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Charge parameterization of the metal centers in cytochrome c oxidase
Author(s) -
Johansson Mikael P.,
Kaila Ville R. I.,
Laakkonen Liisa
Publication year - 2007
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20835
Subject(s) - charge (physics) , force field (fiction) , point particle , chemistry , chemical physics , metal , stability (learning theory) , field (mathematics) , atomic charge , cytochrome c oxidase , computational chemistry , statistical physics , atomic physics , physics , molecule , computer science , quantum mechanics , mathematics , pure mathematics , biochemistry , organic chemistry , machine learning , mitochondrion
Reliable atomic point charges are of key importance for a correct description of the electrostatic interactions when performing classical, force field based simulations. Here, we present a systematic procedure for point charge derivation, based on quantum mechanical methodology suited for the systems at hand. A notable difference to previous procedures is to include an outer region around the actual system of interest. At the cost of increasing the system sizes, here up to 265 atoms, including the surroundings achieves near‐neutrality for the systems as well as structural stability, important factors for reliable charge distributions. In addition, the common problem of converting between CH bonds and CC bonds at the border vanishes. We apply the procedure to the four redox‐active metal centers of cytochrome c oxidase: Cu A , haem a , haem a 3 , and Cu B . Several relevant charge and ligand states are considered. Charges for two different force fields, CHARMM and AMBER, are presented. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008