Pub Date : 2024-09-02DOI: 10.1038/s42004-024-01282-4
Kuan-Ting Huang, Yimon Aye
Immune-cell reprogramming driven by mitochondria-derived reactive electrophilic immunometabolites (mt-REMs—e.g., fumarate, itaconate) is an emerging phenomenon of major biomedical importance. Despite their localized production, mt-REMs elicit significantly large local and global footprints within and across cells, through mechanisms involving electrophile signaling. Burgeoning efforts are being put into profiling mt-REMs’ potential protein-targets and phenotypic mapping of their multifaceted inflammatory behaviors. Yet, precision indexing of mt-REMs’ first-responders with spatiotemporal intelligence and locale-specific function assignments remain elusive. Highlighting the latest advances and overarching challenges, this perspective aims to stimulate thoughts and spur interdisciplinary innovations to address these unmet chemical-biotechnological needs at therapeutic immuno-signaling frontiers. Immune-cell reprogramming driven by mitochondria-derived reactive electrophilic immunometabolites (mt-REMs) is an emerging phenomenon of major biomedical importance. Here, the authors highlight the latest advances and overarching challenges in precision indexing of mt-REMs’ cellular responses with spatiotemporal intelligence and locale-specific function assignments.
{"title":"Toward decoding spatiotemporal signaling activities of reactive immunometabolites with precision immuno-chemical biology tools","authors":"Kuan-Ting Huang, Yimon Aye","doi":"10.1038/s42004-024-01282-4","DOIUrl":"10.1038/s42004-024-01282-4","url":null,"abstract":"Immune-cell reprogramming driven by mitochondria-derived reactive electrophilic immunometabolites (mt-REMs—e.g., fumarate, itaconate) is an emerging phenomenon of major biomedical importance. Despite their localized production, mt-REMs elicit significantly large local and global footprints within and across cells, through mechanisms involving electrophile signaling. Burgeoning efforts are being put into profiling mt-REMs’ potential protein-targets and phenotypic mapping of their multifaceted inflammatory behaviors. Yet, precision indexing of mt-REMs’ first-responders with spatiotemporal intelligence and locale-specific function assignments remain elusive. Highlighting the latest advances and overarching challenges, this perspective aims to stimulate thoughts and spur interdisciplinary innovations to address these unmet chemical-biotechnological needs at therapeutic immuno-signaling frontiers. Immune-cell reprogramming driven by mitochondria-derived reactive electrophilic immunometabolites (mt-REMs) is an emerging phenomenon of major biomedical importance. Here, the authors highlight the latest advances and overarching challenges in precision indexing of mt-REMs’ cellular responses with spatiotemporal intelligence and locale-specific function assignments.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":" ","pages":"1-16"},"PeriodicalIF":5.9,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01282-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142117971","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}
Pub Date : 2024-09-01DOI: 10.1038/s42004-024-01261-9
Ta Tang, Sulgiye Park, Thomas Peter Devereaux, Yu Lin, Chunjing Jia
Diamondoids are a class of organic molecules with the carbon skeletons isostructural to nano-diamond, and have been shown to be promising precursors for diamond formation. In this work, the formation of diamond crystals from various diamondoid molecule building blocks was studied using our developed molecular geometry specific Monte Carlo method. We maintained the internal carbon skeletons of the diamondoid molecules, and investigated how the carbon-carbon bonds form between diamondoid molecules and how efficient the process is to form diamond crystals. The simulations show that higher diamondoid molecules can produce structures closer to a diamond crystal compared with lower diamondoid molecules. Specifically, using higher diamondoid molecules, larger bulk diamond crystals are formed with fewer vacancies. The higher propensity of certain diamondoids to form diamond crystals reveals insights into the microscopic processes of diamond formation under high-pressure high-temperature conditions. Diamondoids are a series of hydrogen-terminated nanometer-sized hydrocarbons that can be used to synthesize high-quality diamond crystals. Here, the authors use Monte Carlo simulations to study the potentials of different diamondoids in constructing diamond crystals with the assumption that the carbon skeletons keep intact, and find that higher diamondoid molecules are most suitable.
