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期刊名称:Chemical Science
期刊ISSN:2041-6520
期刊官方网站:http://pubs.rsc.org/en/journals/journalissues/sc
出版商:Royal Society of Chemistry
出版周期:
影响因子:7.6
始发年份:2010
年文章数:1413
是否OA:Yes
Contents list
Chemical Science ( IF 7.6 ) Pub Date : 2024-01-31 , DOI: 10.1039/D4SC90025A
The first page of this article is displayed as the abstract.
Diaryl hypervalent bromines and chlorines: synthesis, structures and reactivities
Chemical Science ( IF 7.6 ) Pub Date : 2024-01-03 , DOI: 10.1039/D3SC05382B
Matteo Lanzi
In the field of modern organic chemistry, hypervalent compounds have become indispensable tools for synthetic chemists, finding widespread applications in both academic research and industrial settings. While iodine-based reagents have historically dominated this research field, recent focus has shifted to the potent yet relatively unexplored chemistry of diaryl λ3-bromanes and -chloranes. Despite their unique reactivities, the progress in their development and application within organic synthesis has been hampered by the absence of straightforward, reliable, and widely applicable preparative methods. However, recent investigations have uncovered innovative approaches and novel reactivity patterns associated with these specialized compounds. These discoveries suggest that we have only begun to tap into their potential, implying that there is much more to be explored in this captivating area of chemistry.
Water-stable metal–organic frameworks (MOFs): rational construction and carbon dioxide capture
Chemical Science ( IF 7.6 ) Pub Date : 2024-01-10 , DOI: 10.1039/D3SC06076D
Jindou Tian
Metal–organic frameworks (MOFs) are considered to be a promising porous material due to their excellent porosity and chemical tailorability. However, due to the relatively weak strength of coordination bonds, the stability (e.g., water stability) of MOFs is usually poor, which severely inhibits their practical applications. To prepare water-stable MOFs, several important strategies such as increasing the bonding strength of building units and introducing hydrophobic units have been proposed, and many MOFs with excellent water stability have been prepared. Carbon dioxide not only causes a range of climate and health problems but also is a by-product of some important chemicals (e.g., natural gas). Due to their excellent adsorption performances, MOFs are considered as a promising adsorbent that can capture carbon dioxide efficiently and energetically, and many water-stable MOFs have been used to capture carbon dioxide in various scenarios, including flue gas decarbonization, direct air capture, and purified crude natural gas. In this review, we first introduce the design and synthesis of water-stable MOFs and then describe their applications in carbon dioxide capture, and finally provide some personal comments on the challenges facing these areas.
Solar-driven CO2-to-ethanol conversion enabled by continuous CO2 transport via a superhydrophobic Cu2O nano fence†
Chemical Science ( IF 7.6 ) Pub Date : 2023-11-27 , DOI: 10.1039/D3SC05702J
Hailing Huo,Hua He,Chengxi Huang,Xin Guan,Fang Wu,Yongping Du,Hongbin Xing,Erjun Kan,Ang Li
The overall photocatalytic CO2 reduction reaction presents an eco-friendly approach for generating high-value products, specifically ethanol. However, ethanol production still faces efficiency issues (typically formation rates <605 μmol g−1 h−1). One significant challenge arises from the difficulty of continuously transporting CO2 to the catalyst surface, leading to inadequate gas reactant concentration at reactive sites. Here, we develop a mesoporous superhydrophobic Cu2O hollow structure (O–CHS) for efficient gas transport. O–CHS is designed to float on an aqueous solution and act as a nano fence, effectively impeding water infiltration into its inner space and enabling CO2 accumulation within. As CO2 is consumed at reactive sites, O–CHS serves as a gas transport channel and diffuser, continuously and promptly conveying CO2 from the gas phase to the reactive sites. This ensures a stable high CO2 concentration at reactive sites. Consequently, O–CHS achieves the highest recorded ethanol formation rate (996.18 μmol g−1 h−1) to the best of our knowledge. This strategy combines surface engineering with geometric modulation, providing a promising pathway for multi-carbon production.
