Baode Zhang, Snežana D Zarić, Sonja S Zrilić, Iosif Gofman, Barbara Heck, Günter Reiter
{"title":"London dispersion forces and steric effects within nanocomposites tune interaction energies and chain conformation.","authors":"Baode Zhang, Snežana D Zarić, Sonja S Zrilić, Iosif Gofman, Barbara Heck, Günter Reiter","doi":"10.1038/s42004-025-01414-4","DOIUrl":"10.1038/s42004-025-01414-4","url":null,"abstract":"<p><p>The interplay between attractive London dispersion forces and steric effects due to repulsive forces resulting from the Pauli principle often determines the geometry and stability of nanostructures. Aromatic polyimides (PI) and carbon nanotubes (CNT) were chosen as building blocks as two components in the hetero delocalized electron nanostructures. Two PIs, having the same diamine part and different linkage substituents between two phenyl rings of dianhydride part, one linked with ether bond (C-O-C) (OPI), the other with C-(CF3)2 (FPI), were investigated. Surprisingly, two CNT/PI nanocomposites show distinct failure mode from CNT yielding to CNT pull-out failure. Calculation of the interaction energy and chain conformations of each PI upon CNT was performed by accurate density functional theory (DFT) calculations and molecular dynamic simulation (MDS). OPI chain adopt helically wrapping conformation around CNT with relatively strong interaction energy. FPI chain take the one-side wavelike conformation upon CNT with relatively weak interaction energy.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"21"},"PeriodicalIF":5.9,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Design of asymmetric electrolytes for aqueous zinc batteries.","authors":"Shengmei Chen, Chunyi Zhi","doi":"10.1038/s42004-024-01405-x","DOIUrl":"10.1038/s42004-024-01405-x","url":null,"abstract":"<p><p>Aqueous Zn batteries are gaining increasing research attention in the energy storage area due to their intrinsic safety, potentially low cost and environmental friendliness; however, the zinc dendrite formation, zinc corrosion, passivation and the hydrogen evolution reaction induced by water at the anode side, and materials dissolution as well as intrinsic poor reaction kinetics at cathode side in aqueous systems, seriously shorten the cycling life and decrease energy density of batteries and greatly hinder their development. Recent advancements in asymmetric electrolytes with various functions are promising to overcome such challenges for zinc batteries at the same time. It has been proved that the applications of asymmetric electrolytes show significant contributions in the field of zinc-based batteries in suppressing side reactions while maintaining electrochemical performance to satisfy both anode and cathode. Therefore, this perspective summarizes recent advancements in asymmetric electrolytes' design and applications for zinc batteries and outlines opportunities and future challenges, expecting continued research attention in this area.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"20"},"PeriodicalIF":5.9,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11759685/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037407","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":"Analytical protocol for measuring micro-molar quantities of sulfur volatile species in experimental high pressure and temperature fluids.","authors":"Arianna Secchiari, Luca Toffolo, Sandro Recchia, Simone Tumiati","doi":"10.1038/s42004-024-01370-5","DOIUrl":"10.1038/s42004-024-01370-5","url":null,"abstract":"<p><p>Validating thermodynamic models is essential in experimental geosciences for exploring increasingly complex systems and developing analytical protocols. However, investigating solid-fluid equilibria in mm<sup>3</sup>-sized experimental capsules poses several challenges, particularly in sulfur-bearing chemical systems. These include maintaining bulk fluid composition and performing quantitative analysis with extremely low amounts of synthesized fluid. We present an innovative methodology for measuring ultra-low amounts of sulfur volatiles (H<sub>2</sub>S and SO<sub>2</sub>) generated during experimental runs at high pressure and temperature conditions of 3 GPa and 700 °C. Using solid sulfides (FeS + FeS<sub>2</sub>) and water as reactants, we performed redox-controlled syntheses employing a piston cylinder apparatus. We demonstrate that ex-situ measurements of these fluids by quadrupole mass spectrometry ensure accurate and precise analysis, confirming predicted thermodynamic compositions. This methodology allows in-depht investigation of sulfide solid-fluid equilibria, shedding light on sulfur volatiles behavior and geochemical cycles under high P-T conditions characteristic of the Earth's interior.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"19"},"PeriodicalIF":5.9,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11758018/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028148","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":"Development and functional evaluation of a psoralen-conjugated nucleoside mimic for triplex-forming oligonucleotides.","authors":"Yu Mikame, Haruki Toyama, Chikara Dohno, Takehiko Wada, Asako Yamayoshi","doi":"10.1038/s42004-025-01416-2","DOIUrl":"10.1038/s42004-025-01416-2","url":null,"abstract":"<p><p>Psoralen-conjugated triplex-forming oligonucleotides (Ps-TFOs) have been employed for the photodynamic regulation of gene expression by the photo-cross-linking of psoralen with the target DNA. However, stable triplex formation requires a consecutive purine base sequence in one strand of the target DNA duplexes. The pyrimidine-base interruption in the consecutive purine base sequence drastically decreases the thermodynamic stability of the corresponding triplex, which hampers the TFO application. Here, we propose a design of the Ps-TFO for stable triplex formation with target DNA sequences containing pyrimidine-base interruptions under physiological conditions. This Ps-TFO, named 1'(one)-psoralen-conjugated triplex-forming oligonucleotide (OPTO), incorporates a synthesized nucleoside mimic 1'-psoralen-conjugated deoxyribose to increase the thermodynamic stability of the corresponding triplex by the intercalation of psoralen. The triplex-forming abilities of the OPTO were successfully demonstrated in combination with LNA and 5-methylcytosine, indicating that the use of OPTO will expand the range of the target sequences of TFO for photodynamic gene regulation.