Literature DB >> 17030307

Description of hydration free energy density as a function of molecular physical properties.

K T No1, S G Kim, K H Cho, H A Scheraga.   

Abstract

A method to calculate the solvation free energy density (SFED) at any point in the cavity surface or solvent volume surrounding a solute is proposed. In the special case in which the solvent is water, the SFED is referred to as the hydration free energy density (HFED). The HFED is described as a function of some physical properties of the molecules. These properties are represented by simple basis functions. The hydration free energy of a solute was obtained by integrating the HFED over the solvent volume surrounding the solute, using a grid model. Of 34 basis functions that were introduced to describe the HFED, only six contribute significantly to the HFED. These functions are representations of the surface area and volume of the solute, of the polarization and dispersion of the solute, and of two types of electrostatic interactions between the solute and its environment. The HFED is described as a linear combination of these basis functions, evaluated by summing the interaction energy between each atom of the solute with a grid point in the solvent, where each grid point is a representation of a finite volume of the solvent. The linear combination coefficients were determined by minimizing the error between the calculated and experimental hydration free energies of 81 neutral organic molecules that have a variety of functional groups. The calculated hydration free energies agree well with the experimental results. The hydration free energy of any other solute molecule can then be calculated by summing the product of the linear combination coefficients and the basis functions for the solute.

Entities:  

Year:  1999        PMID: 17030307     DOI: 10.1016/s0301-4622(98)00225-7

Source DB:  PubMed          Journal:  Biophys Chem        ISSN: 0301-4622            Impact factor:   2.352


  4 in total

1.  Molecular simulation study of cooperativity in hydrophobic association.

Authors:  C Czaplewski; S Rodziewicz-Motowidło; A Liwo; D R Ripoll; R J Wawak; H A Scheraga
Journal:  Protein Sci       Date:  2000-06       Impact factor: 6.725

2.  Parameterization of an empirical model for the prediction of n-octanol, alkane and cyclohexane/water as well as brain/blood partition coefficients.

Authors:  Mohamed Zerara; Jürgen Brickmann; Robert Kretschmer; Thomas E Exner
Journal:  J Comput Aided Mol Des       Date:  2008-09-26       Impact factor: 3.686

3.  A generalized G-SFED continuum solvation free energy calculation model.

Authors:  Sehan Lee; Kwang-Hwi Cho; Young-Mook Kang; Harold A Scheraga; Kyoung Tai No
Journal:  Proc Natl Acad Sci U S A       Date:  2013-02-01       Impact factor: 11.205

Review 4.  A minireview on the perturbation effects of polar groups to direct nanoscale hydrophobic interaction and amphiphilic peptide assembly.

Authors:  Feiyi Zhang; Lanlan Yu; Wenbo Zhang; Lei Liu; Chenxuan Wang
Journal:  RSC Adv       Date:  2021-08-25       Impact factor: 4.036

  4 in total

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