{"title":"Molecular geometry specific Monte Carlo simulation of the efficacy of diamond crystal formation from diamondoids","authors":"Ta Tang, Sulgiye Park, Thomas Peter Devereaux, Yu Lin, Chunjing Jia","doi":"10.1038/s42004-024-01261-9","DOIUrl":"10.1038/s42004-024-01261-9","url":null,"abstract":"Diamondoids are a class of organic molecules with the carbon skeletons isostructural to nano-diamond, and have been shown to be promising precursors for diamond formation. In this work, the formation of diamond crystals from various diamondoid molecule building blocks was studied using our developed molecular geometry specific Monte Carlo method. We maintained the internal carbon skeletons of the diamondoid molecules, and investigated how the carbon-carbon bonds form between diamondoid molecules and how efficient the process is to form diamond crystals. The simulations show that higher diamondoid molecules can produce structures closer to a diamond crystal compared with lower diamondoid molecules. Specifically, using higher diamondoid molecules, larger bulk diamond crystals are formed with fewer vacancies. The higher propensity of certain diamondoids to form diamond crystals reveals insights into the microscopic processes of diamond formation under high-pressure high-temperature conditions. Diamondoids are a series of hydrogen-terminated nanometer-sized hydrocarbons that can be used to synthesize high-quality diamond crystals. Here, the authors use Monte Carlo simulations to study the potentials of different diamondoids in constructing diamond crystals with the assumption that the carbon skeletons keep intact, and find that higher diamondoid molecules are most suitable.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":" ","pages":"1-5"},"PeriodicalIF":5.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01261-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142100550","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}
Pub Date : 2024-08-31DOI: 10.1038/s42004-024-01253-9
Jacob D. Teeter, Mamun Sarker, Wenchang Lu, Chenggang Tao, Arthur P. Baddorf, Jingsong Huang, Kunlun Hong, Jerry Bernholc, Alexander Sinitskii, An-Ping Li
Graphene nanoribbons (GNRs) of precise size and shape, critical for controlling electronic properties and future device applications, can be realized via precision synthesis on surfaces using rationally designed molecular precursors. Fluorine-bearing precursors have the potential to form GNRs on nonmetallic substrates suitable for device fabrication. Here, we investigate the deposition temperature-mediated growth of a new fluorine-bearing precursor, 6,11-diiodo-1,4-bis(2-fluorophenyl)-2,3-diphenyltriphenylene (C42H24F2I2), into helically shaped polymer intermediates and chevron-type GNRs on Au(111) by combining scanning tunneling microscopy, X-ray photoelectron spectroscopy, and density functional theory simulations. The fluorinated precursors do not adsorb on the Au(111) surface at lower temperatures, necessitating an optimum substrate temperature to achieve maximum polymer and GNR lengths. We compare the adsorption behavior with that of pristine chevron precursors and discuss the effects of C-H and C-F bonds. The results elucidate the growth mechanism of GNRs with fluorine-bearing precursors and establish a foundation for future synthesis of GNRs on nonmetallic substrates. Fluorine-bearing precursors offer new opportunities for the on-surface synthesis of graphene nanoribbons, but the growth conditions are critical for achieving optimal results. Here, the authors investigate the deposition temperature-mediated growth of helically shaped polymers and graphene nanoribbons on Au(111) from an internally fluorinated precursor.
