Force fields for divalent cations based on single-ion and ion-pair properties.
نویسندگان
چکیده
We develop force field parameters for the divalent cations Mg(2+), Ca(2+), Sr(2+), and Ba(2+) for molecular dynamics simulations with the simple point charge-extended (SPC/E) water model. We follow an approach introduced recently for the optimization of monovalent ions, based on the simultaneous optimization of single-ion and ion-pair properties. We consider the solvation free energy of the divalent cations as the relevant single-ion property. As a probe for ion-pair properties we compute the activity derivatives of the salt solutions. The optimization of the ionic force fields is done in two consecutive steps. First, the cation solvation free energy is determined as a function of the Lennard-Jones (LJ) parameters. The peak in the ion-water radial distribution function (RDF) is used as a check of the structural properties of the ions. Second, the activity derivatives of the electrolytes MgY(2), CaY(2), BaY(2), SrY(2) are determined through Kirkwood-Buff solution theory, where Y = Cl(-), Br(-), I(-). The activity derivatives are determined for the restricted set of LJ parameters which reproduce the exact solvation free energy of the divalent cations. The optimal ion parameters are those that match the experimental activity data and therefore simultaneously reproduce single-ion and ion-pair thermodynamic properties. For Ca(2+), Ba(2+), and Sr(2+) such LJ parameters exist. On the other hand, for Mg(2+) the experimental activity derivatives can only be reproduced if we generalize the combination rule for the anion-cation LJ interaction and rescale the effective cation-anion LJ radius, which is a modification that leaves the cation solvation free energy invariant. The divalent cation force fields are transferable within acceptable accuracy, meaning the same cation force field is valid for all halide ions Cl(-), Br(-), I(-) tested in this study.
منابع مشابه
MOLECULAR WEIGHT DETERMINATION AND METAL ION REQUIREMENT OF PHOSPHATIDATE PHOSPHOHYDROLASE PURIFIED FROM CYTOSOLIC FRACTION OF RAT LIVER
Phosphatidate phosphohydrolase (PAP) from cytosolic fraction of rat liver was purified to homogeneity having specific activity of 5.14 U/mg protein. An activity staining procedure was developed to determine molecular weight of the enzyme on polyacrylamide gel electrophoresis using Ferguson plot. Molecular Weight (M.W.) of the active PAP was 298 KDa. SDS-PAGE analysis showed a M.W. of 47 KDa for...
متن کاملStructural insights into how the MIDAS ion stabilizes integrin binding to an RGD peptide under force.
Integrin alpha(V)beta(3) binds to extracellular matrix proteins through the tripeptide Arg-Gly-Asp (RGD), forming a shallow crevice rather than a deep binding pocket. A dynamic picture of how the RGD-alpha(V)beta(3) complex resists dissociation by mechanical force is derived here from steered molecular dynamic (SMD) simulations in which the major force peak correlates with the breaking of the c...
متن کاملEnergetics of ion permeation, rejection, binding, and block in gramicidin A from free energy simulations.
The rigid force fields currently used in molecular dynamics (MD) simulations of biomolecules are optimized for globular proteins. Whether they can also be used in MD simulations of membrane proteins is an important issue that needs to be resolved. Here we address this issue using the gramicidin A channel, which provides an ideal test case because of the simplicity of its structure and the avail...
متن کاملIonic force field optimization based on single-ion and ion-pair solvation properties: going beyond standard mixing rules.
Using molecular dynamics (MD) simulations in conjunction with the SPC/E water model, we optimize ionic force-field parameters for seven different halide and alkali ions, considering a total of eight ion-pairs. Our strategy is based on simultaneous optimizing single-ion and ion-pair properties, i.e., we first fix ion-water parameters based on single-ion solvation free energies, and in a second s...
متن کاملEffect of Thickness on Structural and Morphological Properties of AlN Films Prepared Using Single Ion Beam Sputtering
Aluminum nitride (AlN) thin films have potential applications in microelectronic and optoelectronic devices. In this study, AlN thin films with different thicknesses were deposited on silicon substrate by single ion beam sputtering method. The X-ray diffraction (XRD) spectra revealed that the structure of films with thickness of - nm was amorphous, while the polycrystalline hexagonal AlN with a...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- The Journal of chemical physics
دوره 138 2 شماره
صفحات -
تاریخ انتشار 2013