Devesh K Pathak, Rajkumar Jana, Ruth Bello, Kelly White, Kelsey A Stoerzinger
{"title":"Robust catalyst assessment for the electrocatalytic nitrate reduction reaction.","authors":"Devesh K Pathak, Rajkumar Jana, Ruth Bello, Kelly White, Kelsey A Stoerzinger","doi":"10.1038/s42004-025-01691-z","DOIUrl":"10.1038/s42004-025-01691-z","url":null,"abstract":"","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"302"},"PeriodicalIF":6.2,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12514229/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145274015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Progress, pitfalls, and prospects in emerging materials for aluminum-sulfur batteries.","authors":"Brindha Ramasubramanian, Dipsikha Ganguly, Rayavarapu Prasada Rao, Seeram Ramakrishna","doi":"10.1038/s42004-025-01690-0","DOIUrl":"10.1038/s42004-025-01690-0","url":null,"abstract":"<p><p>Aluminium-sulfur (Al-S) batteries have emerged as a promising post-lithium alternative owing to aluminium's abundance, safety, and high theoretical capacity. However, their practical implementation is impeded by key challenges such as sluggish Al<sup>3+</sup> redox kinetics, polysulfide shuttle effects, and volumetric changes of the electrodes during cycling. This review critically analysis recent advancements in host structural design engineering, new electrocatalysts, and electrolyte aimed at overcoming these limitations. Advanced host frameworks include 2D/3D porous structures, MXene-based multilayers, and single-atom doped materials that facilitate efficient sulfur confinement, enhance conductivity, and catalyse redox reactions. Embedded catalysts like Mo<sub>6</sub>S<sub>8</sub> and CoS<sub>2</sub> within nitrogen-doped carbons lower the decomposition barrier of Al<sub>2</sub>S<sub>3</sub>, promote stable Al-polysulfide conversion, and extend cycle life. Electrolyte optimization through ionic liquids, molten salts, and halide-modified systems further enhances ion mobility, suppresses passivation, and supports stable sulfur utilization. Emerging hybrid electrolytes combining high-donicity solvents with ionic or molten salt phases offer synergistic gains in redox kinetics and thermal stability. Density functional theory (DFT) guided designs elucidate key host-electrolyte-polysulfide interactions, revealing pathways for tailored material selection and performance enhancement. These integrated strategies pave the way for high-energy, long-lasting Al-S batteries that perform reliably at both room and elevated temperatures.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"301"},"PeriodicalIF":6.2,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12508050/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145250167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Exploring the macrocyclic chemical space for heuristic drug design with deep learning models.","authors":"Feng Hu, Xiaotong Jia, Wenjie Liao, Ziqi Chen, Hongjie Bi, Huan Ge, Dandan Liu, Rongrong Zhang, Yuting Hu, Wenyi Mei, Zhenjiang Zhao, Kai Zhang, Lili Zhu, Yanyan Diao, Honglin Li","doi":"10.1038/s42004-025-01686-w","DOIUrl":"10.1038/s42004-025-01686-w","url":null,"abstract":"<p><p>Macrocyclic compounds hold great promise as therapeutic agents. However, their structural optimization remains constrained by the limited availability of bioactive candidates, which in turn hampers the systematic exploration of structure-activity relationships. Here we introduce CycleGPT, a generative chemical language model designed specifically to address these challenges. CycleGPT is characterized by a progressive transfer learning paradigm that incrementally transfers knowledge from pre-trained chemical language models to specialized macrocycle generation, thereby overcoming the data shortage issue. Meanwhile, it adopts an innovative probabilistic sampling strategy that effectively improves the structural novelty of generated macrocycles while ensuring domain-specific adaptability. In a prospective drug design based on CycleGPT and a JAK2 activity prediction model, we successfully developed a new JAK2 drug candidate with a good selectivity profile (inhibiting 17 wild-type kinases) and promising potential for treating polycythemia in vivo, demonstrating the practicality of deep learning methods in macrocyclic drug design.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"299"},"PeriodicalIF":6.2,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12504684/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vitaliy G Goncharov, William Smith, Jiahong Li, Jeffrey A Eakin, Erik D Reinhart, James Boncella, Luke D Gibson, Vyacheslav S Bryantsev, Rushi Gong, Shun-Li Shang, Zi-Kui Liu, Hongwu Xu, Aurora Clark, Xiaofeng Guo