{"title":"Deposition temperature-mediated growth of helically shaped polymers and chevron-type graphene nanoribbons from a fluorinated precursor","authors":"Jacob D. Teeter, Mamun Sarker, Wenchang Lu, Chenggang Tao, Arthur P. Baddorf, Jingsong Huang, Kunlun Hong, Jerry Bernholc, Alexander Sinitskii, An-Ping Li","doi":"10.1038/s42004-024-01253-9","DOIUrl":"10.1038/s42004-024-01253-9","url":null,"abstract":"Graphene nanoribbons (GNRs) of precise size and shape, critical for controlling electronic properties and future device applications, can be realized via precision synthesis on surfaces using rationally designed molecular precursors. Fluorine-bearing precursors have the potential to form GNRs on nonmetallic substrates suitable for device fabrication. Here, we investigate the deposition temperature-mediated growth of a new fluorine-bearing precursor, 6,11-diiodo-1,4-bis(2-fluorophenyl)-2,3-diphenyltriphenylene (C42H24F2I2), into helically shaped polymer intermediates and chevron-type GNRs on Au(111) by combining scanning tunneling microscopy, X-ray photoelectron spectroscopy, and density functional theory simulations. The fluorinated precursors do not adsorb on the Au(111) surface at lower temperatures, necessitating an optimum substrate temperature to achieve maximum polymer and GNR lengths. We compare the adsorption behavior with that of pristine chevron precursors and discuss the effects of C-H and C-F bonds. The results elucidate the growth mechanism of GNRs with fluorine-bearing precursors and establish a foundation for future synthesis of GNRs on nonmetallic substrates. Fluorine-bearing precursors offer new opportunities for the on-surface synthesis of graphene nanoribbons, but the growth conditions are critical for achieving optimal results. Here, the authors investigate the deposition temperature-mediated growth of helically shaped polymers and graphene nanoribbons on Au(111) from an internally fluorinated precursor.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":" ","pages":"1-7"},"PeriodicalIF":5.9,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01253-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142100539","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}
Pub Date : 2024-08-30DOI: 10.1038/s42004-024-01281-5
Tomoyasu Noji, Keisuke Saito, Hiroshi Ishikita
Structural differences between illuminated and unilluminated crystal structures led to the proposal that the charge-separated state was stabilized by structural changes in its membrane extrinsic protein subunit H in a bacterial photosynthetic reaction center [Katona, G. et al. Nat. Struct. Mol. Biol. 2005, 12, 630–631]. Here, we explored the proposal by titrating all titratable sites and calculating the redox potential (Em) values in these crystal structures. Contrary to the expected charge-separated states, Em for quinone, Em(QA/QA•–), is even lower in the proposed charge-separated structure than in the ground-state structure. The subunit-H residues, which were proposed to exhibit electron-density changes in the two crystal structures, contribute to an Em(QA/QA•–) difference of only <0.5 mV. Furthermore, the protonation states of the titratable residues in the entire reaction center are practically identical in the two structures. These findings indicate that the proposed structural differences are irrelevant to explaining the significant prolongation of the charge-separated-state lifetime. In bacterial photosynthetic reactions, charge-separated states are thought to be stabilized by structural changes in the membrane extrinsic protein subunit H. Here, the authors probe all titratable sites and calculate values of cofactors, and find that the redox potential for quinone is lower in the proposed charge-separated than in the ground-state structure and that the subunit-H residues contribute to a redox potential difference below 0.5 mV.
发光晶体结构与非发光晶体结构之间的结构差异促使人们提出，电荷分离状态是通过细菌光合作用反应中心膜外蛋白亚基 H 的结构变化来稳定的[Katona, G. et al. Nat. Struct.］在这里，我们通过滴定所有可滴定位点并计算这些晶体结构中的氧化还原电位（Em）值来探索这一提议。与预期的电荷分离状态相反，在拟议的电荷分离结构中，醌的氧化还原电位（Em(QA/QA--)）甚至低于基态结构。亚单位-H残基被认为在两种晶体结构中显示出电子密度的变化，但其导致的Em（QA/QA--）差异仅为0.5 mV。此外，整个反应中心中可滴定残基的质子化状态在两种结构中几乎完全相同。这些发现表明，所提出的结构差异与解释电荷分离态寿命的显著延长无关。在细菌光合作用反应中，电荷分离态被认为是通过膜外蛋白亚基 H 的结构变化来稳定的。在这里，作者探测了所有可滴定位点并计算了辅助因子的值，结果发现，在拟议的电荷分离态结构中，醌的氧化还原电位低于基态结构，亚基 H 残基导致氧化还原电位差低于 0.5 mV。
