Saideep Singh, Joaquín Martínez-Ortigosa, Nuria Ortuño, Vivek Polshettiwar, Javier Garcia-Martinez
By modulating zeolite confinement and improving pore diffusion properties, addressing a significant limitation in current plastic waste upcycling methodologies is essential. In this work, we have developed mesoporous zeolites that exhibit enhanced diffusion capabilities for long-chain polymers without compromising the crystalline structure. The mesopore volume doubled from 0.14 cm3/g (CBV720) to 0.28 cm3/g (M7203h) after zeolite modification. This has enabled to overcome the inefficiencies associated with polymer diffusion in conventional zeolites, significantly advancing the catalytic conversion of plastic waste into valuable products. Catalytic pyrolysis experiments on various polyethylenes underline the superior performance of mesoporous zeolites, especially for highly branched polymer structures where degradation temperatures are reduced by 29.5 °C compared to conventional zeolite, highlighting the importance of pore arrangement. Detailed analysis using NH3-TPD and in-situ DRIFT spectroscopy reveals the crucial role of Brønsted acid sites in enhancing degradation efficiency. The optimized mesoporous zeolite catalyst, M720cit, showed excellent effectiveness in reducing degradation temperatures for a wide array of daily-use plastic waste. The T10 values were significantly reduced for various plastic wastes: food packaging dropped to 193°C (from 341°C), plastic bottles to 319°C (from 373°C), and milk packets to 253°C (from 388°C), among others. Moreover, the well-retained microstructure of the M720 catalyst yielded a very similar product distribution despite the introduction of mesoporosity. This study not only surmounts crucial obstacles in the modulation of zeolite confinement and the enhancement of pore diffusion properties but also augments the economic and environmental sustainability of plastic waste conversion processes.
{"title":"Enhanced Efficiency in Plastic Waste Upcycling: The Role of Mesoporosity and Acidity in Zeolites","authors":"Saideep Singh, Joaquín Martínez-Ortigosa, Nuria Ortuño, Vivek Polshettiwar, Javier Garcia-Martinez","doi":"10.1039/d4sc05121a","DOIUrl":"https://doi.org/10.1039/d4sc05121a","url":null,"abstract":"By modulating zeolite confinement and improving pore diffusion properties, addressing a significant limitation in current plastic waste upcycling methodologies is essential. In this work, we have developed mesoporous zeolites that exhibit enhanced diffusion capabilities for long-chain polymers without compromising the crystalline structure. The mesopore volume doubled from 0.14 cm3/g (CBV720) to 0.28 cm3/g (M7203h) after zeolite modification. This has enabled to overcome the inefficiencies associated with polymer diffusion in conventional zeolites, significantly advancing the catalytic conversion of plastic waste into valuable products. Catalytic pyrolysis experiments on various polyethylenes underline the superior performance of mesoporous zeolites, especially for highly branched polymer structures where degradation temperatures are reduced by 29.5 °C compared to conventional zeolite, highlighting the importance of pore arrangement. Detailed analysis using NH3-TPD and in-situ DRIFT spectroscopy reveals the crucial role of Brønsted acid sites in enhancing degradation efficiency. The optimized mesoporous zeolite catalyst, M720cit, showed excellent effectiveness in reducing degradation temperatures for a wide array of daily-use plastic waste. The T10 values were significantly reduced for various plastic wastes: food packaging dropped to 193°C (from 341°C), plastic bottles to 319°C (from 373°C), and milk packets to 253°C (from 388°C), among others. Moreover, the well-retained microstructure of the M720 catalyst yielded a very similar product distribution despite the introduction of mesoporosity. This study not only surmounts crucial obstacles in the modulation of zeolite confinement and the enhancement of pore diffusion properties but also augments the economic and environmental sustainability of plastic waste conversion processes.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142555711","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}
Jingjing Yu, Marius Gaedke, Satyajit Das, Daniel L. Stares, Christoph A Schalley, Fredrik Schaufelberger
We report on the synthesis of [2]rotaxanes from vicinal diols through dynamic covalent boronic ester templates, as well as the use of the boronic ester for rotaxane post-functionalisation. A boronic acid pincer ligand with two alkene-appended arms was condensed with a linear diol-containing thread, and ring-closing metathesis established a pre-rotaxane architecture along with a non-entangled isomer. Advanced NMR spectroscopy and mass spectrometry unambiguously assigned the isomers and revealed that the pre-rotaxane was in equilibrium with its hydrolyzed free [2]rotaxane form. The boronic ester handle in the pre-rotaxane could be synthetically addressed in a multitude of ways to obtain different endo-functionalised [2]rotaxanes, including with direct oxidation reactions, protodeboronation, functional group interconversions and Pd-catalysed cross-couplings.
