Néstor Gutiérrez-Sánchez, Fernando Mendizábal, Sebastián Miranda-Rojas
Here, an exhaustive exploration of the reaction mechanism toward the chlorination process carried out by SalL, a chlorinase enzyme that catalyzes the conversion of SAM into 5′-chloro-5′-deoxyadenosine through an SN2 reaction, is presented. To this end, molecular dynamics simulations and quantum mechanical/molecular mechanics calculations are performed, and 14 density functionals are benchmarked. Among the tested functionals, TPSSh(BJ) provides the closest energy barrier to experimental value. Three configurations of interaction between chloride and the halogen pocket are found, where the best model exhibits a barrier height of 20.1 kcal mol−1, close to the 19.9 kcal mol−1 experimentally obtained. This model is characterized by the chloride interacting with the backbone-amide of Gly131 and Tyr130. The reaction pathway is calculated through the intrinsic reaction coordinate approach, and it is characterized using reaction force analysis and the activation-strain model with energy decomposition analysis to obtain chemical insights into the inner working of this enzyme. According to the main findings, the overstabilization of the halogen binding on the active site increases the barrier height, explaining the lack of activity against fluoride, while the interaction energy between nucleophile−electrophile is responsible of reducing the barrier height, with the orbital interaction energy as the main stabilizing factor during the chlorination process.
{"title":"Unveiling SalL Chlorinase Reaction Mechanism and Selectivity through Quantum Mechanical/Molecular Mechanics and Activation-Strain Model","authors":"Néstor Gutiérrez-Sánchez, Fernando Mendizábal, Sebastián Miranda-Rojas","doi":"10.1002/cplu.202500344","DOIUrl":"10.1002/cplu.202500344","url":null,"abstract":"<p>Here, an exhaustive exploration of the reaction mechanism toward the chlorination process carried out by SalL, a chlorinase enzyme that catalyzes the conversion of SAM into 5′-chloro-5′-deoxyadenosine through an <i>S</i><sub><i>N</i></sub>2 reaction, is presented. To this end, molecular dynamics simulations and quantum mechanical/molecular mechanics calculations are performed, and 14 density functionals are benchmarked. Among the tested functionals, TPSSh(BJ) provides the closest energy barrier to experimental value. Three configurations of interaction between chloride and the halogen pocket are found, where the best model exhibits a barrier height of 20.1 kcal mol<sup>−1</sup>, close to the 19.9 kcal mol<sup>−1</sup> experimentally obtained. This model is characterized by the chloride interacting with the backbone-amide of Gly131 and Tyr130. The reaction pathway is calculated through the intrinsic reaction coordinate approach, and it is characterized using reaction force analysis and the activation-strain model with energy decomposition analysis to obtain chemical insights into the inner working of this enzyme. According to the main findings, the overstabilization of the halogen binding on the active site increases the barrier height, explaining the lack of activity against fluoride, while the interaction energy between nucleophile−electrophile is responsible of reducing the barrier height, with the orbital interaction energy as the main stabilizing factor during the chlorination process.</p>","PeriodicalId":148,"journal":{"name":"ChemPlusChem","volume":"90 10","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Due to their comparable molecular dimensions and volatility, distinguishing C2H2 from CO2 during purification remains a significant challenge in industrial applications. Achieving effective isolation of C2H2 from binary mixtures of C2H2/CO2 is therefore a critical objective in petrochemical processes. Herein, an adsorption mechanism enabling selective C2H2/CO2 separation has been elucidated in the phosphonate metal–organic framework (MOF) Ni-STA-12. The high C2H2 uptake and remarkable CO2 selectivity of Ni-STA-12 arise from the synergistic effect of diverse adsorption sites distributed throughout its structure, including various oxygen atoms and open metal sites. The adsorbed C2H2 interacts strongly with the exposed adsorption sites in the framework and its binding capacity is much larger than that of CO2. Dynamic breakthrough experiments demonstrated the practical potential for the separation of C2H2 in mixtures, and excellent separation potential (Δq) demonstrating high C2H2 recovery from C2H2/CO2 mixtures. Theoretical calculations show the synergistic interaction of various oxygen atoms of the MOF with the open metal site Ni and the dominant role of uncoordinated oxygen atoms in the adsorption of C2H2.