Hydrous ruthenium oxide triggers template-free and spontaneous growth of metal nanostructures†
Chemical Science ( IF 7.6 ) Pub Date : 2023-12-19 , DOI: 10.1039/D3SC05644A
Faheem Muhammad,Xiwen Chen,Jiayi Tang,Yuan Cheng,Yuyang Li,Chenxin Zhu,Yihong Zhang,Leiying Miao,Yu Deng
Intrinsically conductive ruthenium oxide is an excellent material for energy storage and conversion. Herein, we present hydrous RuO2 (H–RuO2) as a potent reducing agent to achieve spontaneous growth of multiple noble metals at room temperature. Self-assembled gold and platinum, comprising small-sized nanoparticles, are generated on the surface of H–RuO2 without the need for additional templates. Structural analysis reveals that the disordered structure and the presence of oxygen vacancies trigger interfacial redox reactions between H–RuO2 and oxidative metal salts. The resulting integrated nanostructures, consisting of a metal oxide and different metals (H–RuO2@metal), are subsequently used to treat inflammatory bowel diseases. In addition to biomedical applications, our developed synthetic strategy, using reactive oxides to spontaneously generate multicomponent nanostructures, also holds great significance for other catalysis-based applications.
Monitoring the synthesis of neutral lipids in lipid droplets of living human cancer cells using two-color infrared photothermal microscopy†
Chemical Science ( IF 7.6 ) Pub Date : 2023-12-01 , DOI: 10.1039/D3SC04705A
Jong Min Lim
There has been growing interest in the functions of lipid droplets (LDs) due to recent discoveries regarding their diverse roles. These functions encompass lipid metabolism, regulation of lipotoxicity, and signaling pathways that extend beyond their traditional role in energy storage. Consequently, there is a need to examine the molecular dynamics of LDs at the subcellular level. Two-color infrared photothermal microscopy (2C-IPM) has proven to be a valuable tool for elucidating the molecular dynamics occurring in LDs with sub-micrometer spatial resolution and molecular specificity. In this study, we employed the 2C-IPM to investigate the molecular dynamics of LDs in both fixed and living human cancer cells (U2OS cells) using the isotope labeling method. We investigated the synthesis of neutral lipids occurring in individual LDs over time after exposing the cells to excess saturated fatty acids while simultaneously comparing inherent lipid contents in LDs. We anticipate that these research findings will reveal new opportunities for studying lesser-known biological processes within LDs and other subcellular organelles.
Implementing vanadium peroxides as direct air carbon capture materials†
Chemical Science ( IF 7.6 ) Pub Date : 2023-12-21 , DOI: 10.1039/D3SC05381D
Eduard Garrido Ribó,Zhiwei Mao,Jacob S. Hirschi,Taylor Linsday,Karlie Bach,Eric D. Walter,Casey R. Simons,Tim J. Zuehlsdorff,May Nyman
Direct air capture (DAC) removal of anthropogenic CO2 from the atmosphere is imperative to slow the catastrophic effects of global climate change. Numerous materials are being investigated, including various alkaline inorganic metal oxides that form carbonates via DAC. Here we explore metastable early d0 transition metal peroxide molecules that undergo stabilization via multiple routes, including DAC. Specifically here, we describe via experiment and computation the mechanistic conversion of A3V(O2)4 (tetraperoxovanadate, A = K, Rb, Cs) to first a monocarbonate VO(O2)2(CO3)3−, and ultimately HKCO3 plus KVO4. Single crystal X-ray structures of rubidium and cesium tetraperoxovanadate are reported here for the first time, likely prior-challenged by instability. Infrared spectroscopy (FTIR), powder X-ray diffraction (PXRD), 51V solid state NMR (nuclear magnetic resonance), tandem thermogravimetry-mass spectrometry (TGA-MS) along with calculations (DFT, density functional theory) all converge on mechanisms of CO2 capture and release that involve the vanadium centre, despite the end product of a 300 days study being bicarbonate and metavanadate. Electron Paramagnetic Resonance (EPR) Spectroscopy along with a wet chemical assay and computational studies evidence the presense of ∼5% adventitous superoxide, likely formed by peroxide reduction of vanadium, which also stabilizes via the reaction with CO2. The alkalis have a profound effect on the stability of the peroxovanadate compounds, stability trending K > Rb > Cs. While this translates to more rapid CO2 capture with heavier alkalis, it does not necessarily lead to capture of more CO2. All compounds capture approximately two equivalents CO2 per vanadium centre. We cannot yet explain the reactivity trend of the alkali peroxovanadates, because any change in speciation of the alkalis from reactions to product is not quantifiable. This study sets the stage for understanding and implementing transition metal peroxide species, including peroxide-functionalized metal oxides, for DAC.
