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Dohn AO, Jónsson EÖ, Levi G, Mortensen JJ, Lopez-Acevedo O, Thygesen KS, Jacobsen KW, Ulstrup J, Henriksen NE, Møller KB, Jónsson H. Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex. J Chem Theory Comput 2017; 13:6010-6022. [PMID: 29083921 DOI: 10.1021/acs.jctc.7b00621] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H2O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt2(P2O5H2)4]4- complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 Å from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2% from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex.
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Affiliation(s)
- A O Dohn
- Faculty of Physical Sciences and Science Institute, University of Iceland , 107 Reykjavı́k, Iceland
| | - E Ö Jónsson
- Faculty of Physical Sciences and Science Institute, University of Iceland , 107 Reykjavı́k, Iceland
| | - G Levi
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - J J Mortensen
- CAMD, Department of Physics, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - O Lopez-Acevedo
- Department of Applied Physics, Aalto University , 02150 Espoo, Finland
| | - K S Thygesen
- CAMD, Department of Physics, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - K W Jacobsen
- CAMD, Department of Physics, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - J Ulstrup
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - N E Henriksen
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - K B Møller
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - H Jónsson
- Faculty of Physical Sciences and Science Institute, University of Iceland , 107 Reykjavı́k, Iceland.,Department of Applied Physics, Aalto University , 02150 Espoo, Finland
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Recent Progress in Adaptive-Partitioning QM/MM Methods for Born-Oppenheimer Molecular Dynamics. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-21626-3_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Pezeshki S, Lin H. Recent developments in QM/MM methods towards open-boundary multi-scale simulations. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.911870] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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{N-alkyl-N-[pyridin-2-ylmethylene] amine}dichloro palladium(II) complexes: synthesis, crystal structures and evaluation of their catalytic activities for ethylene polymerization. Polyhedron 2003. [DOI: 10.1016/s0277-5387(03)00410-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Niu S, Hall MB. Theoretical studies on reactions of transition-metal complexes. Chem Rev 2000; 100:353-406. [PMID: 11749240 DOI: 10.1021/cr980404y] [Citation(s) in RCA: 743] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S Niu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
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