{"title":"Boronic Ester-Templated Pre-Rotaxanes as Versatile Intermediates for Rotaxane Endo-functionalisation","authors":"Jingjing Yu, Marius Gaedke, Satyajit Das, Daniel L. Stares, Christoph A Schalley, Fredrik Schaufelberger","doi":"10.1039/d4sc04879b","DOIUrl":"https://doi.org/10.1039/d4sc04879b","url":null,"abstract":"We report on the synthesis of [2]rotaxanes from vicinal diols through dynamic covalent boronic ester templates, as well as the use of the boronic ester for rotaxane post-functionalisation. A boronic acid pincer ligand with two alkene-appended arms was condensed with a linear diol-containing thread, and ring-closing metathesis established a pre-rotaxane architecture along with a non-entangled isomer. Advanced NMR spectroscopy and mass spectrometry unambiguously assigned the isomers and revealed that the pre-rotaxane was in equilibrium with its hydrolyzed free [2]rotaxane form. The boronic ester handle in the pre-rotaxane could be synthetically addressed in a multitude of ways to obtain different endo-functionalised [2]rotaxanes, including with direct oxidation reactions, protodeboronation, functional group interconversions and Pd-catalysed cross-couplings.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142556044","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}
Thomas Specht, Mayank Nagda, Sophie Fellenz, Stephan Mandt, Hans Hasse, Fabian Jirasek
We present the first hard-constraint neural network model for predicting activity coefficients (HANNA), a thermodynamic mixture property that is the basis for many applications in science and engineering. Unlike traditional neural networks, which ignore physical laws and result in inconsistent predictions, our model is designed to strictly adhere to all thermodynamic consistency criteria. By leveraging deep-set neural networks, HANNA maintains symmetry under the permutation of the components. Furthermore, by hard-coding physical constraints in the model architecture, we ensure consistency with the Gibbs-Duhem equation and in modeling the pure components. The model was trained and evaluated on 317,421 data points for activity coefficients in binary mixtures from the Dortmund Data Bank, achieving significantly higher prediction accuracies than the current state-of-the-art model UNIFAC. Moreover, HANNA only requires the SMILES of the components as input, making it applicable to any binary mixture of interest. HANNA is fully open-source and available for free use.
