A generalized G-SFED continuum solvation free energy calculation model
- Authors
- Lee, Sehan; Cho, Kwang-Hwi; Kang, Young-Mook; Scheraga, Harold A.; No, Kyoung Tai
- Issue Date
- 19-Feb-2013
- Publisher
- NATL ACAD SCIENCES
- Keywords
- implicit solvent; macromolecules; linear time
- Citation
- PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, v.110, no.8, pp.E662 - E667
- Journal Title
- PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Volume
- 110
- Number
- 8
- Start Page
- E662
- End Page
- E667
- URI
- http://scholarworks.bwise.kr/ssu/handle/2018.sw.ssu/11342
- DOI
- 10.1073/pnas.1221940110
- ISSN
- 0027-8424
- Abstract
- An empirical continuum solvation model, solvation free energy density (SFED), has been developed to calculate solvation free energies of a molecule in the most frequently used solvents. A generalized version of the SFED model, generalized-SFED (G-SFED), is proposed here to calculate molecular solvation free energies in virtually any solvent. G-SFED provides an accurate and fast generalized framework without a complicated description of a solution. In the model, the solvation free energy of a solute is represented as a linear combination of empirical functions of the solute properties representing the effects of solute on various solute-solvent interactions, and the complementary solvent effects on these interactions were reflected in the linear expansion coefficients with a few solvent properties. G-SFED works well for a wide range of sizes and polarities of solute molecules in various solvents as shown by a set of 5,753 solvation free energies of diverse combinations of 103 solvents and 890 solutes. Octanol-water partition coefficients of small organic compounds and peptides were calculated with G-SFED with accuracy within 0.4 log unit for each group. The G-SFED computation time depends linearly on the number of nonhydrogen atoms (n) in a molecule, O(n).
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