Chemical Science最新文献_第2页

Quantum-accurate enhanced sampling and mini-protein folding through replica exchange for multiscale neural network potentials 通过多尺度神经网络电位的副本交换，量子精确增强采样和迷你蛋白质折叠

IF 8.4 1区化学

Chemical Science Pub Date : 2026-11-09 DOI: 10.1039/d6sc04555c

Riccardo Solazzo,Igor Gordiy,Sereina Riniker

{"title":"Quantum-accurate enhanced sampling and mini-protein folding through replica exchange for multiscale neural network potentials","authors":"Riccardo Solazzo,Igor Gordiy,Sereina Riniker","doi":"10.1039/d6sc04555c","DOIUrl":"https://doi.org/10.1039/d6sc04555c","url":null,"abstract":"Neural network potentials (NNPs) have emerged as efficient alternatives to computationally demanding quantum-mechanical (QM) methods. AMPv3-EE-BMS25 (short AMP-BMS) is an equivariant NNP designed for multiscale ML/MM simulations that captures directional and long-range interactions. In classical molecular dynamics (MD) simulations, enhanced-sampling techniques are applied to cross large energy barriers and improve convergence. Among those, replica exchange with solute tempering (REST2) is an efficient method that selectively scales solute interactions while keeping the bath temperature fixed, thereby reducing the number of replicas required. Here, we present a REST2-like algorithm compatible with multiscale ML/MM simulations. This algorithm is combined with AMP-BMS by exploiting the separability of its Hamiltonian into solute–solute, solute–solvent, and solvent–solvent contributions. We validate the REST2–AMP approach on several peptidic systems in explicit solvent and demonstrate folding of the mini-proteins chignolin and CLN025 from extended conformations. Thus, our REST2 approach for ML/MM enables access to biologically relevant timescales while maintaining near-DFT accuracy.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":"237 1","pages":""},"PeriodicalIF":8.4,"publicationDate":"2026-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149368249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hydrogen-bonded organic frameworks materials fabricating luminescent device for smart responsive sensing application 用于智能响应传感应用的发光器件的氢键有机框架材料制造

IF 8.4 1区化学

Chemical Science Pub Date : 2026-11-09 DOI: 10.1039/d6sc07271b

Alituniguli Maimaiti,Bing Yan

{"title":"Hydrogen-bonded organic frameworks materials fabricating luminescent device for smart responsive sensing application","authors":"Alituniguli Maimaiti,Bing Yan","doi":"10.1039/d6sc07271b","DOIUrl":"https://doi.org/10.1039/d6sc07271b","url":null,"abstract":"Hydrogen-bonded organic frameworks (HOFs) provide a distinctive platform for luminescent device development because their organic building blocks can combine molecular recognition, ordered porosity and photophysical activity within reversibly assembled crystalline networks. In selected systems, this reversibility also enables solution-assisted processing, defect repair and material regeneration. However, the practical value of HOFs is determined not only by the properties of the framework itself, but also by how it is integrated with polymers, fibers, porous substrates and optical readout systems. This Review examines the transition from particulate HOF sensors to HOF-based hybrid devices. We first discuss the roles of polymer hosts and interfaces in controlling framework dispersion, analyte transport, mechanical compliance, optical stability and signal reproducibility. We then compare thin films, hydrogels, fabrics, fibers, foams and microneedle architectures, relating their structures to fabrication routes and sensing performance. The resulting devices support ratiometric and multimodal analysis, biomimetic chemical perception, physical-stimulus sensing, anti-counterfeiting and artificial-intelligence-assisted interpretation. Particular attention is given to the limitations that are often obscured by proof-of-concept demonstrations, including water stability, interfacial retention, batch variation, matrix interference, calibration and model transferability. Finally, we propose design principles for connecting framework chemistry, polymer architecture, optical transduction and data analysis. The central challenge is to move HOF devices from responsive laboratory materials towards reproducible, scalable and independently validated intelligent sensing systems.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":"7 1","pages":""},"PeriodicalIF":8.4,"publicationDate":"2026-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149368251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Harnessing Bridge Resonance to Optimise Multiexciton Evolution through Intramolecular Singlet Fission 利用桥共振优化分子内单线态裂变中的多激子演化

IF 8.4 1区化学

Chemical Science Pub Date : 2026-11-06 DOI: 10.1039/d6sc05308d

Kanad Majumder,Soham Mukherjee,Jieun Lee,Jeoungin Yi,Jayashree Nagesh,Namana Venkatareddy,Arup Kundu,Aleesha George,Jyotishman Dasgupta,Manish Jain,Woojae Kim,Andrew J Musser,Satish Amrutrao Patil,Kiser Z Colley