{"title":"A hybrid calorimetry-simulation model of mixing enthalpy for molten salt.","authors":"Vitaliy G Goncharov, William Smith, Jiahong Li, Jeffrey A Eakin, Erik D Reinhart, James Boncella, Luke D Gibson, Vyacheslav S Bryantsev, Rushi Gong, Shun-Li Shang, Zi-Kui Liu, Hongwu Xu, Aurora Clark, Xiaofeng Guo","doi":"10.1038/s42004-025-01688-8","DOIUrl":"10.1038/s42004-025-01688-8","url":null,"abstract":"<p><p>Calorimetric determination of enthalpies of mixing (ΔH<sub>mix</sub>) in multicomponent molten salts is often interpreted using empirical models that lack physically meaningful parameters. However, for improving pyrochemical separation of spent nuclear fuel, where lanthanides are major fission products and critical elements, a deeper thermodynamic understanding of the link between excess thermodynamic properties and solvation structure is critically needed. In this work, we implement a hybrid and physics-informed framework, MIVM+Calorimetry+AIMD, which integrates experimentally measured ΔH<sub>mix</sub> (via high temperature drop calorimetry) with solvation structures from ab initio molecular dynamics (AIMD). This approach is demonstrated using LaCl<sub>3</sub> mixed with eutectic LiCl-KCl (58 mol% - 42 mol%) at 873 K and 1133 K. MIVM-derived parameters enable extrapolation of excess Gibbs energy and La<sup>3+</sup> activity across compositions. In contrast, direct ΔH<sub>mix</sub> predictions from AIMD and polarizable ion model simulations deviate significantly. By incorporating experimentally benchmarked solvation structures into an interpretable thermodynamic model, the MIVM+Calorimetry+AIMD formalism achieves higher accuracy and generalizable method for studying molten salts, offering a robust path for understanding and optimizing molten salt chemistry relevant to nuclear fuel cycles and separation science.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"300"},"PeriodicalIF":6.2,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12504626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
X Mercier, J Bourgalais, A Faccinetto, L-S Tran, J Elias, P Demaux, A Lahccen, B Calimet, L Nahon, G A Garcia
{"title":"Direct observation and identification of resonance-stabilized radicals in a sooting flame.","authors":"X Mercier, J Bourgalais, A Faccinetto, L-S Tran, J Elias, P Demaux, A Lahccen, B Calimet, L Nahon, G A Garcia","doi":"10.1038/s42004-025-01689-7","DOIUrl":"10.1038/s42004-025-01689-7","url":null,"abstract":"<p><p>Understanding the molecular mechanisms governing soot inception is critical for developing accurate models of particulate formation in combustion systems. Polycyclic aromatic hydrocarbons (PAHs) are well established as key precursors/intermediates that participate to soot formation, but the growth reactions towards the particulate phase are still the subject of active debate. Among the proposed chemical mechanisms, aromatic resonance-stabilized radicals (RSRs) offer a promising alternative pathway, but their in situ detection in flames has proven challenging, limiting further mechanistic insight. Here, we report the direct observation and identification of several polycyclic aromatic RSRs, using a combination of synchrotron-based mass-selected vacuum ultraviolet photoelectron spectroscopy and quantum chemical calculations. The existence of both delocalized and localized π-radicals and their specific implication on the different stages of soot formation, via radical-driven PAH reaction mechanisms, is discussed in the context of combustion chemistry.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"295"},"PeriodicalIF":6.2,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12501325/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145238254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Claudia Spallacci, Marco Chino, Antonio Rosato, Ornella Maglio, Ping Huang, Luca D'Amario, Angela Lombardi, Claudia Andreini, Mun Hon Cheah
{"title":"A bioinformatics approach to design minimal biomimetic metal-binding peptides.","authors":"Claudia Spallacci, Marco Chino, Antonio Rosato, Ornella Maglio, Ping Huang, Luca D'Amario, Angela Lombardi, Claudia Andreini, Mun Hon Cheah","doi":"10.1038/s42004-025-01702-z","DOIUrl":"10.1038/s42004-025-01702-z","url":null,"abstract":"<p><p>Nature-inspired or biomimetic catalysts aim to reach the high catalytic performance and selectivity of natural enzymes while possessing the chemical stability and processability of synthetic catalysts. A promising strategy for designing biomimetic catalysts relies on mimicking the structure of the enzyme active site. This can either entail complicated total synthesis of a synthetic catalyst or design of peptide sequences, able to self-assemble in the presence of metal ions, thus forming metallo-peptide complexes that mimic the active sites of natural enzymes. Using a bioinformatics approach, we designed a minimal peptide made up of eight amino acids (H4pep) to act as a functional mimic of the trinuclear Cu site of the laccase enzyme. Cu(II) binding to H4pep results in the formation of a Cu<sup>2+</sup>(H4pep)<sub>2</sub> complex with a β-sheet secondary structure, able to reduce O<sub>2</sub>. Our study demonstrates the viability and potential of using short peptides to mimic the minimal functional site of natural enzymes.