{"title":"HANNA: Hard-constraint Neural Network for Consistent Activity Coefficient Prediction","authors":"Thomas Specht, Mayank Nagda, Sophie Fellenz, Stephan Mandt, Hans Hasse, Fabian Jirasek","doi":"10.1039/d4sc05115g","DOIUrl":"https://doi.org/10.1039/d4sc05115g","url":null,"abstract":"We present the first hard-constraint neural network model for predicting activity coefficients (HANNA), a thermodynamic mixture property that is the basis for many applications in science and engineering. Unlike traditional neural networks, which ignore physical laws and result in inconsistent predictions, our model is designed to strictly adhere to all thermodynamic consistency criteria. By leveraging deep-set neural networks, HANNA maintains symmetry under the permutation of the components. Furthermore, by hard-coding physical constraints in the model architecture, we ensure consistency with the Gibbs-Duhem equation and in modeling the pure components. The model was trained and evaluated on 317,421 data points for activity coefficients in binary mixtures from the Dortmund Data Bank, achieving significantly higher prediction accuracies than the current state-of-the-art model UNIFAC. Moreover, HANNA only requires the SMILES of the components as input, making it applicable to any binary mixture of interest. HANNA is fully open-source and available for free use.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142556045","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}
Explosives as high-energy materials could generate huge destructive explosions along with massive releases of energy. The regulatory or illegal transportation of explosives threatens the peace and stability worldwide. Among the many high-powered explosives, 2,4,6-trinitrophenol (TNP) is not only frequently used in many terrorist attacks, but also seriously jeopardizes environmental safety and human health. Hence, dependable methods for high-sensitivity, rapid and portable detection are desperately needed. Inspired by olfactory sensory neurons (OSNs) in sniffer dogs, we present a nanofluidic sensor for ultrasensitive TNP detection by in situ growing dense UiO-66-NH2 layers on the surface of anodic aluminum oxide (AAO) nanochannels. TNP could be specifically captured by UiO-66-NH2 of the sensor through charge transfer to form Meisenheimer complexes, which cause the ionic current change. The TNP concentrations are quantitatively analyzed by monitoring the changed ionic current. And the detection range is from 10−14 to 10−10 g/mL with limit of detection as low as 6.5 × 10−16 g/mL, which is far beyond the state-of-the-art sensors. This work provides a novel strategy for ultrasensitive TNP detection as well as other explosives, which opens new and promising routes to various breakthroughs in the fields of homeland security, military applications, security inspections and environmental monitoring.
{"title":"Ultrasensitive 2,4,6-trinitrophenol nanofluidic sensor inspired by olfactory sensory neurons in sniffer dogs","authors":"Xin Li, Zhanfang Liu, Linsen Yang, Shengyang Zhou, Yongchao Qian, Yuge Wu, Zidi Yan, Zhehua Zhang, Tingyang Li, Qingchen Wang, Congcong Zhu, Xiang-Yu Kong, Liping Wen","doi":"10.1039/d4sc05493h","DOIUrl":"https://doi.org/10.1039/d4sc05493h","url":null,"abstract":"Explosives as high-energy materials could generate huge destructive explosions along with massive releases of energy. The regulatory or illegal transportation of explosives threatens the peace and stability worldwide. Among the many high-powered explosives, 2,4,6-trinitrophenol (TNP) is not only frequently used in many terrorist attacks, but also seriously jeopardizes environmental safety and human health. Hence, dependable methods for high-sensitivity, rapid and portable detection are desperately needed. Inspired by olfactory sensory neurons (OSNs) in sniffer dogs, we present a nanofluidic sensor for ultrasensitive TNP detection by in situ growing dense UiO-66-NH<small><sub>2</sub></small> layers on the surface of anodic aluminum oxide (AAO) nanochannels. TNP could be specifically captured by UiO-66-NH<small><sub>2</sub></small> of the sensor through charge transfer to form Meisenheimer complexes, which cause the ionic current change. The TNP concentrations are quantitatively analyzed by monitoring the changed ionic current. And the detection range is from 10<small><sup>−14</sup></small> to 10<small><sup>−10</sup></small> g/mL with limit of detection as low as 6.5 × 10<small><sup>−16</sup></small> g/mL, which is far beyond the state-of-the-art sensors. This work provides a novel strategy for ultrasensitive TNP detection as well as other explosives, which opens new and promising routes to various breakthroughs in the fields of homeland security, military applications, security inspections and environmental monitoring.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142556365","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}
Merging the advantages of biocatalysis and chemocatalysis in retrosynthetic analysis can significantly improve the efficiency and selectivity of natural product synthesis. Here, we describe a unified approach for the synthesis of drimane meroterpenoids by combining heterologous biosynthesis, enzymatic hydroxylation, and transition metal catalysis. In phase one, drimenol was produced by engineering a biosynthetic pathway in Escherichia coli. Cytochrome P450BM3 from Bacillus megaterium was engineered to catalyze the C-3 hydroxylation of drimenol. By means of nickel-catalyzed reductive coupling, six drimane meroterpenoids (+)-hongoquercins A and B, (+)-ent-chromazonarol, 8-epi-puupehenol, (−)-pelorol, and (−)-mycoleptodiscin A were synthesized in a concise and enantiospecific manner. This strategy offers facile access to the congeners of the drimane meroterpenoid family and lays the foundation for activity optimization.