{"title":"Absence of a link between stabilized charge-separated state and structural changes proposed from crystal structures of a photosynthetic reaction center","authors":"Tomoyasu Noji, Keisuke Saito, Hiroshi Ishikita","doi":"10.1038/s42004-024-01281-5","DOIUrl":"10.1038/s42004-024-01281-5","url":null,"abstract":"Structural differences between illuminated and unilluminated crystal structures led to the proposal that the charge-separated state was stabilized by structural changes in its membrane extrinsic protein subunit H in a bacterial photosynthetic reaction center [Katona, G. et al. Nat. Struct. Mol. Biol. 2005, 12, 630–631]. Here, we explored the proposal by titrating all titratable sites and calculating the redox potential (Em) values in these crystal structures. Contrary to the expected charge-separated states, Em for quinone, Em(QA/QA•–), is even lower in the proposed charge-separated structure than in the ground-state structure. The subunit-H residues, which were proposed to exhibit electron-density changes in the two crystal structures, contribute to an Em(QA/QA•–) difference of only <0.5 mV. Furthermore, the protonation states of the titratable residues in the entire reaction center are practically identical in the two structures. These findings indicate that the proposed structural differences are irrelevant to explaining the significant prolongation of the charge-separated-state lifetime. In bacterial photosynthetic reactions, charge-separated states are thought to be stabilized by structural changes in the membrane extrinsic protein subunit H. Here, the authors probe all titratable sites and calculate values of cofactors, and find that the redox potential for quinone is lower in the proposed charge-separated than in the ground-state structure and that the subunit-H residues contribute to a redox potential difference below 0.5 mV.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":" ","pages":"1-10"},"PeriodicalIF":5.9,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01281-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142100538","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}
Pub Date : 2024-08-30DOI: 10.1038/s42004-024-01268-2
Rubén López-Sánchez, Douglas V. Laurents, Miguel Mompeán
Hydrogen bond cooperativity (HBC) plays an important role in stabilizing protein assemblies built by α-helices and β-sheets, the most common secondary structures. However, whether HBC exists in other types of protein secondary structures such as polyproline II (PPII) helices remains unexplored. This is intriguing, since PPII systems as assembling blocks are continuously emerging across multiple fields. Here, using a combination of computational chemistry tools and molecular modeling corroborated by experimental observables, we characterize the distinct H-bonding patterns present in PPII helical bundles and establish that HBC stabilizes intermolecular PPII helices as seen in other protein assemblies such as amyloid fibrils. In addition to cooperative interactions in canonical CO···HN H-bonds, we show that analogous interactions in non-canonical CO···HαCα H-bonds are relevant in Gly-rich PPII bundles, thus compensating for the inability of glycine residues to create hydrophobic cores. Our results provide a mechanistic explanation for the assembly of these bundles. Hydrogen bond cooperativity (HBC) plays an important role in the stability of protein assemblies built by α-helices and β-sheets, however, it remains unknown whether HBC also exists in polyproline II (PPII) helices. Here, the authors show that HBC stabilizes intermolecular PPII helices using computational chemistry tools and molecular modeling corroborated by experimental observations.
氢键合作性（HBC）在稳定由α螺旋和β片层（最常见的二级结构）构建的蛋白质组装方面发挥着重要作用。然而，HBC 是否存在于其他类型的蛋白质二级结构（如多脯氨酸 II（PPII）螺旋）中仍有待探索。这一点很耐人寻味，因为作为组装模块的 PPII 系统正在多个领域不断涌现。在这里，我们结合使用计算化学工具和分子建模，并辅以实验观察结果，描述了 PPII 螺旋束中存在的独特 H 键模式，并确定 HBC 可稳定分子间 PPII 螺旋，正如在淀粉样纤维等其他蛋白质组装体中看到的那样。除了规范的 CO-HN H 键中的合作性相互作用外，我们还发现非规范的 CO-HαCα H 键中的类似相互作用也与富含甘氨酸的 PPII 束有关，从而弥补了甘氨酸残基无法形成疏水核心的缺陷。我们的研究结果为这些束的组装提供了一种机理解释。氢键合作性（HBC）在由α螺旋和β片所构建的蛋白质组装的稳定性中起着重要作用，然而，HBC是否也存在于多脯氨酸II（PPII）螺旋中仍是未知数。在本文中，作者利用计算化学工具和分子建模证明了 HBC 能稳定分子间的 PPII 螺旋，并得到了实验观察的证实。
{"title":"Hydrogen bonding patterns and cooperativity in polyproline II helical bundles","authors":"Rubén López-Sánchez, Douglas V. Laurents, Miguel Mompeán","doi":"10.1038/s42004-024-01268-2","DOIUrl":"10.1038/s42004-024-01268-2","url":null,"abstract":"Hydrogen bond cooperativity (HBC) plays an important role in stabilizing protein assemblies built by α-helices and β-sheets, the most common secondary structures. However, whether HBC exists in other types of protein secondary structures such as polyproline II (PPII) helices remains unexplored. This is intriguing, since PPII systems as assembling blocks are continuously emerging across multiple fields. Here, using a combination of computational chemistry tools and molecular modeling corroborated by experimental observables, we characterize the distinct H-bonding patterns present in PPII helical bundles and establish that HBC stabilizes intermolecular PPII helices as seen in other protein assemblies such as amyloid fibrils. In addition to cooperative interactions in canonical CO···HN H-bonds, we show that analogous interactions in non-canonical CO···HαCα H-bonds are relevant in Gly-rich PPII bundles, thus compensating for the inability of glycine residues to create hydrophobic cores. Our results provide a mechanistic explanation for the assembly of these bundles. Hydrogen bond cooperativity (HBC) plays an important role in the stability of protein assemblies built by α-helices and β-sheets, however, it remains unknown whether HBC also exists in polyproline II (PPII) helices. Here, the authors show that HBC stabilizes intermolecular PPII helices using computational chemistry tools and molecular modeling corroborated by experimental observations.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":" ","pages":"1-11"},"PeriodicalIF":5.9,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01268-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142100549","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}