{"title":"Harnessing Multiple Adsorption Sites in a Phosphonate Metal–Organic Framework for Efficient C2H2/CO2 Separation","authors":"Xiangsen Yuan, Wenpeng Xie, Qiuju Fu, Huimin Jiang, Shilong Wen, Xiaokun Yang, Liting Yan, Ling-Zhi Yang, Xuebo Zhao","doi":"10.1002/cplu.202500495","DOIUrl":"10.1002/cplu.202500495","url":null,"abstract":"<p>Due to their comparable molecular dimensions and volatility, distinguishing C<sub>2</sub>H<sub>2</sub> from CO<sub>2</sub> during purification remains a significant challenge in industrial applications. Achieving effective isolation of C<sub>2</sub>H<sub>2</sub> from binary mixtures of C<sub>2</sub>H<sub>2</sub>/CO<sub>2</sub> is therefore a critical objective in petrochemical processes. Herein, an adsorption mechanism enabling selective C<sub>2</sub>H<sub>2</sub>/CO<sub>2</sub> separation has been elucidated in the phosphonate metal–organic framework (MOF) Ni-STA-12. The high C<sub>2</sub>H<sub>2</sub> uptake and remarkable CO<sub>2</sub> selectivity of Ni-STA-12 arise from the synergistic effect of diverse adsorption sites distributed throughout its structure, including various oxygen atoms and open metal sites. The adsorbed C<sub>2</sub>H<sub>2</sub> interacts strongly with the exposed adsorption sites in the framework and its binding capacity is much larger than that of CO<sub>2</sub>. Dynamic breakthrough experiments demonstrated the practical potential for the separation of C<sub>2</sub>H<sub>2</sub> in mixtures, and excellent separation potential (Δ<i>q</i>) demonstrating high C<sub>2</sub>H<sub>2</sub> recovery from C<sub>2</sub>H<sub>2</sub>/CO<sub>2</sub> mixtures. Theoretical calculations show the synergistic interaction of various oxygen atoms of the MOF with the open metal site Ni and the dominant role of uncoordinated oxygen atoms in the adsorption of C<sub>2</sub>H<sub>2</sub>.</p>","PeriodicalId":148,"journal":{"name":"ChemPlusChem","volume":"90 10","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Covalent organic framework (COF)-based memristors are promising for novel storage and neuromorphic computing applications. The ordered porous structure, tunable chemical composition, and exceptional stability of COFs offer an ideal material foundation for the development of high-performance memristors. This review summarizes a classification method for COFs based on their distinctive bonding patterns, with particular emphasis on the key developmental milestones and functional applications of imine, amide, boronic ester, and vinylene-based architectures. Lastly, a thorough discussion of the future challenges and prospects associated with COF-based memristors is provided.
{"title":"Research Progress on Covalent Organic Framework-Based Memristors","authors":"Minghan Xiang, Qiongshan Zhang, Bin Zhang","doi":"10.1002/cplu.202500361","DOIUrl":"10.1002/cplu.202500361","url":null,"abstract":"<p>Covalent organic framework (COF)-based memristors are promising for novel storage and neuromorphic computing applications. The ordered porous structure, tunable chemical composition, and exceptional stability of COFs offer an ideal material foundation for the development of high-performance memristors. This review summarizes a classification method for COFs based on their distinctive bonding patterns, with particular emphasis on the key developmental milestones and functional applications of imine, amide, boronic ester, and vinylene-based architectures. Lastly, a thorough discussion of the future challenges and prospects associated with COF-based memristors is provided.</p>","PeriodicalId":148,"journal":{"name":"ChemPlusChem","volume":"90 10","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144858668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The front cover picture shows a distinct size-dependent affinity of gold (Au)-based materials for dioxygen (O2). Although Au is chemically inert against O2, unique reactivities emerged at the nanometer to the atomic scales. Atomically precise Au nanoclusters and molecular Au complexes with supporting ligands exhibit affinity for O2, and detailed mechanisms for O2-activation by these Au-based nanomaterials can be revealed on the basis of both experimental and theoretical analyses. More details can be found in the Concept by Wataru Suzuki and Toshiharu Teranishi (DOI: 10.1002/cplu.202500244).