H-bond Lifetimes Research Articles

Molecular dynamics study of hydrated imogolite : 2. Structure and dynamics of confined water

The behaviour of water confined in an imogolite nanotube was studied by means of molecular dynamics simulations. The results of the study show an important difference between the interaction of water molecules with the internal and external surfaces of the nanotube. The analysis of the density profiles of confined molecules, of their spatial organisation, of the size of molecular clusters, of the lifetime of H-bonds in the system and of dynamical characteristics of molecules permits us to qualify the external imogolite surface as hydrophobic, whereas the internal surface reveals a hydrophilic character.

Effect of Temperature, Pressure, and Cosolvents on Structural and Dynamic Properties of the Hydration Shell of SNase: A Molecular Dynamics Computer Simulation Study

It is now generally agreed that the hydration water and solvational properties play a crucial role in determining the dynamics and hence the functionality of proteins. We present molecular dynamics computer simulation studies on staphylococcal nuclease (SNase) at various temperatures and pressures as well as in different cosolvent solutions containing various concentrations of urea and glycerol. The aim is to provide a molecular level understanding of how different types of cosolvents (chaotropic and kosmotropic) as well as temperature and high hydrostatic pressure modify the structure and dynamics of the hydration water. Taken together, these three intrinsic thermodynamic variables, temperature, pressure, and chemical potential (or activity) of the solvent, are able to influence the stability and function of the protein by protein-solvent dynamic coupling in different ways. A detailed analysis of the structural and dynamical properties of the water and cosolvents at the protein surface (density profile, coordination numbers, hydrogen-bond distribution, average H-bond lifetimes (water-protein and water-water), and average residence time of water in the hydration shell) was carried out, and differences in the structural and dynamical properties of the hydration water in the presence of the different cosolvents and at temperatures between 300 and 400 K and pressures up to 5000 bar are discussed. Furthermore, the results obtained help understand various thermodynamic properties measured for the protein.

The topological and dynamic characteristics of H-bond networks in water according to computer simulation results

The classic molecular dynamics methods were employed to calculate the topological and dynamic characteristics of H-bond networks in water with the use of various model potentials. The explicit inclusion of specific intermolecular interactions between oxygen and hydrogen atoms additionally stabilized tetrahedrally coordinated molecules and, as a consequence, increased their number in the system. The lifetimes of H-bonds were found to characterize high correlation of movements of nearest environment molecules.

New model pair potential for water. Effect of inclusion of specific O⋯H interactions on the topology and dynamics of the hydrogen-bond network

Classical molecular dynamics was used to calculate the topologic and dynamic characteristics of H-bond networks in water, using various model potentials. The explicit inclusion of intermolecular interactions of oxygen and hydrogen atoms leads to a model involving additional stabilization of tetrahedrally coordinated molecules and, as a consequence, increased number of such molecules in the system. The H-bond lifetimes point to a strongly correlated molecular motion in the immediate environment.

Car–Parrinello molecular dynamics on the S N2 reaction Cl −+CH 3Br in water

The results of the analysis of ab initio molecular dynamics simulations of the transition state of a bimolecular nuclear substitution reaction in water are discussed and a lower limit for the life-time of the hydrogen bonded interactions between the halogens and the surrounding water molecules is estimated. A new function is introduced to compute a lower estimate of the H-bond life-time and compared with the results of the traditional one.

Molecular dynamics simulations of DNA oligomers under various electrostatic parameters

The modelling program AMBER 3.0 has been used to generate molecular dynamics trajectories of d(A-T) and dA-dT oligomers. The simulations were done without explicit solvent molecules but with two different dielectric functions (e(r) = 4r and a sigmoidal distance-dependent dielectric function e(r) = e cal ) as well as with and without derivation of the additional distance-dependence introduced. Best comparisons between experimental (Raman, NMR, X-ray data) and calculated results are obtained with the c dielectric function with derivation of the distance-dependence of the dielectric function. Thus, the pseudorotation phases of the adenine residues are systematically higher (around C 2’ -endo) than those of the thymine residues (close to O 4’ -endo). Also, depending on the dielectric function, the lifetimes of the Watson-Crick H-bonds are 10 to 50 times longer than those of the three-centered H-bonds in the major groove of dA-dT.