| Understanding cross-boundary events in ONIOM QM:QM' calculations. | |
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MedLine Citation:
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PMID: 22109102 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
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QM:QM' models, where QM' is a fast molecular orbital method, offers advantages over standard quantum mechanics: molecular mechanics (QM:MM) models, especially in the description of charge transfer and mutual polarization between layers. The ONIOM QM:QM' scheme also allows for reactions across the layer boundary, but the understanding of these events is limited. To explain the factors that affect cross-boundary events, a set of proton transfer processes, including the acylation reaction in serine protease, have been investigated. For reactions inside out, that is, when a group breaks a bond in the high layer and forms a new bond with a group in the low layer, QM' methods that are overbinding relative to the QM method, for example, Hartree-Fock versus B3LYP, can severely overestimate the exothermicity of the reaction. This might lead to artificial reactivity across the QM:QM' boundary, a phenomenon called model escape. The accuracy for reactions that occur outside in, that is, when a group in the low layer forms a new bond with the high layer, is mainly determined by the QM' calculation. Cross-boundary reactions should generally be avoided in the present ONIOM scheme. Fortunately, a better understanding of these events makes it easy to design stable ONIOM QM:QM' models, for example, by choosing a proper model system. Importantly, an accurate description of cross-boundary reactions would open up possibilities to simulate chemical reactions without a priori limiting the reactivity in the design of the computational model. Challenges to implement a simulation scheme (ONIOM-XR) that can automatically handle chemical reactions between different layers are briefly discussed. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011. |
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Authors:
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Marcus Lundberg |
Publication Detail:
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Type: JOURNAL ARTICLE Date: 2011-11-23 |
Journal Detail:
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Title: Journal of computational chemistry Volume: - ISSN: 1096-987X ISO Abbreviation: - Publication Date: 2011 Nov |
Date Detail:
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Created Date: 2011-11-23 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 9878362 Medline TA: J Comput Chem Country: - |
Other Details:
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Languages: ENG Pagination: - Citation Subset: - |
Copyright Information:
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Copyright © 2011 Wiley Periodicals, Inc. |
Affiliation:
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Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan. marcus.lundberg@kvac.uu.se. |
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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