{"title":"Unified Enantiospecific Synthesis of Drimane Meroterpenoids Enabled by Enzyme Catalysis and Transition Metal Catalysis","authors":"You Yipeng, Xue-Jie Zhang, Wen Xiao, Thittaya Kunthic, Zheng Xiang, Chen Xu","doi":"10.1039/d4sc06060a","DOIUrl":"https://doi.org/10.1039/d4sc06060a","url":null,"abstract":"Merging the advantages of biocatalysis and chemocatalysis in retrosynthetic analysis can significantly improve the efficiency and selectivity of natural product synthesis. Here, we describe a unified approach for the synthesis of drimane meroterpenoids by combining heterologous biosynthesis, enzymatic hydroxylation, and transition metal catalysis. In phase one, drimenol was produced by engineering a biosynthetic pathway in Escherichia coli. Cytochrome P450BM3 from Bacillus megaterium was engineered to catalyze the C-3 hydroxylation of drimenol. By means of nickel-catalyzed reductive coupling, six drimane meroterpenoids (+)-hongoquercins A and B, (+)-ent-chromazonarol, 8-epi-puupehenol, (−)-pelorol, and (−)-mycoleptodiscin A were synthesized in a concise and enantiospecific manner. This strategy offers facile access to the congeners of the drimane meroterpenoid family and lays the foundation for activity optimization.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142555710","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}
Kang Liu, Haikuo Lan, Yuting Chen, Weicheng Tang, Zhenyu Xiao, Yunmei Du, Jun Xing, Zexing Wu, Lei Wang
Metal-organic gels (MOGs) are emerging soft materials with distinct metal active centers, multifunctional ligands and hierarchical porous structures, showing promising potential in the field of electrocatalysis. However, the reconfiguration of MOGs during the electrocatalytic process remains underexplored, with current studies in early developmental stages. To deeply investigate the application of MOG materials in electrocatalysis, the compositional transformations and structural changes under an electrochemical activation method were studied in detail, which leading to high-performance OER pre-electrocatalysts. XRD and HRTEM results demonstrate the complete reconfiguration of amorphous Fe5Ni5-MOG into crystalline NiOOH/FeOOH heterostructures. The synergistic effect of the bimetallic center and the rich NiOOH-FeOOH interface in the reconstituted Re-Fe5Ni5-MOG exhibit excellent OER activity in alkaline electrolytes, with low overpotentials (205 mV at 10 mA cm-2) and a Tafel slope of 58 mV dec-1. In-situ characterization during the electrocatalytic process reveals the gradual transformation of the metal center into metal hydroxyl oxides upon increasing voltage to 1.55 V. DFT analysis suggests that in the Fe-Ni double sites reaction pathway, active substances preferentially adsorb on the Fe site before the Ni sites.
