Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.
Journal Article (Journal Article)
We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.
Full Text
Duke Authors
Cited Authors
- Shen, L; Yang, W
Published Date
- April 2016
Published In
Volume / Issue
- 12 / 4
Start / End Page
- 2017 - 2027
PubMed ID
- 26930454
Pubmed Central ID
- PMC4977206
Electronic International Standard Serial Number (EISSN)
- 1549-9626
International Standard Serial Number (ISSN)
- 1549-9618
Digital Object Identifier (DOI)
- 10.1021/acs.jctc.5b01107
Language
- eng