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"296"},"PeriodicalIF":6.2,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12501389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145238236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lillian Otteson, Gabor Nagy, John Kunkel, Gerdenis Kodis, Lars V Bock, Christophe Bignon, Sonia Longhi, Wenwei Zheng, Helmut Grubmüller, Andrea C Vaiana, Sara M Vaiana
{"title":"Transient non-local interactions dominate the dynamics of measles virus N<sub>TAIL</sub>.","authors":"Lillian Otteson, Gabor Nagy, John Kunkel, Gerdenis Kodis, Lars V Bock, Christophe Bignon, Sonia Longhi, Wenwei Zheng, Helmut Grubmüller, Andrea C Vaiana, Sara M Vaiana","doi":"10.1038/s42004-025-01682-0","DOIUrl":"10.1038/s42004-025-01682-0","url":null,"abstract":"<p><p>The RNA genome of measles virus is encapsidated by the nucleoprotein within a helical nucleocapsid that serves as a template for both transcription and replication. The intrinsically disordered domain of the nucleoprotein (N<sub>TAIL</sub>) is essential for binding the polymerase complex responsible for viral transcription and replication. As for many IDPs, binding of N<sub>TAIL</sub> occurs through a short molecular recognition element (MoRE) that folds upon binding, with the majority of N<sub>TAIL</sub> remaining disordered. Although N<sub>TAIL</sub> regions far from the MoRE influence the binding affinity, interactions between them and the MoRE have not been investigated in depth. Relying on photo-induced electron transfer (PET) experiments between tryptophan and cysteine pairs placed at different positions in the protein under varying salt and pH conditions, combined with analytical models, simulations, and coevolutionary analysis, we identified transient interactions between two disordered regions distant in sequence, which dominate N<sub>TAIL</sub> dynamics, and regulate the conformational preferences of both the MoRE and the entire N<sub>TAIL</sub> domain. We propose mechanisms by which these non-local interactions may regulate binding to the measles phosphoprotein, polymerase recruitment, and ultimately viral transcription and replication. Our findings may be extended to other IDPs, where non-local intra-protein interactions affect the conformational preferences of intermolecular binding sites.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"298"},"PeriodicalIF":6.2,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12501004/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145238226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kiran Reddy Baddigam, Bor Shin Chee, Elodie Guilloud, Chaitra Venkatesh, Helena Koninckx, Kim Windey, Margaret Brennan Fournet, Mikael Hedenqvist, Anna J Svagan
{"title":"High oxygen barrier packaging materials from protein-rich single-celled organisms.","authors":"Kiran Reddy Baddigam, Bor Shin Chee, Elodie Guilloud, Chaitra Venkatesh, Helena Koninckx, Kim Windey, Margaret Brennan Fournet, Mikael Hedenqvist, Anna J Svagan","doi":"10.1038/s42004-025-01720-x","DOIUrl":"10.1038/s42004-025-01720-x","url":null,"abstract":"<p><p>Fossil-based packaging materials pose significant environmental challenges due to their persistence and carbon footprint, resulting in pollution and long-term climate change. Here we develop bioplastic packaging alternatives (films and trays) from protein-rich microbial biomass with glycerol as the plasticizer. The microbial biomass demonstrated excellent film-forming properties through compression molding, and the final materials exhibited good mechanical properties and excellent gas barrier properties - an average oxygen permeability coefficient of 0.33 cm<sup>3 </sup>mm m<sup>-2</sup> day<sup>-1</sup> atm<sup>-1</sup> at 50% relative humidity and 23 °C. The oxygen barrier properties highlight these microbial biomass materials as a promising, sustainable alternative to fossil-based synthetic films like EVOH, which are widely used in multilayer food packaging. Beyond offering a microplastic-free solution, the protein-rich materials present an opportunity to mitigate microplastic pollution at the end of their lifecycle. The current results position bioplastics based on microbial biomass as a critical step forward in addressing environmental sustainability challenges with current commercial packaging materials.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"297"},"PeriodicalIF":6.2,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12500970/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145238284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mana Mohan Mukherjee, Matthew D Watson, Devin Biesbrock, Lara K Abramowitz, Steven K Drake, Jennifer C Lee, John A Hanover