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"18"},"PeriodicalIF":5.9,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11754458/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143022495","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":"Engineering of acyl ligase domain in non-ribosomal peptide synthetases to change fatty acid moieties of lipopeptides.","authors":"Rina Aoki, Eri Kumagawa, Kazuaki Kamata, Hideo Ago, Naoki Sakai, Tomohisa Hasunuma, Naoaki Taoka, Yukari Ohta, Shingo Kobayashi","doi":"10.1038/s42004-024-01379-w","DOIUrl":"10.1038/s42004-024-01379-w","url":null,"abstract":"<p><p>Cyclic lipopeptides (CLPs) produced by the genus Bacillus are amphiphiles composed of hydrophilic amino acid and hydrophobic fatty acid moieties and are biosynthesised by non-ribosomal peptide synthetases (NRPSs). CLPs are produced as a mixture of homologues with different fatty acid moieties, whose length affects CLP activity. Iturin family lipopeptides are a family of CLPs comprising cyclic heptapeptides and β-amino fatty acids and have antimicrobial activity. There is little research on how the length of the fatty acid moiety of iturin family lipopeptides is determined. Here, we demonstrated that the acyl ligase (AL) domain determines the length of the fatty acid moiety in vivo. In addition, enzyme assays revealed how mutations in the substrate-binding pocket of the AL domain affected substrate specificity in vitro. Our findings have implications for the design of fatty acyl moieties for CLP synthesis using NRPS.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"17"},"PeriodicalIF":5.9,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11751314/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143001434","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}
Florian P Weissenboeck, Melissa Pieper, Helena Schepers, Sophie Hötte, Nils Klöcker, Sabine Hüwel, Andreas van Impel, Stefan Schulte-Merker, Andrea Rentmeister
{"title":"Spatiotemporal control of translation in live zebrafish embryos via photoprotected mRNAs.","authors":"Florian P Weissenboeck, Melissa Pieper, Helena Schepers, Sophie Hötte, Nils Klöcker, Sabine Hüwel, Andreas van Impel, Stefan Schulte-Merker, Andrea Rentmeister","doi":"10.1038/s42004-025-01411-7","DOIUrl":"10.1038/s42004-025-01411-7","url":null,"abstract":"<p><p>Translation of mRNA into protein is a fundamental process and tightly controlled during development. Several mechanisms acting on the mRNA level regulate when and where an mRNA is expressed. To explore the effects of conditional and transient gene expression in a developing organism, it is vital to experimentally enable abrogation and restoration of translation. We recently developed the FlashCaps technology allowing preparation of translationally muted mRNAs and their controlled activation by light. Here, we validate its functionality in vivo. We demonstrate that translation of FlashCap-eGFP-mRNA can be triggered in zebrafish embryos with spatiotemporal control. The injected FlashCap-mRNA is stable for hours and remains muted. Light-mediated activation up to 24 h post fertilization produces visible amounts of eGFP and can be restricted to distinct parts of the embryo. This methodology extends the toolbox for vertebrate models by enabling researchers to locally activate mRNA translation at different timepoints during development.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"16"},"PeriodicalIF":5.9,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743775/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143001435","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}
Tomaž Kotnik, Antoine Debuigne, Julien De Winter, Matej Huš, Albin Pintar, Sebastijan Kovačič
{"title":"Unlocking the potential of azide-phosphine Staudinger reaction for the synthesis of poly(arylene iminophosphorane)s and materials therefrom.","authors":"Tomaž Kotnik, Antoine Debuigne, Julien De Winter, Matej Huš, Albin Pintar, Sebastijan Kovačič","doi":"10.1038/s42004-024-01362-5","DOIUrl":"10.1038/s42004-024-01362-5","url":null,"abstract":"<p><p>Iminophosphoranes with the general formula (R<sub>3</sub>P═NR') have great potential in synthetic chemistry as valuable precursors/intermediates in organic synthesis or as building blocks for various organic compounds. However, the synthetic approaches and conditions to prepare iminophosphoranes are still poorly understood, limiting the utility of this chemistry for organic materials. In this article, a simple and efficient synthesis of previously unattainable poly(arylene iminophosphoranes) is reported. The azide-phosphine Staudinger polycondensation is used, and the reaction conditions are carefully studied, including consideration of light and air, the influence of solvent and temperature, and investigation of the electronic and steric effects of multiazides. The newly defined reaction conditions appear to be highly versatile, allowing the use of both electron-rich and electron-deficient arylazides for reaction with phosphines to synthesize a library of poly(arylene iminophosphorane) networks that exhibit exceptional thermal and oxidative stability. Interestingly, despite the ylidic-form of the iminophosphorane linkage as shown by theoretical calculations, these newly developed poly(arylene-iminophosphorane) networks exhibit semiconducting properties, such as absorption band edges up to 800 nm and optical band gaps in the range of 1.70 to 2.40 eV. Finally, we demonstrate the broad applicability of these polymers by processing them into glassy films, creating foam-like structures and synthesizing metallo-polymer hybrids.