{"title":"介氮酶的机制:从捕获 N2 到首次释放 NH3","authors":"Ian Dance","doi":"10.1039/D4DT02606C","DOIUrl":null,"url":null,"abstract":"<p >Mo-nitrogenase hydrogenates N<small><sub>2</sub></small> to NH<small><sub>3</sub></small>. This report continues from the previous paper [I. Dance, <em>Dalton Trans.</em>, 2024, <strong>53</strong>, 14193–14211] that described how the active site FeMo-co of the enzyme is uniquely able to capture and activate N<small><sub>2</sub></small>, forming a key intermediate with Fe-bound HNNH. Density functional simulations with a 485+ atom model of the active site and its surroundings are used to describe here the further reactions of this HNNH intermediate. The first step is hydrogenation to form HNNH<small><sub>2</sub></small> bridging Fe2 and Fe6. Then a single-step reaction breaks the N–N bond, generating an Fe2–NH–Fe6 bridge and forming NH<small><sub>3</sub></small> bound to Fe6. Then NH<small><sub>3</sub></small> dissociates from Fe6. Reaction potential energies and kinetic barriers for all steps are reported for the most favourable electronic states of the system. The steps that follow the Fe2–NH–Fe6 intermediate, forming and dissociating the second NH<small><sub>3</sub></small>, and regenerating the resting state of the enzyme, are outlined. These results provide an interpretation of the recent steady-state kinetics data and analysis by Harris <em>et al</em>., [<em>Biochemistry</em>, 2022, <strong>61</strong>, 2131–2137] who found a slow step after the formation of the HNNH intermediate. The calculated potential energy barriers for the HNNH<small><sub>2</sub></small> → NH + NH<small><sub>3</sub></small> reaction (30–36 kcal mol<small><sup>−1</sup></small>) are larger than the potential energy barriers for the N<small><sub>2</sub></small> → HNNH reaction (19–29 kcal mol<small><sup>−1</sup></small>). I propose that the post-HNNH slow step identified kinetically is the key HNNH<small><sub>2</sub></small> → NH + NH<small><sub>3</sub></small> reaction described here. This step and the N<small><sub>2</sub></small>-capture step are the most difficult in the conversion of N<small><sub>2</sub></small> to 2NH<small><sub>3</sub></small>. The steps in the complete mechanism still to be computationally detailed are relatively straightforward.</p>","PeriodicalId":71,"journal":{"name":"Dalton Transactions","volume":" 48","pages":" 19360-19377"},"PeriodicalIF":3.5000,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"The mechanism of Mo-nitrogenase: from N2 capture to first release of NH3†\",\"authors\":\"Ian Dance\",\"doi\":\"10.1039/D4DT02606C\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p >Mo-nitrogenase hydrogenates N<small><sub>2</sub></small> to NH<small><sub>3</sub></small>. This report continues from the previous paper [I. Dance, <em>Dalton Trans.</em>, 2024, <strong>53</strong>, 14193–14211] that described how the active site FeMo-co of the enzyme is uniquely able to capture and activate N<small><sub>2</sub></small>, forming a key intermediate with Fe-bound HNNH. Density functional simulations with a 485+ atom model of the active site and its surroundings are used to describe here the further reactions of this HNNH intermediate. The first step is hydrogenation to form HNNH<small><sub>2</sub></small> bridging Fe2 and Fe6. Then a single-step reaction breaks the N–N bond, generating an Fe2–NH–Fe6 bridge and forming NH<small><sub>3</sub></small> bound to Fe6. Then NH<small><sub>3</sub></small> dissociates from Fe6. Reaction potential energies and kinetic barriers for all steps are reported for the most favourable electronic states of the system. The steps that follow the Fe2–NH–Fe6 intermediate, forming and dissociating the second NH<small><sub>3</sub></small>, and regenerating the resting state of the enzyme, are outlined. These results provide an interpretation of the recent steady-state kinetics data and analysis by Harris <em>et al</em>., [<em>Biochemistry</em>, 2022, <strong>61</strong>, 2131–2137] who found a slow step after the formation of the HNNH intermediate. The calculated potential energy barriers for the HNNH<small><sub>2</sub></small> → NH + NH<small><sub>3</sub></small> reaction (30–36 kcal mol<small><sup>−1</sup></small>) are larger than the potential energy barriers for the N<small><sub>2</sub></small> → HNNH reaction (19–29 kcal mol<small><sup>−1</sup></small>). I propose that the post-HNNH slow step identified kinetically is the key HNNH<small><sub>2</sub></small> → NH + NH<small><sub>3</sub></small> reaction described here. This step and the N<small><sub>2</sub></small>-capture step are the most difficult in the conversion of N<small><sub>2</sub></small> to 2NH<small><sub>3</sub></small>. The steps in the complete mechanism still to be computationally detailed are relatively straightforward.</p>\",\"PeriodicalId\":71,\"journal\":{\"name\":\"Dalton Transactions\",\"volume\":\" 48\",\"pages\":\" 19360-19377\"},\"PeriodicalIF\":3.5000,\"publicationDate\":\"2024-10-30\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Dalton Transactions\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://pubs.rsc.org/en/content/articlelanding/2024/dt/d4dt02606c\",\"RegionNum\":3,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"CHEMISTRY, INORGANIC & NUCLEAR\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Dalton Transactions","FirstCategoryId":"92","ListUrlMain":"https://pubs.rsc.org/en/content/articlelanding/2024/dt/d4dt02606c","RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"CHEMISTRY, INORGANIC & NUCLEAR","Score":null,"Total":0}
The mechanism of Mo-nitrogenase: from N2 capture to first release of NH3†
Mo-nitrogenase hydrogenates N2 to NH3. This report continues from the previous paper [I. Dance, Dalton Trans., 2024, 53, 14193–14211] that described how the active site FeMo-co of the enzyme is uniquely able to capture and activate N2, forming a key intermediate with Fe-bound HNNH. Density functional simulations with a 485+ atom model of the active site and its surroundings are used to describe here the further reactions of this HNNH intermediate. The first step is hydrogenation to form HNNH2 bridging Fe2 and Fe6. Then a single-step reaction breaks the N–N bond, generating an Fe2–NH–Fe6 bridge and forming NH3 bound to Fe6. Then NH3 dissociates from Fe6. Reaction potential energies and kinetic barriers for all steps are reported for the most favourable electronic states of the system. The steps that follow the Fe2–NH–Fe6 intermediate, forming and dissociating the second NH3, and regenerating the resting state of the enzyme, are outlined. These results provide an interpretation of the recent steady-state kinetics data and analysis by Harris et al., [Biochemistry, 2022, 61, 2131–2137] who found a slow step after the formation of the HNNH intermediate. The calculated potential energy barriers for the HNNH2 → NH + NH3 reaction (30–36 kcal mol−1) are larger than the potential energy barriers for the N2 → HNNH reaction (19–29 kcal mol−1). I propose that the post-HNNH slow step identified kinetically is the key HNNH2 → NH + NH3 reaction described here. This step and the N2-capture step are the most difficult in the conversion of N2 to 2NH3. The steps in the complete mechanism still to be computationally detailed are relatively straightforward.
期刊介绍:
Dalton Transactions is a journal for all areas of inorganic chemistry, which encompasses the organometallic, bioinorganic and materials chemistry of the elements, with applications including synthesis, catalysis, energy conversion/storage, electrical devices and medicine. Dalton Transactions welcomes high-quality, original submissions in all of these areas and more, where the advancement of knowledge in inorganic chemistry is significant.