Molecular dynamics in physiological solutions

Force fields, alkali metal ions, and ionic strength

Chao Zhang, Simone Raugei, Bob Eisenberg, Paolo Carloni

Research output: Contribution to journalArticle

42 Citations (Scopus)

Abstract

The monovalent ions Na+ and K+ and Cl- are present in any living organism. The fundamental thermodynamic properties of solutions containing such ions is given as the excess (electro-)chemical potential differences of single ions at finite ionic strength. This quantity is key for many biological processes, including ion permeation in membrane ion channels and DNA-protein interaction. It is given by a chemical contribution, related to the ion activity, and an electric contribution, related to the Galvani potential of the water/air interface. Here we investigate molecular dynamics based predictions of these quantities by using a variety of ion/water force fields commonly used in biological simulation, namely the AMBER (the newly developed), CHARMM, OPLS, Dang95 with TIP3P, and SPC/E water. Comparison with experiment is made with the corresponding values for salts, for which data are available. The calculations based on the newly developed AMBER force field with TIP3P water agrees well with experiment for both KCl and NaCl electrolytes in water solutions, as previously reported. The simulations based on the CHARMM-TIP3P and Dang95-SPC/E force fields agree well for the KCl and NaCl solutions, respectively. The other models are not as accurate. Single cations excess (electro-)chemical potential differences turn out to be similar for all the force fields considered here. In the case of KCl, the calculated electric contribution is consistent with higher level calculations. Instead, such agreement is not found with NaCl. Finally, we found that the calculated activities for single Cl- ions turn out to depend clearly on the type of counterion used, with all the force fields investigated. The implications of these findings for biomolecular systems are discussed.

Original languageEnglish
Pages (from-to)2167-2175
Number of pages9
JournalJournal of Chemical Theory and Computation
Volume6
Issue number7
DOIs
Publication statusPublished - Jul 13 2010

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Alkali Metals
Alkali metals
Ionic strength
alkali metals
field theory (physics)
Metal ions
Molecular dynamics
metal ions
Ions
molecular dynamics
Water
ions
water
Chemical potential
Ion Channels
organisms
Permeation
Electrolytes
Cations
Thermodynamic properties

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications

Cite this

Molecular dynamics in physiological solutions : Force fields, alkali metal ions, and ionic strength. / Zhang, Chao; Raugei, Simone; Eisenberg, Bob; Carloni, Paolo.

In: Journal of Chemical Theory and Computation, Vol. 6, No. 7, 13.07.2010, p. 2167-2175.

Research output: Contribution to journalArticle

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