Force field independent metal parameters using a nonbonded dummy model
Duarte, Fernanda ; Bauer, Paul ; Barrozo, Alexandre ; Amrein, Beat Anton ; Purg, Miha ; Åqvist, Johan and Kamerlin, Shina Caroline Lynn LU
(2014)
In The Journal of Physical Chemistry Part B
118(16).
p.62-4351
- Abstract
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 Mn(2+), Zn(2+), Mg(2+), and Ca(2+), as well as providing new parameters for Ni(2+), Co(2+), and Fe(2+). In all the cases, we are able to reproduce both M(2+)-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... (More)
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 Mn(2+), Zn(2+), Mg(2+), and Ca(2+), as well as providing new parameters for Ni(2+), Co(2+), and Fe(2+). In all the cases, we are able to reproduce both M(2+)-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 I 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.
(Less)
- author
- Duarte, Fernanda
; Bauer, Paul
; Barrozo, Alexandre
; Amrein, Beat Anton
; Purg, Miha
; Åqvist, Johan
and Kamerlin, Shina Caroline Lynn
LU
- publishing date
- 2014-04-24
- type
- Contribution to journal
- publication status
- published
- keywords
- Catalytic Domain, Cations/chemistry, Escherichia coli, Escherichia coli Proteins/chemistry, Humans, Lactoylglutathione Lyase/chemistry, Metals/chemistry, Models, Chemical, Molecular Dynamics Simulation, Static Electricity, Water/chemistry
- in
- The Journal of Physical Chemistry Part B
- volume
- 118
- issue
- 16
- pages
- 12 pages
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- scopus:84899478992
- pmid:24670003
- ISSN
- 1520-5207
- DOI
- 10.1021/jp501737x
- language
- English
- LU publication?
- no
- id
- 4e94f593-40a5-4063-8588-3a22fd19b002
- date added to LUP
- 2025-01-11 21:53:57
- date last changed
- 2025-06-01 15:16:01
@article{4e94f593-40a5-4063-8588-3a22fd19b002,
abstract = {{<p>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 Mn(2+), Zn(2+), Mg(2+), and Ca(2+), as well as providing new parameters for Ni(2+), Co(2+), and Fe(2+). In all the cases, we are able to reproduce both M(2+)-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 I 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.</p>}},
author = {{Duarte, Fernanda and Bauer, Paul and Barrozo, Alexandre and Amrein, Beat Anton and Purg, Miha and Åqvist, Johan and Kamerlin, Shina Caroline Lynn}},
issn = {{1520-5207}},
keywords = {{Catalytic Domain; Cations/chemistry; Escherichia coli; Escherichia coli Proteins/chemistry; Humans; Lactoylglutathione Lyase/chemistry; Metals/chemistry; Models, Chemical; Molecular Dynamics Simulation; Static Electricity; Water/chemistry}},
language = {{eng}},
month = {{04}},
number = {{16}},
pages = {{62--4351}},
publisher = {{The American Chemical Society (ACS)}},
series = {{The Journal of Physical Chemistry Part B}},
title = {{Force field independent metal parameters using a nonbonded dummy model}},
url = {{http://dx.doi.org/10.1021/jp501737x}},
doi = {{10.1021/jp501737x}},
volume = {{118}},
year = {{2014}},
}