Pub Date : 2024-08-28DOI: 10.1038/s42004-024-01275-3
Manasa Yerragunta, Akash Tiwari, Rajshree Chakrabarti, Jeffrey D. Rimer, Bart Kahr, Peter G. Vekilov
Organic solvents host the synthesis of high-value crystals used as pharmaceuticals and optical devices, among other applications. A knowledge gap persists on how replacing the hydrogen bonds and polar attraction that dominate aqueous environments with the weaker van der Waals forces affects the growth mechanism, including its defining feature, whether crystals grow classically or nonclassically. Here we demonstrate a rare dual growth mode of etioporphyrin I crystals, enabled by liquid precursors that associate with crystal surfaces to generate stacks of layers, which then grow laterally by incorporating solute molecules. Our findings reveal the precursors as mesoscopic solute-rich clusters, a unique phase favored by weak bonds such as those between organic solutes. The lateral spreading of the precursor-initiated stacks of layers crucially relies on abundant solute supply directly from the solution, bypassing diffusion along the crystal surface; the direct incorporation pathway may, again, be unique to organic solvents. Clusters that evolve to amorphous particles do not seamlessly integrate into crystal lattices. Crystals growing fast and mostly nonclassically at high supersaturations are not excessively strained. Our findings demonstrate that the weak interactions typical of organic systems promote nonclassical growth modes by supporting liquid precursors and enabling the spreading of multilayer stacks. Organic solvents are used to produce high-value crystals such as pharmaceuticals, organic semiconductors, and optical devices, but our understanding of the fundamental processes of crystal growth from organic solutions is limited. Here, the authors use time-resolved in situ atomic force microscopy to show a nonclassical, dual growth mode of etioporphyrin I crystals from mesoscopic solute-rich clusters.
有机溶剂是合成用于制药和光学设备等用途的高价值晶体的主要载体。在用较弱的范德华力取代水环境中占主导地位的氢键和极性吸引力如何影响晶体生长机制（包括其决定性特征，即晶体是经典生长还是非经典生长）方面，仍然存在知识空白。在这里，我们展示了依托卟啉 I 晶体罕见的双重生长模式，即液态前驱体与晶体表面结合生成层叠，然后通过结合溶质分子横向生长。我们的研究结果表明，前驱体是介观的富溶质团簇，这是一种受有机溶质之间的弱键等因素影响的独特阶段。前驱体引发的层状堆叠的横向扩散主要依赖于直接从溶液中提供的大量溶质，绕过了沿晶体表面的扩散；这种直接结合途径可能也是有机溶剂所独有的。演变为非晶粒子的晶簇不会无缝地融入晶格。在高过饱和度条件下快速生长的晶体，大多是非经典晶体，不会产生过度应变。我们的研究结果表明，有机体系中典型的弱相互作用通过支持液态前驱体和促成多层堆叠的扩散，促进了非经典生长模式。
{"title":"A dual growth mode unique for organic crystals relies on mesoscopic liquid precursors","authors":"Manasa Yerragunta, Akash Tiwari, Rajshree Chakrabarti, Jeffrey D. Rimer, Bart Kahr, Peter G. Vekilov","doi":"10.1038/s42004-024-01275-3","DOIUrl":"10.1038/s42004-024-01275-3","url":null,"abstract":"Organic solvents host the synthesis of high-value crystals used as pharmaceuticals and optical devices, among other applications. A knowledge gap persists on how replacing the hydrogen bonds and polar attraction that dominate aqueous environments with the weaker van der Waals forces affects the growth mechanism, including its defining feature, whether crystals grow classically or nonclassically. Here we demonstrate a rare dual growth mode of etioporphyrin I crystals, enabled by liquid precursors that associate with crystal surfaces to generate stacks of layers, which then grow laterally by incorporating solute molecules. Our findings reveal the precursors as mesoscopic solute-rich clusters, a unique phase favored by weak bonds such as those between organic solutes. The lateral spreading of the precursor-initiated stacks of layers crucially relies on abundant solute supply directly from the solution, bypassing diffusion along the crystal surface; the direct incorporation pathway may, again, be unique to organic solvents. Clusters that evolve to amorphous particles do not seamlessly integrate into crystal lattices. Crystals growing fast and mostly nonclassically at high supersaturations are not excessively strained. Our findings demonstrate that the weak interactions typical of organic systems promote nonclassical growth modes by supporting liquid precursors and enabling the spreading of multilayer stacks. Organic solvents are used to produce high-value crystals such as pharmaceuticals, organic semiconductors, and optical devices, but our understanding of the fundamental processes of crystal growth from organic solutions is limited. Here, the authors use time-resolved in situ atomic force microscopy to show a nonclassical, dual growth mode of etioporphyrin I crystals from mesoscopic solute-rich clusters.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":" ","pages":"1-12"},"PeriodicalIF":5.9,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01275-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142092495","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}