Keeping an “eye” on the experiment: computer vision for real-time monitoring and control†
Chemical Science ( IF 7.6 ) Pub Date : 2023-11-27 , DOI: 10.1039/D3SC05491H
Rama El-khawaldeh,Mason Guy,Finn Bork,Nina Taherimakhsousi,Kris N. Jones,Joel M. Hawkins,Lu Han,Robert P. Pritchard,Blaine A. Cole,Sebastien Monfette
This work presents a generalizable computer vision (CV) and machine learning model that is used for automated real-time monitoring and control of a diverse array of workup processes. Our system simultaneously monitors multiple physical outputs (e.g., liquid level, homogeneity, turbidity, solid, residue, and color), offering a method for rapid data acquisition and deeper analysis from multiple visual cues. We demonstrate a single platform (consisting of CV, machine learning, real-time monitoring techniques, and flexible hardware) to monitor and control vision-based experimental techniques, including solvent exchange distillation, antisolvent crystallization, evaporative crystallization, cooling crystallization, solid–liquid mixing, and liquid–liquid extraction. Both qualitative (video capturing) and quantitative data (visual outputs measurement) were obtained which provided a method for data cross-validation. Our CV model's ease of use, generalizability, and non-invasiveness make it an appealing complementary option to in situ and real-time analytical monitoring tools and mathematical modeling. Additionally, our platform is integrated with Mettler-Toledo's iControl software, which acts as a centralized system for real-time data collection, visualization, and storage. With consistent data representation and infrastructure, we were able to efficiently transfer the technology and reproduce results between different labs. This ability to easily monitor and respond to the dynamic situational changes of the experiments is pivotal to enabling future flexible automation workflows.
A four-component reaction to access 3,3-disubstituted indolines via the palladium–norbornene-catalyzed ortho amination/ipso conjunctive coupling†
Chemical Science ( IF 7.6 ) Pub Date : 2023-12-14 , DOI: 10.1039/D3SC06409C
Alexander J. Rago,Rong Ye,Xin Liu,Guangbin Dong
As an important class of multicomponent reactions, the palladium/norbornene (Pd/NBE) cooperative catalysis has been mainly restricted to the coupling of an aryl halide, an electrophile and a nucleophile. Here, we report the development of a Pd/NBE-catalyzed four-component reaction, which involves ortho C–H amination/ipso conjunctive coupling using an alkene and an external nucleophile. The use of alkene-tethered nitrogen electrophiles provides a rapid and modular synthesis of 3,3-disubstituted indolines from readily available aryl iodides. The reaction exhibits broad functional group tolerance, and its utility is exemplified in a streamlined formal synthesis of a rhodamine dye. Preliminary results of the asymmetric version of this reaction have also been obtained.
Harnessing the electronic structure of active metals to lower the overpotential of the electrocatalytic oxygen evolution reaction†
Chemical Science ( IF 7.6 ) Pub Date : 2023-12-12 , DOI: 10.1039/D3SC05891C
Lorenzo Baldinelli,Gabriel Menendez Rodriguez,Iolanda D'Ambrosio,Amalia Malina Grigoras,Riccardo Vivani,Loredana Latterini,Alceo Macchioni,Giovanni Bistoni
Despite substantial advancements in the field of the electrocatalytic oxygen evolution reaction (OER), the efficiency of earth-abundant electrocatalysts remains far from ideal. The difficulty stems from the complex nature of the catalytic system, which limits our fundamental understanding of the process and thus the possibility of a rational improvement of performance. Herein, we shed light on the role played by the tunable 3d configuration of the metal centers in determining the OER catalytic activity by combining electrochemical and spectroscopic measurements with an experimentally validated computational protocol. One-dimensional coordination polymers based on Fe, Co and Ni held together by an oxonato linker were selected as a case study because of their well-defined electronic and geometric structure in the active site, which can be straightforwardly correlated with their catalytic activity. Novel heterobimetallic coordination polymers were also considered, in order to shed light on the cooperativity effects of different metals. Our results demonstrate the fundamental importance of electronic structure effects such as metal spin and oxidation state evolutions along the reaction profile to modulate ligand binding energies and increase catalyst efficiency. We demonstrated that these effects could in principle be exploited to reduce the overpotential of the electrocatalytic OER below its theoretical limit, and we provide basic principles for the development of coordination polymers with a tailored electronic structure and activity.
