPs enabled by high-valent copper catalysis, which allows exclusive activation of the congested proximal C─C bond is presented. The reaction that achieves fluoroarylation of gem-DFCPs uses NFSI (N-fluorobenzenesulfonimide) as electrophilic fluoro reagent and arenes as the C─H nucleophiles, enabling the synthesis of diverse CF<sub>3</sub>-containing scaffolds. It is proposed that a high-valent copper species plays an important role in the regioselective activation of the proximal C─C bond possibly via a σ-bond metathesis. Regioselectivity ; Nucleophile ; Chemistry ; Electrophile ; Catalysis ; Metathesis ; Combinatorial chemistry ; Reactivity (psychology) ; Salt metathesis reaction ; Reagent ; Copper ; Bond cleavage ; Nucleophilic addition ; Reductive elimination ; Medicinal chemistry ; Organic chemistry Cyclopropane Reaction Mechanisms ; Fluorine in Organic Chemistry ; Catalytic Cross-Coupling Reactions
Authors: Haritha Asokan‐Sheeja | Kamal Awad | Jiazhu Xu | Myan Le | Jenny N. Nguyen | Na Nguyen | Tam Nguyen | Kytai T. Nguyen | Yi Hong | Venu Varanasi | Xiaohua Liu | He Dong
Source: Biomacromolecules (article, 2024-04-10)
Field: Materials Science — Biomaterials

In Situ Synthesis and Self-Assembly of Peptide–PEG Conjugates: A Facile Method for the Construction of Fibrous Hydrogels Peptide-based hydrogels have gained considerable attention as a compelling platform for various biomedical applications in recent years. Their attractiveness stems from their ability to seamlessly integrate diverse properties, such as biocompatibility, biodegradability, easily adjustable hydrophilicity/hydrophobicity, and other functionalities. However, a significant drawback is that most of the functional self-assembling peptides cannot form robust hydrogels suitable for biological applications. In this study, we present the synthesis of novel peptide-PEG conjugates and explore their comprehensive hydrogel properties. The hydrogel comprises double networks, with the first network formed through the self-assembly of peptides to create a β-sheet secondary structure. The second network is established through covalent bond formation via <i>N</i>-hydroxysuccinimide chemistry between peptides and a 4-arm PEG to form a covalently linked network. Importantly, our findings reveal that this hydrogel formation method can be applied to other peptides containing lysine-rich sequences. Upon encapsulation of the hydrogel with antimicrobial peptides, the hydrogel retained high bacterial killing efficiency while showing minimum cytotoxicity toward mammalian cells. We hope that this method opens new avenues for the development of a novel class of peptide-polymer hydrogel materials with enhanced performance in biomedical contexts, particularly in reducing the potential for infection in applications of tissue regeneration and drug delivery. Self-healing hydrogels ; Biocompatibility ; Peptide ; Self-assembling peptide ; Covalent bond ; Chemistry ; PEG ratio ; Drug delivery ; Self-assembly ; Nanotechnology ; Tissue engineering ; PEGylation ; Combinatorial chemistry ; Materials science ; Biochemistry ; Polyethylene glycol ; Organic chemistry ; Biomedical engineering Supramolecular Self-Assembly in Materials ; Polydiacetylene-based materials and applications ; RNA Interference and Gene Delivery
Authors: Qiao Zheng | Shengnan Jing | Lin Hu | Xiangrui Meng
Source: Journal of Cancer (article, 2024-01-01)
Field: Chemistry — Organic Chemistry