金属有机凝胶（MOGs）是一种新兴的软材料，具有独特的金属活性中心、多功能配体和分层多孔结构，在电催化领域具有广阔的应用前景。然而，MOGs 在电催化过程中的重构仍未得到充分探索，目前的研究还处于早期发展阶段。为了深入研究 MOG 材料在电催化中的应用，我们详细研究了其在电化学活化方法下的组成转变和结构变化，从而制备出高性能的 OER 预电催化剂。XRD 和 HRTEM 结果表明，无定形的 Fe5Ni5-MOG 完全重构为结晶的 NiOOH/FeOOH 异质结构。重构的 Re-Fe5Ni5-MOG 中的双金属中心和丰富的 NiOOH-FeOOH 界面产生了协同效应，在碱性电解质中表现出优异的 OER 活性，过电位低（10 mA cm-2 时为 205 mV），塔菲尔斜率为 58 mV dec-1。电催化过程中的原位表征显示，当电压升高到 1.55 V 时，金属中心逐渐转变为金属羟基氧化物。DFT 分析表明，在铁镍双位点反应途径中，活性物质优先吸附在铁位点上，然后才吸附在镍位点上。
{"title":"Electrochemical reconstruction of metal-organic gels into crystalline oxy-hydroxide heterostructures for efficient oxygen evolution electrocatalysis","authors":"Kang Liu, Haikuo Lan, Yuting Chen, Weicheng Tang, Zhenyu Xiao, Yunmei Du, Jun Xing, Zexing Wu, Lei Wang","doi":"10.1039/d4sc05799f","DOIUrl":"https://doi.org/10.1039/d4sc05799f","url":null,"abstract":"Metal-organic gels (MOGs) are emerging soft materials with distinct metal active centers, multifunctional ligands and hierarchical porous structures, showing promising potential in the field of electrocatalysis. However, the reconfiguration of MOGs during the electrocatalytic process remains underexplored, with current studies in early developmental stages. To deeply investigate the application of MOG materials in electrocatalysis, the compositional transformations and structural changes under an electrochemical activation method were studied in detail, which leading to high-performance OER pre-electrocatalysts. XRD and HRTEM results demonstrate the complete reconfiguration of amorphous Fe5Ni5-MOG into crystalline NiOOH/FeOOH heterostructures. The synergistic effect of the bimetallic center and the rich NiOOH-FeOOH interface in the reconstituted Re-Fe5Ni5-MOG exhibit excellent OER activity in alkaline electrolytes, with low overpotentials (205 mV at 10 mA cm-2) and a Tafel slope of 58 mV dec-1. In-situ characterization during the electrocatalytic process reveals the gradual transformation of the metal center into metal hydroxyl oxides upon increasing voltage to 1.55 V. DFT analysis suggests that in the Fe-Ni double sites reaction pathway, active substances preferentially adsorb on the Fe site before the Ni sites.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142556094","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}
The internal rotation of triplet-generating molecules is detrimental to room temperature phosphorescence (RTP) radiation, which is always mentioned and usually mitigated by doping into rigid microenvironments. The chemical locking of internal rotation units in advance should be an effective strategy but is rarely studied in comparison. Herein, a triplet-generating molecule with two rotatable phenyls (DIA) is designed, synthesized, and then cyclized by two kinds of bonding bridge. We find that DIA/PMMA film hardly shows observable RTP afterglow despite 148 ms of lifetime, whereas carbon bridge cyclized DIA (CDIA) and oxygen bridge cyclized DIA (ODIA) emit green and blue ultralong RTP in PMMA film with lifetimes of 2146 ms and 2656 ms, respectively, demonstrating the potent role of pre-locking of internal rotation unit in promoting RTP. Benefited from the good spectral overlaps between the RTP emissions of dopants and the absorption of perylene red (PR) in PMMA film, the almost complete triplet-to-singlet Förster resonance energy transfer is achieved under trace doping (0.1%), providing red room temperature afterglow materials with lifetimes of 1567‒1800 ms. The preliminary applications of blue, green, and red afterglow materials in optical encryption and anti-counterfeiting are demonstrated. This work not only develops new triplet generating and radiating molecules but also guides an effective molecular strategy of achieving ultralong RTP polymers.
