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Abstract: Nucleic acids are highly charged biopolymers whose secondary structure is strongly dependent on electrostatic interactions. Solvent molecules and ions are also believed to play an important role in mediating [...]

The constant pressure constant temperature molecular dynamics simulations at ambient conditions were carried out to evaluate three different potential models for dimethyl sulfoxide (DMSO), both as pure liquid and in the (1:3) DMSO-H2O mixture, based on structural, thermodynamical and dynamical properties. It helps to reveal the spatial solvation structure and topological features in the 1:3 molar mixture of dimethyl sulfoxide and water.

Research was conducted to examine the diffusional mobility of water, Cs and Li counterions in oriented DNA fibers using NMR self-diffusion calculations as a function of varying water content and salt concentration. A detailed study of the hydration structure and the counterion coordination was carried out based on the molecular dynamics simulation trajectories. Simulation and experimental results are in agreement that Li ion diffusion is considerably slower than the Cs ion diffusion.

Molecular dynamics (MD) simulation is used for the analysis of NMR dipolar couplings in a bilayer formed by dimyristoylphosphatidylcholine (DMPC). The results have shown that the additive potential (AP) model and the maximum entropy (ME) method (APME) is a good tool for interpreting the results in bilayers, liquid crystals and other complex chemical systems.

The structural and dynamical properties of dimyristoylphosphatidylcholine lipid bilayers at different levels of hydration and temperatures are studied by using a series of molecular dynamics simulations. The dynamical properties such as lipid diffusion and relaxation of reorientation time correlation functions are found to become slower with the removal of water.

Car-Parrinello molecular dynamics simulations of a hydroxyl radical in liquid water are performed where the structural and dynamical properties of the solvated structure are studied in detail. Results reveal that the partial atom-atom radial distribution functions for the hydrated hydroxyl do not show drastic differences with the radial distributed functions for liquid water.

Water clusters, formed on the aqueous ions OH(super -) and H3O(super O+) are investigated using the molecular dynamics simulation method and the temperature dependence of various cluster properties is studied from 150 to 300 K. The nucleation barrier is found to be lower for clusters around hydronium ion than those formed around the hydroxyl ions on the bases of work-of-cluster formation and its size dependent.

An expanded ensemble method provides a way to calculate solvation free energies and the partition coefficients for typical and complex drug structures based on atomistic molecular dynamic simulations. The expanded ensemble technique, implemented within molecular dynamic scheme, is adapted to treat molecules and the solvation free energy of organic solute molecules is found to be sensitive.

MD simulations of neat liquid tert-butyl alcohol (TBA) are done with two different potential models constructed for TBA: a simple rigid three-site model and a fully flexible all-atom 15-site model. The 15-site model is found to be superior, providing reasonable agreement with experimentally derived data, while the three-site model is only able to reproduce qualitatively the competitive hydrophobic and hydrophilic aspects of the intermolecular interactions.

MD simulations of tert-butyl alcohol(TBA) dissolved in water are carried out. The hydration structure of both simple rigid three-site model and the flexible all-atom 15-site model of TBA is seen to be different from that of methanol, so the steric bulk of a tert-butyl group can have large, though indirect, effect on hydrogen bonding is indicated.

The Monte Carlo approach with the approximation of a dielectric continuum and radii of the small ions obtained from modeling of simple electrolyte solutions can give a reason for the selectivity of DNA for Li+, Na+ and K+ in oriented DNA fibers.