نتایج جستجو برای: solvation energy
تعداد نتایج: 669961 فیلتر نتایج به سال:
We present PAFMPB, an updated and parallel version of the AFMPB software package for fast calculation of molecular solvation-free energy. The new version has the following new features: (1) The adaptive fast multipole method and the boundary element methods are parallelized; (2) A tool is embedded for automatic molecular VDW/SAS surface mesh generation, leaving the requirement for a mesh file a...
We address the response of a random heteropolymer to preferential solvation of certain monomer types at the globule-solvent interface. For each set of monomers that can comprise the molecule's surface, we represent the ensemble of allowed configurations by a Gaussian distribution of energy levels, whose mean and variance depend on the set's composition. Within such a random energy model, mean s...
We employ the entire experimentally determined protein structure for the KcsA potassium channel from Streptomyces lividans in molecular dynamics calculations to observe hydrated channel protein structure, ion solvation, selectivity, multiple ion configurations, and diffusion. Free energy perturbation calculations display a significant ion discrimination of ;9 kT in favor of the larger K ion. Th...
The water solubility of salts is ordinarily dictated by lattice energy and ion solvation. However, in the case of low melting salts also known as ionic liquids, lattice energy is immaterial and differences in hydrophobicity largely account for differences in their water solubility. In this contribution, the activity coefficients of ionic liquids in water are split into cation and anion contribu...
In the first part of this paper I review the understanding of anomalous properties of water in terms of particles interacting by core-softened potentials. I discuss the origin of the bulk anomalies in terms of the two different configurations of neighbor particles: low energy–high volume and high energy–low volume. In the second part I study some anomalies of water under strong spatial confinem...
The free energy of solvation, DeltaGS0, in octanol of organic compounds is quantitatively predicted from the molecular structure. The model, involving only three molecular descriptors, is obtained by multiple linear regression analysis from a data set of 147 compounds containing diverse organic functions, namely, halogenated and non-halogenated alkanes, alkenes, alkynes, aromatics, alcohols, al...
A new theory of solutions, the method of energy representation, is introduced by adopting the solute-solvent interaction energy as the coordinate of distribution functions. The density-functional theory is formulated over the energy coordinate, and an approximate functional for the solvation free energy is given in terms of energy distribution functions in the solution and reference solvent sys...
Free energy calculations based on molecular dynamics (MD) simulations have seen a tremendous growth in the last decade. However, it is still difficult and tedious to set them up in an automated manner, as the majority of the present-day MD simulation packages lack that functionality. Relative free energy calculations are a particular challenge for several reasons, including the problem of findi...
Objective(s): First principles calculations were performed to study four multiple sclerosis drugs namely, Ampyra, Fingolimod, Mitoxantrone and Eliprodil in gas and liquid phases using Density Functional Theory (DFT). Computational chemistry simulations were carried out to compare calculated quantum chemical parameters for Ampyra, Fingolimod, Mitoxantrone and Eliprodil. Materials and Methods: Al...
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