{"title":"Organic Dopant Cyclization and Significantly Improved RTP Properties","authors":"Shiguo Zhang, Guanyu Liu, Zhichao Mao, Shanfeng Xue, Qikun Sun, Wenjun Yang","doi":"10.1039/d4sc06213b","DOIUrl":"https://doi.org/10.1039/d4sc06213b","url":null,"abstract":"The internal rotation of triplet-generating molecules is detrimental to room temperature phosphorescence (RTP) radiation, which is always mentioned and usually mitigated by doping into rigid microenvironments. The chemical locking of internal rotation units in advance should be an effective strategy but is rarely studied in comparison. Herein, a triplet-generating molecule with two rotatable phenyls (DIA) is designed, synthesized, and then cyclized by two kinds of bonding bridge. We find that DIA/PMMA film hardly shows observable RTP afterglow despite 148 ms of lifetime, whereas carbon bridge cyclized DIA (CDIA) and oxygen bridge cyclized DIA (ODIA) emit green and blue ultralong RTP in PMMA film with lifetimes of 2146 ms and 2656 ms, respectively, demonstrating the potent role of pre-locking of internal rotation unit in promoting RTP. Benefited from the good spectral overlaps between the RTP emissions of dopants and the absorption of perylene red (PR) in PMMA film, the almost complete triplet-to-singlet Förster resonance energy transfer is achieved under trace doping (0.1%), providing red room temperature afterglow materials with lifetimes of 1567‒1800 ms. The preliminary applications of blue, green, and red afterglow materials in optical encryption and anti-counterfeiting are demonstrated. This work not only develops new triplet generating and radiating molecules but also guides an effective molecular strategy of achieving ultralong RTP polymers.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142541266","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}
Zhihang Chen, Menglin Ji, Jie Qian, Zhe Zhang, Xiangying Zhang, Haojie Wang, Haotian Gao, Renxiao Wang, Yifei Qi
Protein-protein interactions are pivotal in numerous biological processes. The computational design of these interactions facilitates the creation of novel binding proteins, crucial for advancing biopharmaceutical products. With the evolution of artificial intelligence (AI), protein design tools have swiftly transitioned from scoring-function-based to AI-based models. However, many AI models for protein design are constrained by assuming complete unfamiliarity with the amino acid sequence of the input protein, a feature most suited for de novo design but posing challenges in designing protein-protein interactions when the receptor sequence is known. To bridge this gap in computational protein design, we introduce ProBID-Net. Trained using natural protein-protein complex structures and protein domain-domain interface structures, ProBID-Net can discern features from known target protein structures to design specific binding proteins based on their binding sites. In independent tests, ProBID-Net achieved interface sequence recovery rates of 52.7%, 43.9%, and 37.6%, surpassing or being on par with ProteinMPNN in binding protein design. Validated using AlphaFold-Multimer, the sequences designed by ProBID-Net demonstrated a close correspondence between the design target and the predicted structure. Moreover, the model's output can predict changes in binding affinity upon mutations in protein complexes, even in scenarios where no data on such mutations were provided during training (zero-shot prediction). In summary, the ProBID-Net model is poised to significantly advance the design of protein-protein interactions.
