the molecular geometry of complex of adenine with 8 water molecules was calculated with hartree-fock (hf). the standard 6-31g(d) basis set has been employed. the existence of c-h…o hydrogen bonds between the water molecules and the hydrophobic part of nucleobase is stablished. we optimized structures and computed interaction energies of all complexes of adenine with water molecules step by step...

The molecular geometry of complex of adenine with 8 water molecules was calculated with Hartree-Fock (HF). The standard 6-31G(d) basis set has been employed. The existence of C-H…O Hydrogen bonds between the water molecules and the hydrophobic part of nucleobase is stablished. We optimized structures and computed interaction energies of all complexes of adenine with water molecules step by step...

Raman spectroscopy is used to probe the nature of the hydrogen bonds which hold the water of hydration to DNA. The ∼ 3450 cm(-1) molecular O-H stretching mode shows that the first six water molecules per base pair of the primary hydration shell are very strongly bound to the DNA. The observed shift in the peak position of this mode permits a determination of the length of the hydrogen bonds for...

The heat capacities of hydration (∆Cp) of the first four of the linear alkane series, methane, ethane, propane, and butane, were calculated by a combination of Monte Carlo simulations and the random network model (RNM) of water. The contribution from the water-water interaction and the solute-water interaction accounted for about 45% and 20%, respectively, of the experimental values. The water-...

We have studied the hydration and diffusion of the hydroxyl radical OH0 in water using classical molecular dynamics. We report the atomic radial distribution functions, hydrogen-bond distributions, angular distribution functions, and lifetimes of the hydration structures. The most frequent hydration structure in the OH0 has one water molecule bound to the OH0 oxygen (57% of the time), and one w...

The energetics of water proximal to apolar groups is analyzed from a statistical perspective in the realistic context of polypeptide hydration. Analysis of a series of molecular dynamics simulations of a 16-residue polypeptide in water reveals a correlation between hydrogen bond energy and local packing when there is overcoordination of the water molecules around hydrogen bonds. We show that th...

A theoretical study of vibrational spectral diffusion in aqueous NaBr solutions is presented by means of ab initio molecular dynamics simulations and time series analysis. The OD stretch frequencies of deuterated water hydrogen bonded to the bromide ions are found to be higher than those in the bulk which implies a somewhat weaker Br–water hydrogen bonds than those between water molecules. The ...

The mechanism for the hydration of CO2 within a Keplerate nanocapsule is presented. A network of hydrogen bonds across the water layers in the first metal coordination sphere facilitates the proton abstraction and nucleophilic addition of water. The highly acidic properties of the polyoxometalate cluster are crucial for explaining the catalysed hydration.

Molecular dynamics (MD) simulation of the Mg/Al (3:1) layered double hydroxide (LDH), hydrotalcite (HT), containing citrate, C6H5O7(3-), as the charge balancing interlayer anion provides new molecular scale insight into the interlayer structure, hydrogen bonding, and energetics of the hydration and consequent swelling of LDH compounds containing organic and biomolecules. Citrate-HT exhibits aff...

We present results of molecular dynamics simulations of water confined in a silica pore. A cylindrical cavity is created inside a vitreous silica cell with geometry and size similar to the pores of real Vycor glass. The simulations are performed at different hydration levels. At all hydration levels water adsorbs strongly on the Vycor surface; a double layer structure is evident at higher hydra...