Using the molecular dynamics simulations with separate thermostats for translational and rotational degrees of freedom, we investigate the effects of water’s rotational motion on the interaction among Lennard–Jones solutes. The situation with rotational temperature higher than the translational one (Tr ) Tt) is mimicking the effects of microwaves on model solutions. Molecular dynamics simulations suggest that solutions of Lennard–Jones solutes become increasingly more structured with the rise in Tr, while keeping the Tt constant. This is evidenced by an increase of the first and the second peak of the solute–solute radial distribution function. In addition, the first peak moves toward slightly larger distances; the effect seems to be caused by the destabilization of water molecules in the first hydration shell around hydrophobic solutes. More evidence of strong effects of the rotationally excited water is provided by the simulations of short hydrophobic polymers, which upon an increase in Tr assume more compact conformations. In these simulations, we see the re-distribution of water molecules, which escape from hydrophobic “pockets” to better solvate the solvent exposed monomers.
COBISS.SI-ID: 1536690627
We employed molecular dynamics simulations with separate thermostats for translational and rotational temperatures in order to study the effects of these degrees of freedom on the hydration of ions. In this work we examine how water models, differing in charge distribution, respond to the rise of rotational temperature. The study shows that, with respect to the distribution of negative charge, popular water models lead to different responses upon an increase of the rotational temperature. The differences arise in hydration of cations, as the negative charge distribution on the model solvent represents the determining factor in such cases. The cation-water correlation increases with the increasing rotational temperature if negative charge is placed in (or close to) the centre of the water molecule (a typical example is the SPC water model) and decreases, when the negative charge is shifted from the centre (as in the TIP5P model of water). Because all the water models examined here have similar distributions of positive charge, they all exhibit similar trends in solvation of anions. In contrast to above, the effect of translational temperature variation is similar for all water-solute pairs; any increase in translational temperature decreases the solute-water correlations.
COBISS.SI-ID: 1536357059
Enzymes are one of the most important groups of drug targets, and identifying possible ligand-enzyme interactions is of major importance in many drug discovery processes. Novel computational methods have been developed that can apply the information from the increasing number of resolved and available ligand-enzyme complexes to model new unknown interactions and therefore contribute to answer open questions in the field of drug discovery like the identification of unknown protein functions, chemical carcinogenesis, off-target binding, ligand 3D homology modeling and induced-fit simulations.
COBISS.SI-ID: 5782298