{"title":"ProBID-Net: A Deep Learning Model for Protein-Protein Binding Interface Design","authors":"Zhihang Chen, Menglin Ji, Jie Qian, Zhe Zhang, Xiangying Zhang, Haojie Wang, Haotian Gao, Renxiao Wang, Yifei Qi","doi":"10.1039/d4sc02233e","DOIUrl":"https://doi.org/10.1039/d4sc02233e","url":null,"abstract":"Protein-protein interactions are pivotal in numerous biological processes. The computational design of these interactions facilitates the creation of novel binding proteins, crucial for advancing biopharmaceutical products. With the evolution of artificial intelligence (AI), protein design tools have swiftly transitioned from scoring-function-based to AI-based models. However, many AI models for protein design are constrained by assuming complete unfamiliarity with the amino acid sequence of the input protein, a feature most suited for de novo design but posing challenges in designing protein-protein interactions when the receptor sequence is known. To bridge this gap in computational protein design, we introduce ProBID-Net. Trained using natural protein-protein complex structures and protein domain-domain interface structures, ProBID-Net can discern features from known target protein structures to design specific binding proteins based on their binding sites. In independent tests, ProBID-Net achieved interface sequence recovery rates of 52.7%, 43.9%, and 37.6%, surpassing or being on par with ProteinMPNN in binding protein design. Validated using AlphaFold-Multimer, the sequences designed by ProBID-Net demonstrated a close correspondence between the design target and the predicted structure. Moreover, the model's output can predict changes in binding affinity upon mutations in protein complexes, even in scenarios where no data on such mutations were provided during training (zero-shot prediction). In summary, the ProBID-Net model is poised to significantly advance the design of protein-protein interactions.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142541213","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}
Molecule-based hybrid layered magnets provide an ideal platform for investigating the long-range spin-ordering process in low-dimensional magnetic systems. Within this context, a promising area of research is spin-sandwiched hybrid layered magnets. These materials offer the potential to explore how the spin, which is sandwiched between magnetic layers, is influenced by the internal magnetic fields generated by the magnetic layers. Herein, we report a layered ferrimagnet with intercalated biferrocenium ([bifc]+) radicals, [bifc][{Ru2(2,3,5,6-F4ArCO2)4}2(TCNQF2)] (1, TCNQF2 = 2,5-difluorotetracyano-p-quinodimethane). The [{Ru2(2,3,5,6-F4ArCO2)4}2(TCNQF2)]– moiety acts as a ferrimagnetic layer with ST = 3/2, composed of a paddlewheel [Ru2II,II(2,3,5,6-F4ArCO2)4] (2,3,5,6-F4ArCO2– = 2,3,5,6-tetrafluorobenzoate) with S = 1 and 2,5-difluoro-7,7,8,8-tetracyanoquinodimethanate (TCNQF2•–) units with S = 1/2 in a 2:1 ratio. The isostructural paramagnetic compound [bifc][{Rh2(2,3,5,6-F4ArCO2)4}2(TCNQF2)] (2) consisting of diamagnetic [Rh2II,II(2,3,5,6-F4ArCO2)4] components was also synthesized. An investigation of the properties of 2 revealed minimal magnetic interaction between the [bifc]+ and TCNQF2•– components. Compound 1 displayed long-range ferrimagnetic ordering at the Curie temperature of 105 K without any frequency dependence on alternating current (AC) susceptibility, due to the combination of predominant ferrimagnetic ordering within the layer and interlayer ferromagnetic dipole interactions. However, subsequent stepwise magnetic ordering involving a strong AC frequency dependence was observed upon further cooling. These dynamic behaviors are associated with the ordering of two types of anisotropic [bifc]+ spins between the ferrimagnetic layers, indicating that [bifc]+ spin ordering is sensitive to anisotropic internal magnetic fields generated by the ferrimagnetic layers.