Evodiamine Inhibits Colorectal Cancer Growth via RTKs Mediated PI3K/AKT/p53 Signaling Pathway <b>Objective:</b> To investigate the inhibitory effect of EVO on colorectal cancer (CRC) growth and further explore the potential mechanism involving the RTKs-mediated PI3K/AKT/p53 signaling pathway. <b>Methods:</b> Firstly, the inhibitory effect of EVO on CRC cells was detected <i>in vitro</i> by cell viability assay and colony formation assay. The effects of EVO on spatial migration and invasion capacity of cells were detected by Transwell assay. The effects of EVO on apoptosis and cycle of cells were detected by flow cytometry. Then, the molecular mechanism of EVO against CRC was revealed by qRT-PCR and Western blot. Finally, the excellent anti-tumour activity of EVO was verified by <i>in vivo</i> experiments. <b>Results:</b> The results demonstrated that EVO exerts inhibitory effects on CRC cell proliferation, invasion, and colony formation. The cell cycle assay revealed that EVO induces G1/S phase arrest. Through RNA seq, we explored the influence of EVO on the transcriptional profile of colon cancer and observed significant activation of RTKs and the PI3K/AKT pathway, along with its downstream signaling pathways. Furthermore, we observed upregulation of p53 proteins by EVO, which led to the inhibition of Bcl-2 expression and an increase in Bax expression. Consistently, EVO exhibited remarkable suppression of tumor xenograft growth in nude mice. <b>Conclusion:</b> This study confirmed that EVO inhibits the proliferation of CRC cells and promotes cell apoptosis. The possible mechanism of action is inhibiting the expression of the RTK protein family, activating the PI3K/AKT/p53 apoptotic signaling pathway, thereby inhibiting Bcl-2 expression and increasing Bax expression, promoting apoptosis of CRC cells. As a natural product, EVO has very high potential application value. PI3K/AKT/mTOR pathway ; Protein kinase B ; Apoptosis ; Cell growth ; Cell cycle ; Cancer research ; Signal transduction ; Chemistry ; Cell cycle checkpoint ; Cell biology ; Downregulation and upregulation ; Flow cytometry ; Biology ; Molecular biology ; Biochemistry ; Gene Quinazolinone synthesis and applications ; Synthesis and Biological Evaluation ; Synthesis and biological activity
Authors: Ferran Nadal‐Bufí | Raj V. Nithun | Fabio De Moliner | Xiaoxi Lin | Shaimaa Habiballah | Muhammad Jbara | Marc Vendrell
Source: ACS Central Science (article, 2024-11-26)
Field: Chemistry — Organic Chemistry

Late-Stage Minimal Labeling of Peptides and Proteins for Real-Time Imaging of Cellular Trafficking The cellular uptake routes of peptides and proteins are complex and diverse, often handicapping therapeutic success. Understanding their mechanisms of internalization requires chemical derivatization with approaches that are compatible with wash-free and real-time imaging. In this work, we developed a new late-stage labeling strategy for unprotected peptides and proteins, which retains their biological activity while enabling live-cell imaging of uptake and intracellular trafficking. Benzo-2,1,3-thiadiazoles were selectively incorporated into Cys residues of both linear and cyclic peptides via Pd-mediated arylation with good yields and high purities. The resulting labeled peptides are chemically stable under physiological conditions and display strong fluorogenic character for wash-free imaging studies. We utilized this approach to prepare native-like analogues of cell-penetrating peptides and performed time-course analysis of their internalization routes in live cells by fluorescence lifetime imaging. Furthermore, we applied our strategy to label the chemokine protein mCCL2 and monitor its internalization via receptor-mediated endocytosis in live macrophages. This study provides a straightforward strategy for late-stage fluorogenic labeling of intact peptides and small proteins and direct visualization of dynamic intracellular events. Internalization ; Live cell imaging ; Endocytosis ; Intracellular ; Chemistry ; Fluorescence-lifetime imaging microscopy ; Cell biology ; Biochemistry ; Cell ; Biophysics ; Fluorescence ; Biology Click Chemistry and Applications ; Chemical Synthesis and Analysis ; Nanoplatforms for cancer theranostics
Authors: Brenda S. Ferrari | Matteo Manica | Ronaldo Giro | Teodoro Laino | M. Steiner
Source: npj Computational Materials (article, 2024-06-04)
Field: Materials Science — Materials Chemistry

Predicting polymerization reactions via transfer learning using chemical language models Abstract Polymers are candidate materials for a wide range of sustainability applications such as carbon capture and energy storage. However, computational polymer discovery lacks automated analysis of reaction pathways and stability assessment through retro-synthesis. Here, we report an extension of transformer-based language models to polymerization for both reaction and retrosynthesis tasks. To that end, we have curated a polymerization dataset for vinyl polymers covering reactions and retrosynthesis for representative homo-polymers and co-polymers. Overall, we obtain a forward model Top-4 accuracy of 80% and a backward model Top-4 accuracy of 60%. We further analyze the model performance with representative polymerization examples and evaluate its prediction quality from a materials science perspective. To enable validation and reuse, we have made our models and data available in public repositories. Polymerization ; Transfer of learning ; Computer science ; Chemistry ; Artificial intelligence ; Organic chemistry ; Polymer Machine Learning in Materials Science ; Computational Drug Discovery Methods