Delving into the Catalytic Mechanism of Molybdenum Cofactors: A Novel Coupled Cluster Study
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arXiv
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| Format: | Preprint |
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2024
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| author | Gałyńska, Marta de Moraes, Matheus Morato F. Tecmer, Paweł Boguslawski, Katharina |
| author_facet | Gałyńska, Marta de Moraes, Matheus Morato F. Tecmer, Paweł Boguslawski, Katharina |
| contents | In this work, we use modern electronic structure methods to model the catalytic mechanism of different variants of the molybdenum cofactor (Moco). We investigate the dependence of various Moco model systems on structural relaxation and the importance of environmental effects for five critical points along the reaction coordinate with the DMSO and NO$_3^-$ substrates. Furthermore, we scrutinize the performance of various coupled-cluster approaches for modeling the relative energies along the investigated reaction paths, focusing on several pair coupled cluster doubles (pCCD) flavors and conventional coupled cluster approximations. Moreover, we elucidate the Mo--O bond formation using orbital-based quantum information measures, which highlight the flow of $σ_{\rm M-O}$ bond formation and $σ_{\rm N/S-O}$ bond breaking. Our study shows that pCCD-based models are a viable alternative to conventional methods and offer us unique insights into the bonding situation along a reaction coordinate. Finally, this work highlights the importance of environmental effects or changes in the core and, consequently, in the model itself to elucidate the change in activity of different Moco variants. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2406_14037 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Delving into the Catalytic Mechanism of Molybdenum Cofactors: A Novel Coupled Cluster Study Gałyńska, Marta de Moraes, Matheus Morato F. Tecmer, Paweł Boguslawski, Katharina Chemical Physics Biological Physics Computational Physics In this work, we use modern electronic structure methods to model the catalytic mechanism of different variants of the molybdenum cofactor (Moco). We investigate the dependence of various Moco model systems on structural relaxation and the importance of environmental effects for five critical points along the reaction coordinate with the DMSO and NO$_3^-$ substrates. Furthermore, we scrutinize the performance of various coupled-cluster approaches for modeling the relative energies along the investigated reaction paths, focusing on several pair coupled cluster doubles (pCCD) flavors and conventional coupled cluster approximations. Moreover, we elucidate the Mo--O bond formation using orbital-based quantum information measures, which highlight the flow of $σ_{\rm M-O}$ bond formation and $σ_{\rm N/S-O}$ bond breaking. Our study shows that pCCD-based models are a viable alternative to conventional methods and offer us unique insights into the bonding situation along a reaction coordinate. Finally, this work highlights the importance of environmental effects or changes in the core and, consequently, in the model itself to elucidate the change in activity of different Moco variants. |
| title | Delving into the Catalytic Mechanism of Molybdenum Cofactors: A Novel Coupled Cluster Study |
| topic | Chemical Physics Biological Physics Computational Physics |
| url | https://arxiv.org/abs/2406.14037 |