{"title":"Dynamic Spin Reordering in a Hybrid Layered Ferrimagnet with Intercalated Biferrocenium Radicals","authors":"Qingxin Liu, Wataru Kosaka, Hitoshi Miyasaka","doi":"10.1039/d4sc04722b","DOIUrl":"https://doi.org/10.1039/d4sc04722b","url":null,"abstract":"Molecule-based hybrid layered magnets provide an ideal platform for investigating the long-range spin-ordering process in low-dimensional magnetic systems. Within this context, a promising area of research is spin-sandwiched hybrid layered magnets. These materials offer the potential to explore how the spin, which is sandwiched between magnetic layers, is influenced by the internal magnetic fields generated by the magnetic layers. Herein, we report a layered ferrimagnet with intercalated biferrocenium ([bifc]+) radicals, [bifc][{Ru2(2,3,5,6-F4ArCO2)4}2(TCNQF2)] (1, TCNQF2 = 2,5-difluorotetracyano-p-quinodimethane). The [{Ru2(2,3,5,6-F4ArCO2)4}2(TCNQF2)]– moiety acts as a ferrimagnetic layer with ST = 3/2, composed of a paddlewheel [Ru2II,II(2,3,5,6-F4ArCO2)4] (2,3,5,6-F4ArCO2– = 2,3,5,6-tetrafluorobenzoate) with S = 1 and 2,5-difluoro-7,7,8,8-tetracyanoquinodimethanate (TCNQF2•–) units with S = 1/2 in a 2:1 ratio. The isostructural paramagnetic compound [bifc][{Rh2(2,3,5,6-F4ArCO2)4}2(TCNQF2)] (2) consisting of diamagnetic [Rh2II,II(2,3,5,6-F4ArCO2)4] components was also synthesized. An investigation of the properties of 2 revealed minimal magnetic interaction between the [bifc]+ and TCNQF2•– components. Compound 1 displayed long-range ferrimagnetic ordering at the Curie temperature of 105 K without any frequency dependence on alternating current (AC) susceptibility, due to the combination of predominant ferrimagnetic ordering within the layer and interlayer ferromagnetic dipole interactions. However, subsequent stepwise magnetic ordering involving a strong AC frequency dependence was observed upon further cooling. These dynamic behaviors are associated with the ordering of two types of anisotropic [bifc]+ spins between the ferrimagnetic layers, indicating that [bifc]+ spin ordering is sensitive to anisotropic internal magnetic fields generated by the ferrimagnetic layers.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142541272","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}
Matthew Garrett Miyada, Yuran Choi, Kyle Rich, James J LaClair, Michael Burkart
Carrier protein-dependent synthases are ubiquitous enzymes involved both in primary and secondary metabolism. Biocatalysis within these synthases is governed by key interactions between the carrier protein, substrate, and partner enzymes. The weak and transient nature of these interactions has rendered them difficult to study. Here we develop a useful fluorescent solvatochromic probe, dapoxyl-pantetheinamide, to monitor and quantify carrier protein interactions in vitro. Upon loading with target carrier proteins, we observe dramatic shifts in fluorescent emission wavelength and intensity and further demonstrate that this tool has the potential to be applied across numerous biosynthetic pathways. The environmental sensitivity of this probe allows rapid characterization of carrier protein interactions, with the ability to quantitatively determine inhibition of protein-protein interactions. We anticipate future application of these probes for inhibitor screening and in vivo characterization.
{"title":"Differentiating carrier protein interactions in biosynthetic pathways using dapoxyl solvatochromism","authors":"Matthew Garrett Miyada, Yuran Choi, Kyle Rich, James J LaClair, Michael Burkart","doi":"10.1039/d4sc05499g","DOIUrl":"https://doi.org/10.1039/d4sc05499g","url":null,"abstract":"Carrier protein-dependent synthases are ubiquitous enzymes involved both in primary and secondary metabolism. Biocatalysis within these synthases is governed by key interactions between the carrier protein, substrate, and partner enzymes. The weak and transient nature of these interactions has rendered them difficult to study. Here we develop a useful fluorescent solvatochromic probe, dapoxyl-pantetheinamide, to monitor and quantify carrier protein interactions <em>in vitro</em>. Upon loading with target carrier proteins, we observe dramatic shifts in fluorescent emission wavelength and intensity and further demonstrate that this tool has the potential to be applied across numerous biosynthetic pathways. The environmental sensitivity of this probe allows rapid characterization of carrier protein interactions, with the ability to quantitatively determine inhibition of protein-protein interactions. We anticipate future application of these probes for inhibitor screening and <em>in vivo</em> characterization.","PeriodicalId":9909,"journal":{"name":"Chemical Science","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542177","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}
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