Pub Date : 2024-08-27DOI: 10.1038/s42004-024-01278-0
Masaki Akaogi, Takayuki Ishii, Kazunari Yamaura
Post-spinel-type AB2O4 compounds are stable at higher pressures than spinel phases. These compounds have garnered much interest in geo- and materials science for their geochemical importance as well as potential application as high ionic conductors and materials with strongly correlated electrons. Here, large-volume high-pressure syntheses, structural features and properties of post-spinels are reviewed. Prospects are discussed for future searches for post-spinel-type phases by applying advanced large-volume high-pressure technology. Post-spinel transition-metal oxides have emerged as potential candidates for high ionic conductors and materials with strongly correlated electrons. In this Review, the authors discuss recent developments in large-volume high-pressure technology, crystal structural features of post-spinel phases and their geochemical significance, and weigh the challenges and opportunities post-spinel phases entail for material applications.
{"title":"Post-spinel-type AB2O4 high-pressure phases in geochemistry and materials science","authors":"Masaki Akaogi, Takayuki Ishii, Kazunari Yamaura","doi":"10.1038/s42004-024-01278-0","DOIUrl":"10.1038/s42004-024-01278-0","url":null,"abstract":"Post-spinel-type AB2O4 compounds are stable at higher pressures than spinel phases. These compounds have garnered much interest in geo- and materials science for their geochemical importance as well as potential application as high ionic conductors and materials with strongly correlated electrons. Here, large-volume high-pressure syntheses, structural features and properties of post-spinels are reviewed. Prospects are discussed for future searches for post-spinel-type phases by applying advanced large-volume high-pressure technology. Post-spinel transition-metal oxides have emerged as potential candidates for high ionic conductors and materials with strongly correlated electrons. In this Review, the authors discuss recent developments in large-volume high-pressure technology, crystal structural features of post-spinel phases and their geochemical significance, and weigh the challenges and opportunities post-spinel phases entail for material applications.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":" ","pages":"1-12"},"PeriodicalIF":5.9,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11349911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142079518","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}
Pub Date : 2024-08-27DOI: 10.1038/s42004-024-01276-2
Anushree Dutta, Milan Ončák, Farhad Izadi, Eugene Arthur-Baidoo, João Ameixa, Stephan Denifl, Ilko Bald
Plasmon-driven chemical conversion is gaining burgeoning interest in the field of heterogeneous catalysis. Herein, we study the reactivity of N-methyl-4-sulfanylbenzamide (NMSB) at nanocavities of gold and silver nanoparticle aggregates under plasmonic excitation to gain understanding of the respective reaction mechanism. NMSB is a secondary amide, which is a frequent binding motive found in peptides and a common coupling product of organic molecules and biomolecules. Surface-enhanced Raman scattering (SERS) is used as a two-in-one in-situ spectroscopic tool to initiate the molecular transformation process and simultaneously monitor and analyze the reaction products. Supported by dissociative electron attachment (DEA) studies with the gas phase molecule, a hot electron-mediated conversion of NMSB to p-mercaptobenzamide and p-mercaptobenzonitrile is proposed at the plasmonic nanocavities. The reaction rate showed negligible dependence on the external temperature, ruling out the dominant role of heat in the chemical transformation at the plasmonic interface. This is reflected in the absence of a superlinear relationship between the reaction rate constant and the laser power density, and DEA and SERS studies indicate a hot-electron mediated pathway. We conclude that the overall reaction rate is limited by the availability of energetic hot electrons to the NMSB molecule. Photocatalysis driven by surface plasmons is a promising approach for light-driven chemical conversions of molecules under mild conditions. Here, the authors study the reactivity of N-methyl-4-sulfanylbenzamide (NMSB) at the nanocavities of gold and silver nanoparticle aggregates under plasmonic excitation and propose a hot electron-mediated conversion of NMSB to p-mercaptobenzamide and p-mercaptobenzonitrile.