Anion-templated synthesis of a switchable fluorescent [2]catenane with sulfate sensing capability†
Chemical Science ( IF 7.6 ) Pub Date : 2023-12-18 , DOI: 10.1039/D3SC05086F
Bartosz Trzaskowski
Anion templation strategies have facilitated the synthesis of various catenane and rotaxane hosts capable of strong and selective binding of anions in competitive solvents. However, this approach has primarily relied on positively charged precursors, limiting the structural diversity and the range of potential applications of the anion-templated mechanically interlocked molecules. Here we demonstrate the synthesis of a rare electroneutral [2]catenane using a powerful, doubly charged sulfate template and a complementary diamidocarbazole-based hydrogen bonding precursor. Owing to the unique three-dimensional hydrogen bonding cavity and the embedded carbazole fluorophores, the resulting catenane receptor functions as a sensitive fluorescent turn-ON sensor for the highly hydrophilic sulfate, even in the presence of a large excess of water. Importantly, the [2]catenane exhibits enhanced binding affinity and selectivity for sulfate over its parent macrocycle and other acyclic diamidocarbazole-based receptors. We demonstrate also, for the first time, that the co-conformation of the catenane may be controlled by reversible acid/base induced protonation and deprotonation of the anionic template, SO42−. This approach pioneers a new strategy to induce molecular motion of interlocked components using switchable anionic templates.
Mechanistic insights into radical formation and functionalization in copper/N-fluorobenzenesulfonimide radical-relay reactions†
Chemical Science ( IF 7.6 ) Pub Date : 2023-12-12 , DOI: 10.1039/D3SC03597B
Joshua A. Buss,Si-Jie Chen,Christopher J. Cramer,Shannon S. Stahl
Copper-catalysed radical-relay reactions that employ N-fluorobenzenesulfonimide (NFSI) as the oxidant have emerged as highly effective methods for C(sp3)–H functionalization. Herein, computational studies are paired with experimental data to investigate a series of key mechanistic features of these reactions, with a focus on issues related to site-selectivity, enantioselectivity, and C–H substrate scope. (1) The full reaction energetics of enantioselective benzylic C–H cyanation are probed, and an adduct between Cu and the N-sulfonimidyl radical (˙NSI) is implicated as the species that promotes hydrogen-atom transfer (HAT) from the C–H substrate. (2) Benzylic versus 3° C–H site-selectivity is compared with different HAT reagents: Cu/˙NSI, ˙OtBu, and Cl˙, and the data provide insights into the high selectivity for benzylic C–H bonds in Cu/NFSI-catalyzed C–H functionalization reactions. (3) The energetics of three radical functionalization pathways are compared, including radical–polar crossover (RPC) to generate a carbocation intermediate, reductive elimination from a formal CuIII organometallic complex, and radical addition to a Cu-bound ligand. The preferred mechanism is shown to depend on the ligands bound to copper. (4) Finally, the energetics of three different pathways that convert benzylic C–H bonds into benzylic cations are compared, including HAT/ET (ET = electron transfer), relevant to the RPC mechanism with Cu/NFSI; hydride transfer, involved in reactions with high-potential quinones; and sequential ET/PT/ET (PT = proton transfer), involved in catalytic photoredox reactions. Collectively, the results provide mechanistic insights that establish a foundation for further advances in radical-relay C–H functionalization reactions.