{"title":"Harnessing Bridge Resonance to Optimise Multiexciton Evolution through Intramolecular Singlet Fission","authors":"Kanad Majumder,Soham Mukherjee,Jieun Lee,Jeoungin Yi,Jayashree Nagesh,Namana Venkatareddy,Arup Kundu,Aleesha George,Jyotishman Dasgupta,Manish Jain,Woojae Kim,Andrew J Musser,Satish Amrutrao Patil,Kiser Z Colley","doi":"10.1039/d6sc05308d","DOIUrl":"https://doi.org/10.1039/d6sc05308d","url":null,"abstract":"The central question in the study of singlet fission remains how to control the interchromophore couplings that govern the formation, spin evolution and decay of triplet pairs through molecular design. In intramolecular singlet fission materials, this control is achieved by tethering chromophores with a range of bridging units. These small bridges typically serve as inert structural scaffolds or provide pathways for conjugation between chromophores but usually are not directly involved in the fission pathway due to large orbital offsets. Here, we explore control of iSF rates by using a resonant bridge, in which the linker's frontier orbitals are more closely aligned with those of the chromophore subunits.Through careful spectroscopic and computational comparison between analogous pentacene dimers bridged by strongly electron-withdrawing benzothiadiazole or passive phenyl bridges, we decouple the electronic contributions of bridge resonance from standard geometric and conjugative effects. Our investigations reveal that the benzothiadiazole moiety reconfigures the singlet potential energy surface of the covalently linked dimer, introducing significant orbital hybridisation between pentacenes and the bridge. This hybridisation can lead to new parasitic decay channels, but when the coupling is optimised it results in more rapid triplet-pair formation and suppressed triplet-pair decay in a manner that is remarkably robust against changes to the dielectric environment. Our findings thus demonstrate that resonant bridges rather than passive linkers is a powerful strategy for optimising multiexciton generation and utilisation in pi-conjugated chromophores.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":"23 1","pages":""},"PeriodicalIF":8.4,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149360155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Azobenzene-Mediated Reversible Conformational Switching in 9,9′-Bifluorenylidene-Based Molecular Machines 偶氮苯介导的9,9 ' -二氟乙烯基分子机器的可逆构象开关

IF 8.4 1区化学

Chemical Science Pub Date : 2026-11-06 DOI: 10.1039/d6sc07394h

Sohail Mahajan,Reese Rich,Lin Jiao,Duhan Zhang,Wendu Ding,Jinjia Xu

{"title":"Azobenzene-Mediated Reversible Conformational Switching in 9,9′-Bifluorenylidene-Based Molecular Machines","authors":"Sohail Mahajan,Reese Rich,Lin Jiao,Duhan Zhang,Wendu Ding,Jinjia Xu","doi":"10.1039/d6sc07394h","DOIUrl":"https://doi.org/10.1039/d6sc07394h","url":null,"abstract":"Intrinsically dynamic molecules offer attractive building blocks for molecular machines, yet controlling their conformational motion with external stimuli remains a fundamental challenge. Here, we report Azo-BF-Azo, a visible-light-driven molecular machine in which an intrinsically dynamic 9,9′-bifluorenylidene (BF) core is coupled to two photoswitchable tetraortho-fluorinated azobenzene (Azo) units that act as molecular actuators. By using variabletemperature NMR spectroscopy and UV-vis spectroscopy, together with computational studies, we demonstrate that irradiation at 525 nm induces Azo trans-cis photoisomerization and shifts the BF conformational equilibrium from the closed toward the open state, whereas 456 nm irradiation reverses Azo isomerization and promotes recovery of the BF-closed state. DFT calculations reveal that the extended trans-Azo units favor intramolecular π-π interactions that stabilize the closed BF conformation, while their conversion to the folded cis state disrupts these interactions and alters the steric environment surrounding the BF core. Variable-temperature NMR spectroscopy provides experimental support for the role of these intramolecular interactions in regulating the BF conformational equilibrium. The photoinduced metastable state further undergoes spontaneous thermal relaxation in the dark, recovering approximately 65% of the initial state. Together, these results demonstrate that local photoisomerization can reshape the conformational energy landscape of a second, intrinsically dynamic molecular degree of freedom through switchable noncovalent interactions. This work provides a strategy for converting intrinsic molecular dynamics into externally programmable motion and establishes a design principle for constructing integrated molecular machines in which one type of molecular motion regulates another.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":"1 1","pages":""},"PeriodicalIF":8.4,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149360211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Decoupled Electro-Biosynthesis of High-Value Bioproducts from CO2 and N2 CO2和N2高价值生物产品的解耦电-生物合成

IF 8.4 1区化学

Chemical Science Pub Date : 2026-11-06 DOI: 10.1039/d6sc05584b

Qianzi Hou,Yizhou Dai,Chenyue Zhang,Zixi Gao,Shuqi Guo,Chengbo Li,Tingting Zheng,Xiaohan Huang,Chuan Xia,Qiang Fei

