The thermodynamic properties of a selected set of benchmark hydrogen-bonded systems (acetic acid dimer and the complexes of acetic acid with acetamide and methanol) was studied with the goal of obtaining detailed information on solvent effects on the hydrogen-bonded interactions using water, chloroform, and n-heptane as representatives for a wide range in the dielectric constant. Solvent effect...

To understand the nonexponential relaxation associated with solvation dynamics in the ionic liquid 1-ethyl-3-methylimidazolium hexafluorophosphate, we study power spectra of the fluctuating Franck-Condon energy gap of a diatomic probe solute via molecular dynamics simulations. Results show 1f dependence in a wide frequency range over 2-3 decades, indicating distributed relaxation times. We anal...

The hydration of biomolecules is vitally important in molecular biology, so in this paper thesolvation energy and radial distribution function of DNA bases have been calculated by theMonte Carlo simulation.The geometries of isolated Adenine, Guanine, Cytosine, and Thyminehave been optimized using 6-31+G(d,p) basis function sets. These geometries then will be used inthe Monte Carlo calculation o...

A new method for calculating the total conformational free energy of proteins in water solvent is presented. The method consists of a relatively brief simulation by molecular dynamics with explicit solvent (ES) molecules to produce a set of microstates of the macroscopic conformation. Conformational energy and entropy are obtained from the simulation, the latter in the quasi-harmonic approximat...

The interface between the vapor and liquid phase of quadrupolar-dipolar fluids is the seat of an electric interfacial potential whose influence on ion solvation and distribution is not yet fully understood. To obtain further microscopic insight into water specificity we first present extensive classical molecular dynamics simulations of a series of model liquids with variable molecular quadrupo...

Using’the concepts of scaled particle theory, an analytical theory is developed to investigate the limiting behavior of solvation free energies at the particle creation limit. The new theory directly incorporates the weakly attractive, dispersion interaction terms into the analytical calculations. For neutral molecular systems, the effects of longer ranged electrostatic interactions are also in...

A model is described which explains drag reduction (DR) in dilute polymer solutions in terms of solvation of macromolecular chains and formation of relatively stable domains. The domains partly suppress the vortex formation, act as energy sinks, and also play a role in mechanical degradation in flow (MDF). We report ultrasonically determined solvation numbers for a series of copolymers with the...

We implement a well-established concept to consider dispersion effects within a PoissonBoltzmann approach of continuum solvation of proteins. The theoretical framework is particularly suited for boundary element methods. Free parameters are determined by comparison to experimental data as well as high level Quantum Mechanical reference calculations. The method is general and can be easily exten...

The temperature and length scale dependence of solvation properties of spherical hard solvophobic solutes is investigated in the Jagla liquid, a simple liquid that consists of particles interacting via a spherically symmetric potential combining a hard core repulsion and a longer ranged soft core interaction, yet exhibits water-like anomalies. The results are compared with equivalent calculatio...

The expulsion of water from surfaces upon molecular recognition and nonspecific association makes a major contribution to the free energy changes of these processes. In order to facilitate the characterization of water structure and thermodynamics on surfaces, we have incorporated Grid Inhomogeneous Solvation Theory (GIST) into the CPPTRAJ toolset of AmberTools. GIST is a grid-based implementat...