Molecular dynamics simulations of Ca2+ in water: Comparison of a classical simulation including three-body corrections and Born–Oppenheimer ab initio and density functional theory quantum mechanical/molecular mechanics simulations

Abstract

A classical molecular dynamics simulation including three-body corrections was compared with combined ab initio quantum mechanics/molecular mechanics molecular dynamics simulations (QM/MM–MD), which were carried out at Hartree–Fock (HF) and density functional theory (DFT) level for Ca2+ in water. In the QM approach the region of primary interest—the first hydration sphere of the calcium ion—was treated by Born–Oppenheimer quantum mechanics, while the rest of the system was described by classical pair potentials. Coordination numbers of 7.1, 7.6, and 8.1 were found in the classical, the HF, and the DFT simulation, respectively, using the same double-ζ basis set in both QM methods. The CPU time for one DFT step was about 50% above the time for a HF step, but due to a smaller number of steps needed for equilibration in the DFT case, there was no significant difference in the overall simulation time.

Secretion machinery at the cell plasma membrane

“…Calcium ion exists in its hydrated state within cells. The properties of hydrated calcium have been extensively studied using x-ray diffraction, neutron scattering, in combination with molecular dynamics simulations [38][39][40][41]. The molecular dynamic simulations include three-body corrections compared with ab initio quantum mechanics/molecular mechanics molecular dynamics simulations.…”

Cellular calcium pathways and isotope fractionation in Emiliania huxleyi

“…Schwenk et al, 2001). At the cell membrane, the water-shell of the Ca is stripped off, and Ca enters the cell through Ca-selective channels (Brownlee and Taylor, 2004).…”

Ab initio QM/MM MD simulations of the hydrated Ca2+ ion

“…Various classical molecular dynamics simulations yielded coordination numbers between 7.9 and 9.3 [4,5,7,14]. Previous quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulations showed a preference of the eightfold-coordinated square antiprismatic structure of the [Ca(H 2 O) 8 ] 2+ complex with average coordination numbers of 7.6 [12] and 8.3 [11] for QM/MM Hartree-Fock (HF) and 8.1 [12] for QM/MM density functional theory (DFT).…”

“…Numerous experimental and theoretical reports [4][5][6][7][8][9][10][11][12] provide an inhomogeneous picture even for such rough structural data as the average number of coordinated water molecules. The preferred coordination number in crystal structures ranges from 6 to 8 [10].…”