Dynamics of ion solvation in a Stockmayer fluid

Molecular dynamics computer simulations were performed to study the dynamics of the ionic solvation in a Stockmayer fluid. The simulations show that the solvent relaxation proceeds in two time regimes. Most of the relaxation occurs in a short time period during which the relaxation process can be described by a gaussian function. The long time regime can be described by an exponential relaxation. The decay exponent of the relaxation function in this regime is the same as the exponent describing the decay of the single dipole correlation function. In addition, the contribution of the rotational and translational modes of the solvent to the energy relaxation was investigated. It was found that when the rotational mode is the dominant mode of the solvent motion the relaxation occurs from the outside-in, in accordance with the Onsager snowball picture. When the influence of the translational mode is increased the Onsager picture breaks down

Structure and dynamics of Cl − (H 2 O) 20 clusters: The effect of the polarizability and the charge of the ion

The effect of the polarizability and the sign of the ionic charge were studied in C1(H2O)20 clusters using molecular dynamics computer simulation technique. From our simulations we concluded that the reduction in the ionic polarizability did not significantly change the structure and dynamics of the Cl - (H20)20 cluster, but the inversion of the sign of the ionic charge produced a large effect. The energetic considerations helped us to understand why CIis located on the surface of the cluster. By being on the surface the anion permits the creation of the hydrogen bonded network between water molecules and that lowers the total energy of the cluster. Simulations with the inverted sign of the ionic charge correspond to that with a hypothetical "Cl + " ion which is similar in size and polarizability to a Cs + ion. The dynamical structures and the quenched structures ofCl + (H20)20 clusters are compared with the idealized structure of the Cs + (HZO)20 cluster proposed recently [A. Selinger and A. W. Castleman, Jr., J. Phys. Chern. 95, 8442 (1991)]

Structures of Cl − (H 2 O) n and F − (H 2 O) n ( n =2,3,...,15) clusters. Molecular dynamics computer simulations

We have performed molecular dynamics calculations on Cl−(H2O) n and F−(H2O) n (n=2,3,...,15) clusters. The calculations show that the F− ion is solvated in these clusters, while Cl− remains attached to the water in the clusters. We also obtained the minimum energy structures for the Cl−(H2O) n and F−(H2O) n (n=6,7,8) clusters. From the comparison of these structures with the dynamical structures we conclude that the solvation of the F− ion is due to the entropy effect

Stabilization energies of Cl − , Br − , and I − ions in water clusters

Molecular dynamics computer simulations were performed on clusters of Cl-(H20)n (n =2, ... ,15). From the simulations we calculated the stabilization energies of the anion in the cluster. These energies were compared with the values of stabilization energies obtained from the photodetachment spectra of X-(H20)n clusters (X=CI-, Br-, or 1-). The comparison confirms the hypothesis that the anion is attached to the water cluster

Molecular Dynamics Simulation of Dipalmitoylphosphatidylserine Bilayer with Na+ Counterions

AbstractWe performed a molecular dynamics simulation of dipalmitoylphosphatidylserine (DPPS) bilayer with Na+ counterions. We found that hydrogen bonding between the NH3+ group and the phosphate group leads to a reduction in the area per headgroup when compared to the area in dipalmitoylphosphatidylcholine bilayer. The Na+ ions bind to the oxygen in the carboxyl group of serine, thus giving rise to a dipolar bilayer similar to dipalmitoylphosphatidylethanolamine bilayer. The results of the simulation show that counterions play a crucial role in determining the structural and electrostatic properties of DPPS bilayer

Cube to cage transitions in (H 2 O) n ( n =12, 16, and 20)

Molecular dynamics computer simulations were performed for (H2O)n (n=12, 16, and 20) followed by systematic quenching under a polarizable and a nonpolarizable model to determine the minimum energy structures each favored. Ab initio calculations were done on several minima for (H2O)12 to determine their relative energies. The polarizable model prefers cagelike structures for all cluster sizes, whereas the nonpolarizable model predicts minima of fused cubes for (H2O)12 and (H2O)16 but makes the transition to a cagelike minimum at (H2O)20