{"title":"Decoupled Electro-Biosynthesis of High-Value Bioproducts from CO2 and N2","authors":"Qianzi Hou,Yizhou Dai,Chenyue Zhang,Zixi Gao,Shuqi Guo,Chengbo Li,Tingting Zheng,Xiaohan Huang,Chuan Xia,Qiang Fei","doi":"10.1039/d6sc05584b","DOIUrl":"https://doi.org/10.1039/d6sc05584b","url":null,"abstract":"The conversion of atmospheric carbon dioxide (CO2) and nitrogen (N2) into high-value bioproducts offers a promising pathway for sustainable chemistry, food, and material production. However, existing approaches remain constrained by narrow product scopes, inefficient biological fixation, and poor scalability. Here, we present a spatially decoupled electro-biosystem that converts CO₂ and N₂ into poly-γ-glutamic acid (γ-PGA), while co-generating microbial biomass with cell-protein valorization potential. A Cu-N2 single-atom catalyst and plasma processes generate methane and nitrate from CO2 and N2, providing highly reduced carbon and oxidized nitrogen sources. The engineered methanotrophs heterologously expressing γ-PGA biosynthesis genes were designed to convert methane and nitrate into γ-PGA with a molecular weight of up to 700 kDa. Systematic optimization of carbon, nitrogen, and energy fluxes boosted γ-PGA titer by 125% to 142.84 mg L-1 in a 30-L bioreactor, accompanied by 9.47 g L⁻¹ of cell protein. Importantly, the modular design allows the outputs of the electrocatalytic and plasma-assisted units to be adjusted according to the measured carbon, nitrogen, and oxygen demands of the biological module, thereby supporting supply–demand matching across the spatially decoupled system. Techno-economic analysis and life-cycle assessment identify key determinants of process economics and indicate the potential environmental benefits of the electro-biosystem, respectively. This study demonstrates a decoupled platform for high-value bioproduct production, providing a modular basis for process scale-up and advancing customizable, air-derived biomanufacturing from CO2 and N2.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":"34 1","pages":""},"PeriodicalIF":8.4,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149360156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

IF 8.4 1区化学

Chemical Science Pub Date : 2026-11-05 DOI: 10.1039/d6sc06544a

Shuran Ma,Shuyang Sun,Dengyao Yu,Xue Cong,Yanchao Wang,Yuanzheng Chen,Zhen Liu

{"title":"","authors":"Shuran Ma,Shuyang Sun,Dengyao Yu,Xue Cong,Yanchao Wang,Yuanzheng Chen,Zhen Liu","doi":"10.1039/d6sc06544a","DOIUrl":"https://doi.org/10.1039/d6sc06544a","url":null,"abstract":"High‑pressure unconventional oxidation states are attributed to exceptional charge transfer, which is itself induced by the differential pressure response of atomic orbital energy levels. The high oxidation states observed in heavy alkali metals (Cs, Ba, Ra) exemplify this behavior, as their semi-core p-states surpass the valence orbital levels of oxidants, e.g., the 2p-orbital of F, at high pressure. However, semi-core p-electron activation in lighter alkali metals, such as Rb, is hindered because the relative orbitals lie at intrinsically lower energies due to their smaller radii, making pressure‑induced upshift challenging. We demonstrate that crystal‑field splitting of alkali‑metal semi-core p‑orbitals selectively elevates a portion of these states, substantially lowering the pressure threshold for their chemical activation. Here, our computations reveal that the semi-core 4p-electrons of Rb form weak metallic bonds with F in P21/c-RbBF5 at around 250 GPa, a pressure accessible in modern high‑pressure experiments. Extending to Cs-B-F systems, the crystal‑field splitting drives 5p participation in Cs-F bond formation in CsBF5. These findings unveil a new paradigm for semi-core or inner-shell chemistry, providing a unifying framework for semi-core electron activation and bonding. Crucially, they establish that semi-core electrons of light main‑group elements, including Rb, are accessible at experimentally feasible pressures.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":"24 1","pages":""},"PeriodicalIF":8.4,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149359913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Catalytic borylation of the high-global-warming-potential refrigerant HFC-143a. 高全球变暖潜势制冷剂HFC-143a的催化硼化反应。

IF 8.1 1区化学

Chemical Science Pub Date : 2026-11-05 DOI: 10.1039/d6sc07134a

Luc A Mauro, Anthony T Paolo, Cristabella R Fortna, Josie B Rojo, Agustin P Bravo, Eric Sanchez Josa, Elizabeth R Young, Lisa A Fredin, David A Vicic

引用次数: 0

Bioinspired Metal-Free Carbazole-Guanine Quadruplex Gel for Ambient Room-Temperature Phosphorescence 用于室温磷光的仿生无金属咔唑-鸟嘌呤四联凝胶