{"title":"A dual fluorescent-Raman bioorthogonal probe for specific biosynthetic labeling of intracellular gangliosides.","authors":"Mana Mohan Mukherjee, Matthew D Watson, Devin Biesbrock, Lara K Abramowitz, Steven K Drake, Jennifer C Lee, John A Hanover","doi":"10.1038/s42004-025-01685-x","DOIUrl":"10.1038/s42004-025-01685-x","url":null,"abstract":"<p><p>Gangliosides are sialic acid-containing glycosphingolipids integral to the cell membrane, and they are particularly abundant in the nervous system. Aberrant ganglioside metabolism contributes to pathological conditions, including neurodegenerative diseases, lysosomal storage disorders, and cancer. A critical precursor for sialic acid biosynthesis is N-acetyl-D-mannosamine (ManNAc), which can be epimerized from the corresponding UDP-GlcNAc or exogenously supplied through ManNAc derivatives. Currently, tools to visualize and detect gangliosides are very limited and non-specific. Here, we describe a dual fluorescent and Raman-active ManNAlk derivative, phenanthrene-9-Pr<sub>4</sub>ManNAlk (MM-JH-2), capable of one-step selective labeling of gangliosides in cells. This modified ManNAlk derivative produces a biologically unique Raman spectral signature, which arises from the carbon-carbon triple bond augmented by conjugation to a fluorescent phenanthrene moiety. Raman maps generated using the alkyne stretching frequency indicate a distribution of MM-JH-2 overlapping with intracellular membrane lipids. Using confocal fluorescence imaging, the cellular transport of labeled gangliosides was tracked. Notably, MM-JH-2 can differentiate between cells that differ in ganglioside biosynthetic flux, such as malignant and nonmalignant cells, as well as distinguish between B cells and T cells. Thus, MM-JH-2 is a next-generation metabolic chemical reporter (MCR) that is Raman-active, fluorescent, and can be broadly applied to cellular studies investigating ganglioside biosynthetic flux.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"293"},"PeriodicalIF":6.2,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12494992/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lewis G Parker, Frances K Towers Tompkins, Jake M Seymour, Najaat Alblewi, Ekaterina Gousseva, Megan R Daw, Shusaku Hayama, Richard P Matthews, Adam E A Fouda, Joshua D Elliott, Christopher D Smith, Kevin R J Lovelock
{"title":"Determining structure and Zn-specific Lewis acid-base descriptors for diorganozincs in non-coordinating solvents using X-ray spectroscopy.","authors":"Lewis G Parker, Frances K Towers Tompkins, Jake M Seymour, Najaat Alblewi, Ekaterina Gousseva, Megan R Daw, Shusaku Hayama, Richard P Matthews, Adam E A Fouda, Joshua D Elliott, Christopher D Smith, Kevin R J Lovelock","doi":"10.1038/s42004-025-01704-x","DOIUrl":"10.1038/s42004-025-01704-x","url":null,"abstract":"<p><p>Diorganozinc reagents (ZnR<sub>2</sub>, e.g. R = Et, Ph, C<sub>6</sub>F<sub>5</sub>) are widely used as Lewis acid catalysts or Lewis base reagents in their own right. However, descriptors for predicting the influence of the R substituent on ZnR<sub>2</sub> Lewis acidity/basicity are very sparse. This is because ZnR<sub>2</sub> liquid-phase speciation and electronic structure are unknown to date due to zinc's 'spectroscopically quiet' nature and inability to measure 'at zinc'. Here, we identify the geometric structures of ZnR<sub>2</sub> in weakly coordinating solvents, demonstrating that electronic structure factors will dominate reactivity. We quantify the electronic structure properties that dictate ZnR<sub>2</sub> Lewis acidity/basicity using three newly developed zinc-specific descriptors by combining the results from three zinc-specific X-ray spectroscopy methods and calculations. We provide accessible methods to pre-screen ZnR<sub>2</sub> reactivity. Furthermore, our X-ray spectroscopy toolkit offers opportunities to develop liquid-phase descriptors that dictate reactivity for other zinc species, e.g. zinc bis-amides, battery electrolytes and enzymes.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"294"},"PeriodicalIF":6.2,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12494758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}