Force Field Independent Metal Parameters Using a Nonbonded Dummy Model
2014 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 16, 4351-4362 p.Article in journal (Refereed) Published
The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn2+, Zn2+, Mg2+, and Ca2+, as well as providing new parameters for Ni2+, Co2+, and Fe2+. In all the cases, we are able to reproduce both M2+-O distances and experimental solvation free energies, which has not been achieved to date for transition metals using any other model. The parameters have also been tested using two different water models and show consistent performance. Therefore, our parameters are easily transferable to any force field that describes nonbonded interactions using Coulomb and Lennard-Jones potentials. Finally, we demonstrate the stability of our parameters in both the human and Escherichia coli variants of the enzyme glyoxalase 1 as showcase systems, as both enzymes are active with a range of transition metals. The parameters presented in this work provide a valuable resource for the molecular simulation community, as they extend the range of metal ions that can be studied using classical approaches, while also providing a starting point for subsequent parametrization of new metal centers.
Place, publisher, year, edition, pages
2014. Vol. 118, no 16, 4351-4362 p.
IdentifiersURN: urn:nbn:se:uu:diva-225523DOI: 10.1021/jp501737xISI: 000335113600010OAI: oai:DiVA.org:uu-225523DiVA: diva2:727956
FunderSwedish National Infrastructure for Computing (SNIC), 2013/26-1