The solvation of Cl − , Br − , and I − in acetonitrile clusters: Photoelectron spectroscopy and molecular dynamics simulations

We present the photoelectron spectra of Cl−, Br−, and I− solvated in acetonitrile clusters (CH3CN) n with n=1–33, 1–40, and 1–55, respectively, taken with 7.9 eV photon energy. Anion–solvent electrostatic stabilization energies are extracted from the measured vertical electron binding energies. The leveling of stabilization energies beyond n=10–12 for the three halides signifies the completion of the first solvation layer. This is different from the behavior of anion–water clusters which probably do not fill the first solvation layer, but rather form surface solvation states. Classical molecular dynamics simulations of halide–acetonitrile clusters reproduce the measured stabilization energies and generate full solvation shells of 11–12, 12, and 12–13 solvent molecules for Cl−, Br−, and I−, respectively. Ordered shell structures with high stability were found for the clusters of Cl−, Br−, and I− with n=9, 9, and 12. This special stability is reflected in the intensity distribution of the clusters in the mass spectra. Larger anion–acetonitrile clusters have the molecules beyond the first solvation layer packed in a small droplet which is attached to the first layer. It is suggested that in general, anions solvated in large clusters of polar solvents, might be located close to their surface

Mobility of stretched water

To study the mobility of stretched SPC/E water and its dependence on temperature and density, five molecular dynamics computer simulation runs were performed. Three runs were performed at temperature 300 K and densities 1.0, 0.9, and 0.8 g/cc. Two more runs were performed at temperature 273 K and densities 1.0 and 0.9 g/cc. At temperature 300 K, the translational diffusion coefficient of the stretched SPC/E water increased with the stretch, at temperature 273 K the translational diffusion decreased with the stretch. This behavior is correlated with the observed changes in the hydrogen bonding pattern of water.To study the mobility of stretched SPC/E water and its dependence on temperature and density, five molecular dynamics computer simulation runs were performed. Three runs were performed at temperature 300 K and densities 1.0, 0.9, and 0.8 g/cc. Two more runs were performed at temperature 273 K and densities 1.0 and 0.9 g/cc. At temperature 300 K, the translational diffusion coefficient of the stretched SPC/E water increased with the stretch, at temperature 273 K the translational diffusion decreased with the stretch. This behavior is correlated with the observed changes in the hydrogen bonding pattern of water

Shock Wave-Induced Damage of a Protein by Void Collapse

In this study, we report on a series of molecular dynamics simulations that were used to examine the effects of shock waves on a membrane-bound ion channel. A planar shock wave was found to compress the ion channel upon impact, but the protein geometry resembles the crystal structure as soon as the solvent density begins to dissipate. When a void was placed in close proximity to the membrane, the shock wave proved to be more destructive to the protein due to formation of a nanojet that results from the asymmetric collapse of the void. The nanojet was able to cause significant structural changes to the protein even at low piston velocities that are not able to directly cause poration of the membrane

Structure of Dipalmitoylphosphatidylcholine/Cholesterol Bilayer at Low and High Cholesterol Concentrations: Molecular Dynamics Simulation

By using molecular dynamics simulation technique we studied the changes occurring in membranes constructed of dipalmitoylphosphatidylcholine (DPPC) and cholesterol at 8:1 and 1:1 ratios. We tested two different initial arrangements of cholesterol molecules for a 1:1 ratio. The main difference between two initial structures is the average number of nearest-neighbor DPPC molecules around the cholesterol molecule. Our simulations were performed at constant temperature (T = 50 degrees C) and pressure (P = 0 atm). Durations of the runs were 2 ns. The structure of the DPPC/cholesterol membrane was characterized by calculating the order parameter profiles for the hydrocarbon chains, atom distributions, average number of gauche defects, and membrane dipole potentials. We found that adding cholesterol to membranes results in a condensing effect: the average area of membrane becomes smaller, hydrocarbon chains of DPPC have higher order, and the probability of gauche defects in DPPC tails is lower. Our results are in agreement with the data available from experiments