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Csizi K, Reiher M. Universal
QM
/
MM
approaches for general nanoscale applications. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Markus Reiher
- Laboratorium für Physikalische Chemie ETH Zürich Zürich Switzerland
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Kawashima Y, Ishimura K, Shiga M. Ab initio quantum mechanics/molecular mechanics method with periodic boundaries employing Ewald summation technique to electron-charge interaction: Treatment of the surface-dipole term. J Chem Phys 2019; 150:124103. [DOI: 10.1063/1.5048451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Y. Kawashima
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - K. Ishimura
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - M. Shiga
- CCSE, Japan Atomic Energy Agency (JAEA), 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
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Moeljadi AMP, Schmid R, Hirao H. Dioxygen binding to Fe-MOF-74: microscopic insights from periodic QM/MM calculations. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0284] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Accurate MOF-FF parameter sets were determined for the ferrous and ferric forms of an iron-based metal–organic framework (MOF) called Fe-MOF-74. For this purpose, density functional theory (DFT) calculations were applied to truncated cluster models of Fe-MOF-74, and the DFT-calculated geometries and energy derivatives were used for the force-field parameterization. The resultant parameter sets performed remarkably well in reproducing the experimentally determined structure of the MOF. We also performed periodic quantum mechanics (QM) / molecular mechanics (MM) calculations employing a subtractive scheme called ONIOM, with the optimized MOF-FF parameters used for the MM calculations, in an attempt to evaluate the binding energies between O2 and several Fe-MOF-74 variants. The calculated binding energy for Fe-MOF-74 agreed very well with the experimental value, and QM/MM geometry optimization calculations confirmed that the O2-bound complex has a side-on geometry. Our calculations also predicted that, when the two neighboring iron ions around the O2-binding site are replaced with other metal ions (Mg2+, Ni2+, Zn2+, Co2+, or Mn2+), there are noticeable variations in the binding energy, indicating that these substituted metal ions affect the O2 binding indirectly.
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Affiliation(s)
- Adhitya Mangala Putra Moeljadi
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Rochus Schmid
- Computational Materials Chemistry Group, Chair of Inorganic Chemistry 2, Ruhr-University Bochum, D-44801 Bochum, Germany
| | - Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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Vasilevskaya T, Thiel W. Periodic Boundary Conditions in QM/MM Calculations: Implementation and Tests. J Chem Theory Comput 2016; 12:3561-70. [DOI: 10.1021/acs.jctc.6b00269] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Walter Thiel
- Max-Planck-Institut
für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
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