IF 8.4 1区化学

Chemical Science Pub Date : 2026-11-05 DOI: 10.1039/d6sc05787j

Sona Saji,Ariharasudhan R.,Jibin Jibin Sivanarayanan,Mahesh Hariharan

{"title":"Bioinspired Metal-Free Carbazole-Guanine Quadruplex Gel for Ambient Room-Temperature Phosphorescence","authors":"Sona Saji,Ariharasudhan R.,Jibin Jibin Sivanarayanan,Mahesh Hariharan","doi":"10.1039/d6sc05787j","DOIUrl":"https://doi.org/10.1039/d6sc05787j","url":null,"abstract":"Organic room-temperature phosphorescence (RTP) from metal-free supramolecular biomimetic systems remains challenging because of the rapid non-radiative deactivation of triplet excitons under ambient conditions. Herein, we report a structurally modified guanine-carbazole molecule (GC) that spontaneously self-assembles into a metal-free gel (GCG) and exhibits RTP under ambient conditions. Variable-temperature NMR, DOSY NMR, circular dichroism, and high-resolution mass spectrometry measurements collectively confirm the formation of hydrogen-bonded tetrameric G-quartets in solution without the assistance of metal ions. Single-crystal X-ray diffraction of GC reveals cyclic Hoogsteen hydrogen-bonded tetrads that further propagate into ordered helical supramolecular arrays. Gelation induces ordered J-type aggregation and conformational rigidification, and suppresses non-radiative decay pathways. Both dilute and concentrated solutions of GC in THF are non-phosphorescent at room temperature and display only fluorescence. However, upon ageing, the concentrated solution undergoes gelation to form GCG, leading to the emergence of distinct RTP with a phosphorescence lifetime of 170 μs under ambient conditions. These findings demonstrate that G-quadruplex assemblies are a supramolecular scaffold for controlling triplet excited-state dynamics and establish nucleobase-chromophore coupling as a promising strategy for the development of heavy-atom-free phosphorescent soft materials.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":"34 1","pages":""},"PeriodicalIF":8.4,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149359869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Total synthesis of cochinmicin I and V. 红霉素I和V的全合成。

IF 8.1 1区化学

Chemical Science Pub Date : 2026-11-05 DOI: 10.1039/d6sc05662h

Jade C Williams, Preston C Gourville, Chase K Pyrah, William J Stark, Jade A Bing, Jeffrey N Johnston

引用次数: 0

Genetic code expansion for site-specific encoding of a switchable, intrinsic fluorophore-quencher pair to monitor protein dynamics. 遗传密码扩展的位点特异性编码的一个可切换的，固有的荧光团猝灭对，以监测蛋白质动力学。

IF 8.1 1区化学

Chemical Science Pub Date : 2026-11-04 DOI: 10.1039/d6sc06723a

Priyanda Giri, Yarra Venkatesh, Moriah H Mathis, Christina M Hurley, Chloe M Jones, Olivier Ndogo Eteme, Zachary M Hostetler, Richard B Cooley, Rahul M Kohli, Ryan A Mehl, E James Petersson

{"title":"Genetic code expansion for site-specific encoding of a switchable, intrinsic fluorophore-quencher pair to monitor protein dynamics.","authors":"Priyanda Giri, Yarra Venkatesh, Moriah H Mathis, Christina M Hurley, Chloe M Jones, Olivier Ndogo Eteme, Zachary M Hostetler, Richard B Cooley, Rahul M Kohli, Ryan A Mehl, E James Petersson","doi":"10.1039/d6sc06723a","DOIUrl":"10.1039/d6sc06723a","url":null,"abstract":"Precisely modifying proteins at multiple sites in their native, folded structures offers unique opportunities to answer molecular and cellular-level biological questions. Here, we present a genetic code expansion strategy for site-specific integration of a fluorophore-quencher pair comprising two non-canonical amino acids-acridonylalanine (Acd) and methyltetrazinyl phenylalanine (Tet)-into a protein expressed in E. coli. The Acd and Tet pair requires no post-translational labeling, and quenching can be switched off by bioorthogonal or photochemical reactions of Tet for convenient internal control experiments. Mechanistic studies based on Stern-Volmer quenching, fluorescence lifetime measurements, and \"proline ruler\" peptides established the distance dependence of quenching. As proof-of-concept, we applied this strategy to study: (1) calmodulin, a calcium-sensing protein, (2) RecA, a DNA damage sensor in bacteria, and (3) LexA, a transcriptional repressor whose activation by RecA governs acquired antibiotic resistance in bacteria. Using these proteins, we demonstrate that dual Acd/Tet labeling provides molecular-level insights into protein dynamics, shows potential for adaptation to high-throughput drug screening, and advances tools for studying protein structure-function relationships.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":" ","pages":""},"PeriodicalIF":8.1,"publicationDate":"2026-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13732730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149332722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0