Ligand field design enables quantum manipulation of spins in Ni2+ complexes†
Chemical Science ( IF 7.6 ) Pub Date : 2023-12-08 , DOI: 10.1039/D3SC04919A
Michael K. Wojnar,Krishnendu Kundu,Arailym Kairalapova,Xiaoling Wang,Andrew Ozarowski,Timothy C. Berkelbach,Danna E. Freedman
Creating the next generation of quantum systems requires control and tunability, which are key features of molecules. To design these systems, one must consider the ground-state and excited-state manifolds. One class of systems with promise for quantum sensing applications, which require water solubility, are d8 Ni2+ ions in octahedral symmetry. Yet, most Ni2+ complexes feature large zero-field splitting, precluding manipulation by commercial microwave sources due to the relatively large spin–orbit coupling constant of Ni2+ (630 cm−1). Since low lying excited states also influence axial zero-field splitting, D, a combination of strong field ligands and rigidly held octahedral symmetry can ameliorate these challenges. Towards these ends, we performed a theoretical and computational analysis of the electronic and magnetic structure of a molecular qubit, focusing on the impact of ligand field strength on D. Based on those results, we synthesized 1, [Ni(ttcn)2](BF4)2 (ttcn = 1,4,7-trithiacyclononane), which we computationally predict will have a small D (Dcalc = +1.15 cm−1). High-field high-frequency electron paramagnetic resonance (EPR) data yield spin Hamiltonian parameters: gx = 2.1018(15), gx = 2.1079(15), gx = 2.0964(14), D = +0.555(8) cm−1 and E = +0.072(5) cm−1, which confirm the expected weak zero-field splitting. Dilution of 1 in the diamagnetic Zn analogue, [Ni0.01Zn0.99(ttcn)2](BF4)2 (1′) led to a slight increase in D to ∼0.9 cm−1. The design criteria in minimizing D in 1via combined computational and experimental methods demonstrates a path forward for EPR and optical addressability of a general class of S = 1 spins.
A Ru/RuO2 heterostructure boosting electrochemistry-assisted selective benzoic acid hydrogenation†
Chemical Science ( IF 7.6 ) Pub Date : 2023-12-21 , DOI: 10.1039/D3SC05312A
Zifan Cao,Chenhui Wang,Yifan Sun,Menghui Liu,Wei Li,Yan Fu
Electrocatalytic hydrogenation of benzoic acid (BA) to cyclohexanecarboxylic acid (CCA) at ambient temperature and pressure has been recognized as a promising alternative to thermal hydrogenation since water is required as the hydrogen source. So far, only a few Pt-based electrocatalysts have been developed in acidic electrolyte. To overcome the limitations of reactant solubility and catalyst corrosion, herein, carbon fiber-supported Ru electrocatalysts with abundant Ru/RuO2 heterojunctions were fabricated via cyclic electrodeposition between −0.8 and 1.1 V vs. Ag/AgCl. In an alkaline environment, a Ru/RuO2 catalyst achieves an excellent ECH reactivity in terms of high BA conversion (100%) and selectivity towards CCA (100%) within 180 min at a current density of 200/3 mA cm−2, showing exceptional reusability and long-term stability. 1-Cyclohexenecarboxylic acid (CEA) was identified as the reaction intermediate, whose the selectivity is governed by the applied potential. Kinetic studies demonstrate that ECH of BA over Ru/RuO2 follows a Langmuir–Hinshelwood (L–H) mechanism. In situ Raman spectroscopy and theoretical calculations reveal that the Ru/RuO2 interface enhances the adsorption strength of CEA, thereby facilitating the production of fully hydrogenated CCA. This work provides a deep understanding of the ECH pathway of BA in alkaline media, and gives a new methodology to fabricate heterostructure electrocatalysts.
