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Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical–Molecular Mechanical Simulations of Proton Transfer in DNA
Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Chemistry and Biochemistry, University of Texas at Arlington, United States.
2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 3, p. 1695-1705Article in journal (Refereed) Published
Abstract [en]

In recent years, a number of quantum mechanical-molecular mechanical (QM/MM) enzyme studies have investigated the dependence of reaction energetics on the size of the QM region using energy and free energy calculations. In this study, we revisit the question of QM region size dependence in QM/MM simulations within the context of energy and free energy calculations using a proton transfer in a DNA base pair as a test case. In the simulations, the QM region was treated with a dispersion-corrected AM1/d-PhoT Hamiltonian, which was developed to accurately describe phosphoryl and proton transfer reactions, in conjunction with an electrostatic embedding scheme using the particle-mesh Ewald summation method. With this rigorous QM/MM potential, we performed rather extensive QM/MM sampling, and found that the free energy reaction profiles converge rapidly with respect to the QM region size within ca. +/- 1 kcal/mol. This finding suggests that the strategy of QM/MM simulations with reasonably sized and selected QM regions, which has been employed for over four decades, is a valid approach for modeling complex biomolecular systems. We point to possible causes for the sensitivity of the energy and free energy calculations to the size of the QM region, and potential implications.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2018. Vol. 14, no 3, p. 1695-1705
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:umu:diva-146449DOI: 10.1021/acs.jctc.7b00964ISI: 000427661400047PubMedID: 29446946OAI: oai:DiVA.org:umu-146449DiVA, id: diva2:1203610
Available from: 2018-05-03 Created: 2018-05-03 Last updated: 2018-06-09Bibliographically approved

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Nam, Kwangho

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CiteExportLink to record
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