Assessing the accuracy and efficacy of multiscale computational methods in predicting reaction mechanisms and kinetics of SN2 reactions and Claisen rearrangement

This study investigates the application of quantum mechanical (QM) and multiscale computational methods in understanding the reaction mechanisms and kinetics of S N 2 reactions involving methyl iodide with NH 2 OH and NH 2 O − , as well as the Claisen rearrangement of 8-(vinyloxy)dec-9-enoate. Our a...

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Veröffentlicht in:Scientific reports Jg. 14; H. 1; S. 16791 - 13
Hauptverfasser: Haji Dehabadi, Maryam, Saidi, Hamid, Zafari, Faezeh, Irani, Mehdi
Format: Journal Article
Sprache:Englisch
Veröffentlicht: London Nature Publishing Group UK 22.07.2024
Nature Publishing Group
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Schlagworte:
639/638/403
639/638/563
Accuracy
Computer applications
Humanities and Social Sciences
Hybrids
Iodides
Kinetics
multidisciplinary
Multiscale modeling
ORCA software
Python scripting
QM/MM
Reaction mechanism
Reaction mechanisms
Science
Science (multidisciplinary)
Solvents
Reaction mechanism
ORCA software
QM/MM
Multiscale modeling
Python scripting
ISSN:2045-2322, 2045-2322
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Zusammenfassung:This study investigates the application of quantum mechanical (QM) and multiscale computational methods in understanding the reaction mechanisms and kinetics of S N 2 reactions involving methyl iodide with NH 2 OH and NH 2 O − , as well as the Claisen rearrangement of 8-(vinyloxy)dec-9-enoate. Our aim is to evaluate the accuracy and effectiveness of these methods in predicting experimental outcomes for these organic reactions. We achieve this by employing QM-only calculations and several hybrids of QM and molecular mechanics (MM) methods, namely QM/MM, QM1/QM2, and QM1/QM2/MM methodologies. For the S N 2 reactions, our results demonstrate the importance of explicitly including solvent effects in the calculations to accurately reproduce the transition state geometry and energetics. The multiscale methods, particularly QM/MM and QM1/QM2, show promising performance in predicting activation energies. Moreover, we observe that the size of the MM active region significantly affects the accuracy of calculated activation energies, highlighting the need for careful consideration during the setup of multiscale calculations. In the case of the Claisen rearrangement, both QM-only and multiscale methods successfully reproduce the proposed reaction mechanism. However, the activation free energies calculated using a continuum solvation model, based on single-point calculations of QM-only structures, fail to account for solvent effects. On the other hand, multiscale methods more accurately capture the impact of solvents on activation free energies, with systematic error correction enhancing the accuracy of the results. Furthermore, we introduce a Python code for setting up multiscale calculations with ORCA, which is available on GitHub at https://github.com/iranimehdi/pdbtoORCA .
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ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-024-67468-x