The Effects of Conformational Sampling and QM Region Size in QM/MM Simulations : An Adaptive QM/MM Study With Model Systems
© 2025 The Author(s). Journal of Computational Chemistry published by Wiley Periodicals LLC.
| Publié dans: | Journal of computational chemistry. - 1984. - 46(2025), 11 vom: 30. Apr., Seite e70109 |
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| Auteur principal: | |
| Autres auteurs: | , , , |
| Format: | Article en ligne |
| Langue: | English |
| Publié: |
2025
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| Accès à la collection: | Journal of computational chemistry |
| Sujets: | Journal Article Adaptive QM/MM Combined QM/MM Minimum Energy Paths Potential of Mean Force QM Region Size |
| Résumé: | © 2025 The Author(s). Journal of Computational Chemistry published by Wiley Periodicals LLC. Molecular properties in combined quantum mechanics and molecular mechanics (QM/MM) simulations have been shown to be dependent on the size of the quantum mechanical (QM) region and the amount of conformational sampling. Previous studies have largely focused on enzymatic systems, which have made it difficult to distinguish the effects of QM region size and conformational sampling from other factors including QM-MM boundary artifacts and the boundary effects. This study uses the difference-based adaptive solvation QM/MM method to investigate the tautomerization reactions of alanine and aspartate in explicit solvent. The choice of computationally tractable systems enables the decoupling of QM region size effects from other factors and a direct comparison of free energy surfaces with potential energy surfaces (PESs). The results show that (1) it is crucial to properly account for thermal fluctuations along the reaction pathways, and (2) free energy surfaces converge rapidly with increasing QM region size, whereas charge transfer requires a slightly larger QM region to achieve convergence. These findings are expected to guide future studies of enzymatic systems and other complex systems where QM/MM methods are applied |
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| Description: | Date Revised 21.04.2025 published: Print Citation Status PubMed-not-MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.70109 |