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Pub Date : 2024-08-24DOI: 10.1038/s42004-024-01269-1
Lynn Buyachuihan, Simon Reiners, Yue Zhao, Martin Grininger
Modular polyketide synthases (PKSs) play a vital role in the biosynthesis of complex natural products with pharmaceutically relevant properties. Their modular architecture makes them an attractive target for engineering to produce platform chemicals and drugs. In this study, we demonstrate that the promiscuous malonyl/acetyl-transferase domain (MAT) from murine fatty acid synthase serves as a highly versatile tool for the production of polyketide analogs. We evaluate the relevance of the MAT domain using three modular PKSs; the short trimodular venemycin synthase (VEMS), as well as modules of the PKSs deoxyerythronolide B synthase (DEBS) and pikromycin synthase (PIKS) responsible for the production of the antibiotic precursors erythromycin and pikromycin. To assess the performance of the MAT-swapped PKSs, we analyze the protein quality and run engineered polyketide syntheses in vitro. Our experiments include the chemoenzymatic synthesis of fluorinated macrolactones. Our study showcases MAT-based reprogramming of polyketide biosynthesis as a facile option for the regioselective editing of substituents decorating the polyketide scaffold. Modular polyketide synthases (PKSs) play a vital role in the biosynthesis of complex natural products with pharmaceutically relevant properties, and their modular architecture makes them an attractive target for engineering to produce platform chemicals and drugs. In this study, the authors demonstrate that the promiscuous malonyl/acetyl-transferase domain (MAT) from murine fatty acid synthase serves as a highly versatile tool for the production of polyketide analogs.
模块化多酮合成酶（PKSs）在具有医药相关特性的复杂天然产物的生物合成过程中发挥着至关重要的作用。它们的模块化结构使其成为生产平台化学品和药物的有吸引力的工程目标。在本研究中，我们证明小鼠脂肪酸合成酶中的杂合丙二酰/乙酰转移酶结构域（MAT）是生产多酮类似物的多功能工具。我们利用三个模块化 PKS 评估了 MAT 结构域的相关性；短的三模块化文尼霉素合成酶（VEMS），以及负责生产抗生素前体红霉素和匹红霉素的 PKS 模块脱氧红霉素内酯 B 合成酶（DEBS）和匹红霉素合成酶（PIKS）。为了评估 MAT 交换 PKS 的性能，我们分析了蛋白质质量，并在体外进行了工程多酮合成。我们的实验包括氟化大内酯的化学合成。我们的研究展示了基于 MAT 的多酮苷生物合成重编程是对装饰多酮苷支架的取代基进行区域选择性编辑的一种简便选择。
{"title":"The malonyl/acetyl-transferase from murine fatty acid synthase is a promiscuous engineering tool for editing polyketide scaffolds","authors":"Lynn Buyachuihan, Simon Reiners, Yue Zhao, Martin Grininger","doi":"10.1038/s42004-024-01269-1","DOIUrl":"10.1038/s42004-024-01269-1","url":null,"abstract":"Modular polyketide synthases (PKSs) play a vital role in the biosynthesis of complex natural products with pharmaceutically relevant properties. Their modular architecture makes them an attractive target for engineering to produce platform chemicals and drugs. In this study, we demonstrate that the promiscuous malonyl/acetyl-transferase domain (MAT) from murine fatty acid synthase serves as a highly versatile tool for the production of polyketide analogs. We evaluate the relevance of the MAT domain using three modular PKSs; the short trimodular venemycin synthase (VEMS), as well as modules of the PKSs deoxyerythronolide B synthase (DEBS) and pikromycin synthase (PIKS) responsible for the production of the antibiotic precursors erythromycin and pikromycin. To assess the performance of the MAT-swapped PKSs, we analyze the protein quality and run engineered polyketide syntheses in vitro. Our experiments include the chemoenzymatic synthesis of fluorinated macrolactones. Our study showcases MAT-based reprogramming of polyketide biosynthesis as a facile option for the regioselective editing of substituents decorating the polyketide scaffold. Modular polyketide synthases (PKSs) play a vital role in the biosynthesis of complex natural products with pharmaceutically relevant properties, and their modular architecture makes them an attractive target for engineering to produce platform chemicals and drugs. In this study, the authors demonstrate that the promiscuous malonyl/acetyl-transferase domain (MAT) from murine fatty acid synthase serves as a highly versatile tool for the production of polyketide analogs.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":" ","pages":"1-15"},"PeriodicalIF":5.9,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01269-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142055159","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}
