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

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)]

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

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

A molecular dynamics study of the early stages of amyloid-β(1-42) oligomerization: The role of lipid membranes

As research progresses towards understanding the role of the amyloid-β (Aβ) in Alzheimer’s disease, certain aspects of the aggregation process for Aβ are still not clear. In particular, the accepted constitution of toxic aggregates in neurons has shifted towards small oligomers. However, the process of forming these oligomers in cells is still not fully clear. Even more interestingly, it has been implied that cell membranes, and, in particular, anionic lipids within those membranes, play a key role in the progression of Aβ aggregation, but the exact nature of the Aβ-membrane interaction in this process is still unknown. In this work, we use a thermodynamic cycle and umbrella sampling molecular dynamics to investigate dimerization of the 42-residue Aβ peptide on model zwitterionic dipalmitoylphosphatidylcholine (DPPC) or model anionic dioleoylphosphatidylserine (DOPS) bilayer surfaces. We determined that Aβ dimerization was strongly favored through interactions with the DOPS bilayer. Further, our calculations showed that the DOPS bilayer promoted strong protein-protein interactions within the Aβ dimer, while DPPC favored strong protein-lipid interactions. By promoting dimer formation and subsequent dimer release into the solvent, the DOPS bilayer acts as a catalyst in Aβ aggregation through converting Aβ monomers in solution into Aβ dimers in solution without substantial a free energy cost

Interaction Between Amyloid-

The amyloid