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"15"},"PeriodicalIF":5.9,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11739626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143001401","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":"Discovery of bicyclic borane molecule B<sub>14</sub>H<sub>26</sub>.","authors":"Xiaoni Zhang, Tomoko Fujino, Yasunobu Ando, Yuki Tsujikawa, Tianle Wang, Takeru Nakashima, Haruto Sakurai, Kazuki Yamaguchi, Masafumi Horio, Hatsumi Mori, Jun Yoshinobu, Takahiro Kondo, Iwao Matsuda","doi":"10.1038/s42004-025-01409-1","DOIUrl":"10.1038/s42004-025-01409-1","url":null,"abstract":"<p><p>The discovery of fullerene following the synthesis of graphene marked a paradigm shift in chemistry. Here, we report the discovery of biycycloborane, arising from the synthesis of borophane (hydrogen boride). Uniquely, this synthesis method involves a decomposition mechanism rather than traditional atom-by-atom assembly, marking an unique approach to constructing complex borane structures. The mass spectrometry unveiled that the stable molecule has a mass of 178 in atomic mass unit with a stoichiometry of B<sub>14</sub>H<sub>26</sub>. Optical spectra and simulations further evidenced its bicyclic structure, featuring fulvene-like heptagons or octagons. This borane molecule, analogous to cyclic hydrocarbons, adopts a unit configuration with a three-center two-electron (3c-2e) bonding, akin to diborane. The B<sub>14</sub>H<sub>26</sub> molecule has been historically anticipated as a distant descendant of the dodecahedron borane, but it was born from the hydrogen boride sheet with a non-symmorphic symmetry. The discovery of biycycloborane expands the frontiers of boron chemistry, promising advancements in boron-based nanomaterials and beyond.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"14"},"PeriodicalIF":5.9,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11739403/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143001430","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}
Manuel David Peris-Díaz, Artur Krężel, Perdita Barran
{"title":"Deciphering the safeguarding role of cysteine residues in p53 against H<sub>2</sub>O<sub>2</sub>-induced oxidation using high-resolution native mass spectrometry.","authors":"Manuel David Peris-Díaz, Artur Krężel, Perdita Barran","doi":"10.1038/s42004-024-01395-w","DOIUrl":"10.1038/s42004-024-01395-w","url":null,"abstract":"<p><p>The transcription factor p53 is exquisitely sensitive and selective to a broad variety of cellular environments. Several studies have reported that oxidative stress weakens the p53-DNA binding affinity for certain promoters depending on the oxidation mechanism. Despite this body of work, the precise mechanisms by which the physiologically relevant DNA-p53 tetramer complex senses cellular stresses caused by H<sub>2</sub>O<sub>2</sub> are still unknown. Here, we employed native mass spectrometry (MS) and ion mobility (IM)-MS coupled to chemical labelling and H<sub>2</sub>O<sub>2</sub>-induced oxidation to examine the mechanism of redox regulation of the p53-p21 complex. Our approach has found that two reactive cysteines in p53 protect against H<sub>2</sub>O<sub>2</sub>-induced oxidation by forming reversible sulfenates.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"13"},"PeriodicalIF":5.9,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11736120/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143001415","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}
Aini Vuorinen, Cassandra R Kennedy, Katherine A McPhie, William McCarthy, Jonathan Pettinger, J Mark Skehel, David House, Jacob T Bush, Katrin Rittinger
{"title":"Enantioselective OTUD7B fragment discovery through chemoproteomics screening and high-throughput optimisation.","authors":"Aini Vuorinen, Cassandra R Kennedy, Katherine A McPhie, William McCarthy, Jonathan Pettinger, J Mark Skehel, David House, Jacob T Bush, Katrin Rittinger","doi":"10.1038/s42004-025-01410-8","DOIUrl":"10.1038/s42004-025-01410-8","url":null,"abstract":"<p><p>Deubiquitinating enzymes (DUBs) are key regulators of cellular homoeostasis, and their dysregulation is associated with several human diseases. The ovarian tumour protease (OTU) family of DUBs are biochemically well-characterised and of therapeutic interest, yet only a few tool compounds exist to study their cellular function and therapeutic potential. Here we present a chemoproteomics fragment screening platform for identifying novel DUB-specific hit matter, that combines activity-based protein profiling with high-throughput chemistry direct-to-biology optimisation to enable rapid elaboration of initial fragment hits against OTU DUBs. Applying these approaches, we identify an enantioselective covalent fragment for OTUD7B, and validate it using chemoproteomics and biochemical DUB activity assays.</p>","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":"8 1","pages":"12"},"PeriodicalIF":5.9,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11732987/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982896","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}