Prolonged near-infrared fluorescence imaging of microRNAs and proteases in vivo by aggregation-enhanced emission from DNA-AuNC nanomachines†
Chemical Science ( IF 7.6 ) Pub Date : 2023-12-21 , DOI: 10.1039/D3SC05887E
Ting Wang,Kai Jiang,Yifan Wang,Limei Xu,Yingqi Liu,Shiling Zhang,Weiwei Xiong,Yemei Wang,Fenfen Zheng,Jun-Jie Zhu
Developing a comprehensive strategy for imaging various biomarkers (i.e., microRNAs and proteases) in vivo is an exceptionally formidable task. Herein, we have designed a deoxyribonucleic acid-gold nanocluster (DNA-AuNC) nanomachine for detecting tumor-related TK1 mRNA and cathepsin B in living cells and in vivo. The DNA-AuNC nanomachine is constructed using AuNCs and DNA modules that incorporate a three component DNA hybrid (TD) and a single-stranded fuel DNA (FD). Upon being internalized into tumor cells, the TK1 mRNA initiates the DNA-AuNC nanomachine through DNA strand displacement cascades, leading to the amplified self-assembly and the aggregation-enhanced emission of AuNCs for in situ imaging. Furthermore, with the aid of a protease nanomediator consisting of a mediator DNA/peptide complex and AuNCs (DpAuNCs), the DNA-AuNC nanomachine can be triggered by the protease-activated disassembly of the DNA/peptide complex on the nanomediator, resulting in the aggregation of AuNCs for in vivo protease amplified detection. It is worth noting that our study demonstrates the impressive tumor permeability and accumulation capabilities of the DNA-AuNC nanomachines via in situ amplified self-assembly, thereby facilitating prolonged imaging of TK1 mRNA and cathepsin B both in vitro and in vivo. This strategy presents a versatile and biomarker-specific paradigm for disease diagnosis.
Two active species from a single metal halide precursor: a case study of highly productive Mn-catalyzed dehydrogenation of amine-boranes via intermolecular bimetallic cooperation†
Chemical Science ( IF 7.6 ) Pub Date : 2023-12-07 , DOI: 10.1039/D3SC05356C
Elena S. Osipova,Sergey A. Kovalenko,Oleg A. Filippov,Natalia V. Belkova,Laure Vendier,Yves Canac,Elena S. Shubina,Dmitry A. Valyaev
Metal–metal cooperation for inert bond activation is a ubiquitous concept in coordination chemistry and catalysis. While the great majority of such transformations proceed via intramolecular mode in binuclear complexes, to date only a few examples of intermolecular small molecule activation using usually bimetallic frustrated Lewis pairs (Mδ+⋯M′δ−) have been reported. We introduce herein an alternative approach for the intermolecular bimetallic cooperativity observed in the catalytic dehydrogenation of amine-boranes, in which the concomitant activation of N–H and B–H bonds of the substrate via the synergetic action of Lewis acidic (M+) and basic hydride (M–H) metal species derived from the same mononuclear complex (M–Br). It was also demonstrated that this system generated in situ from the air-stable Mn(I) complex fac-[(CO)3(bis(NHC))MnBr] and NaBPh4 shows high activity for H2 production from several substrates (Me2NHBH3, tBuNH2BH3, MeNH2BH3, NH3BH3) at low catalyst loading (0.1% to 50 ppm), providing outstanding efficiency for Me2NHBH3 (TON up to 18 200) that is largely superior to all known 3d-, s-, p-, f-block metal derivatives and frustrated Lewis pairs (FLPs). These results represent a step forward towards more extensive use of intermolecular bimetallic cooperation concepts in modern homogeneous catalysis.
Photochemical H2 activation by an Zn–Fe heterometallic: a mechanistic investigation†
Chemical Science ( IF 7.6 ) Pub Date : 2023-12-14 , DOI: 10.1039/D3SC05966A
Marina Perez-Jimenez,Mark R. Crimmin
Addition of H2 to a Zn–Fe complex was observed to occur under photochemical conditions (390 or 428 nm LED) and leads to the formation of a heterometallic dihydride complex. The reaction does not occur under thermal conditions and DFT calculations suggest this is an endergonic, light driven process. Through a combined experimental and computational approach, the plausible mechanisms for H2 activation were investigated. Inhibition experiments, double-label cross-over experiments, radical trapping experiments, EPR spectroscopy and DFT calculations were used to gain insight into this system. The combined data are consistent with two plausible mechanisms, the first involving ligand dissociation followed by oxidative addition of H2 at the Fe centre, the second involving homolytic fragmentation of the Zn–Fe heterometallic and formation of radical intermediates.