Ionic polymers are intriguing materials whose functionality arises from the synergy between ionic polymer backbones and counterions. A key method for enhancing their functionality is the post-synthetic ion-exchange reaction, which is instrumental in improving the chemical and physical properties of polymer backbones and introducing of the functionalities of the counterions. Electronic interaction between host polymer backbone and guest ions plays pivotal roles in property modulation. The current study highlights the modulation of responses to external electric field in cationic bis(terpyridine)cobalt(II) polymer nanofilms through anion-exchange reactions. Initially, as-prepared chloride-containing polymers exhibited supercapacitor behaviour. Introducing anionic metalladithiolenes into the polymers altered the behaviour to either conductive or insulative, depending on the valence of the metalladithiolenes. This modulation was accomplished by fine tuning of charge-transfer interactions between the bis(terpyridine)cobalt(II) complex moieties and redox-active anions. Our findings open up new avenue for ionic polymers, showcasing their potential as versatile platform in materials science. Post-synthetic ion-exchange is a key method for tuning the chemical and physical properties of ionic polymers, but achieving control over functionality through ion-exchange remains challenging. Here, anion-exchange within a redox-active bis(terpyridine)cobalt(II) polymer enables modulation between capacitor and conductor behaviours in response to an external electric field.
{"title":"Modulation between capacitor and conductor for a redox-active 2D bis(terpyridine)cobalt(II) nanosheet via anion-exchange","authors":"Kenji Takada, Miyu Ito, Naoya Fukui, Hiroshi Nishihara","doi":"10.1038/s42004-024-01274-4","DOIUrl":"10.1038/s42004-024-01274-4","url":null,"abstract":"Ionic polymers are intriguing materials whose functionality arises from the synergy between ionic polymer backbones and counterions. A key method for enhancing their functionality is the post-synthetic ion-exchange reaction, which is instrumental in improving the chemical and physical properties of polymer backbones and introducing of the functionalities of the counterions. Electronic interaction between host polymer backbone and guest ions plays pivotal roles in property modulation. The current study highlights the modulation of responses to external electric field in cationic bis(terpyridine)cobalt(II) polymer nanofilms through anion-exchange reactions. Initially, as-prepared chloride-containing polymers exhibited supercapacitor behaviour. Introducing anionic metalladithiolenes into the polymers altered the behaviour to either conductive or insulative, depending on the valence of the metalladithiolenes. This modulation was accomplished by fine tuning of charge-transfer interactions between the bis(terpyridine)cobalt(II) complex moieties and redox-active anions. Our findings open up new avenue for ionic polymers, showcasing their potential as versatile platform in materials science. Post-synthetic ion-exchange is a key method for tuning the chemical and physical properties of ionic polymers, but achieving control over functionality through ion-exchange remains challenging. Here, anion-exchange within a redox-active bis(terpyridine)cobalt(II) polymer enables modulation between capacitor and conductor behaviours in response to an external electric field.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":" ","pages":"1-8"},"PeriodicalIF":5.9,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01274-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142035384","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}
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