Access to pyrrolines and fused diaziridines by selective radical addition to homoallylic diazirines†‡
Chemical Science ( IF 7.6 ) Pub Date : 2023-12-29 , DOI: 10.1039/D3SC04886A
Zhigang Ma,Xinxin Wu,Haotian Li,Zhu Cao
Pyrroline derivatives are common in bioactive natural products and therapeutic agents. We report here a synthesis of pyrrolines and fused diaziridines by divergent radical cyclization of homoallylic diazirines, which can serve as an internal radical trap and a nitrogen source. This reaction proceeds by selective radical addition to CC or NN bonds followed by intramolecular cyclization. Frontier molecular orbital analysis provides a deep insight into the origin of the selectivity. The reaction demonstrates a new cyclization mode, broad functional group compatibility and high product diversity, and reveals a much broader chemical space for diazirine studies.
Selective recognition and discrimination of single isomeric changes in peptide strands with a host : guest sensing array†
Chemical Science ( IF 7.6 ) Pub Date : 2024-01-02 , DOI: 10.1039/D3SC06087J
Junyi Chen,Parisa Fasihianifard,Alexie Andrea P. Raz,Briana L. Hickey,Jose L. Moreno, Jr.,Chia-En A. Chang
An indirect competitive binding mechanism can be exploited to allow a combination of cationic fluorophores and water-soluble synthetic receptors to selectively recognize and discriminate peptide strands containing a single isomeric residue in the backbone. Peptide isomerization occurs in long-lived proteins and has been linked with diseases such as Alzheimer's, cataracts and cancer, so isomers are valuable yet underexplored targets for selective recognition. Planar cationic fluorophores can selectively bind hydrophobic, Trp-containing peptide strands in solution, and when paired with receptors that provide a competitive host for the fluorophore, can form a differential sensing array that enables selective discrimination of peptide isomers. Residue variations such as D- and L-Asp, D- and L-isoAsp, D-Ser and D-Glu can all be recognized, simply by their effects on the folded structure of the flexible peptide. Molecular dynamics simulations were applied to determine the most favorable conformation of the peptide : fluorophore conjugate, indicating that favorable π-stacking with internal tryptophan residues in a folded binding pocket enables micromolar binding affinity.
CarsiDock: a deep learning paradigm for accurate protein–ligand docking and screening based on large-scale pre-training†
Chemical Science ( IF 7.6 ) Pub Date : 2023-12-19 , DOI: 10.1039/D3SC05552C
Heng Cai,Tianye Jian,Xujun Zhang,Tong Chen,Xiaoqi Han,Zhuo Yang,Wei Dang,Yu Kang,Peichen Pan,Xiangyang Ji,Jianfei Song,Yafeng Deng
The expertise accumulated in deep neural network-based structure prediction has been widely transferred to the field of protein–ligand binding pose prediction, thus leading to the emergence of a variety of deep learning-guided docking models for predicting protein–ligand binding poses without relying on heavy sampling. However, their prediction accuracy and applicability are still far from satisfactory, partially due to the lack of protein–ligand binding complex data. To this end, we create a large-scale complex dataset containing ∼9 M protein–ligand docking complexes for pre-training, and propose CarsiDock, the first deep learning-guided docking approach that leverages pre-training of millions of predicted protein–ligand complexes. CarsiDock contains two main stages, i.e., a deep learning model for the prediction of protein–ligand atomic distance matrices, and a translation, rotation and torsion-guided geometry optimization procedure to reconstruct the matrices into a credible binding pose. The pre-training and multiple innovative architectural designs facilitate the dramatically improved docking accuracy of our approach over the baselines in terms of multiple docking scenarios, thereby contributing to its outstanding early recognition performance in several retrospective virtual screening campaigns. Further explorations demonstrate that CarsiDock can not only guarantee the topological reliability of the binding poses but also successfully reproduce the crucial interactions in crystalized structures, highlighting its superior applicability.
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