Department of Biotechnology, Yonsei University, Seoul 120-749, Korea.
Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):E662-7. doi: 10.1073/pnas.1221940110. Epub 2013 Feb 1.
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).
一种经验连续溶剂化模型，溶剂化自由能密度（SFED），已被开发用于计算最常用溶剂中分子的溶剂化自由能。本文提出了 SFED 模型的广义版本，广义-SFED（G-SFED），用于计算实际上任何溶剂中分子的溶剂化自由能。G-SFED 提供了一个准确且快速的通用框架，而无需对溶液进行复杂的描述。在该模型中，溶质的溶剂化自由能表示为溶质性质的经验函数的线性组合，这些函数代表溶质对各种溶质-溶剂相互作用的影响，以及对这些相互作用的补充溶剂效应反映在具有少数溶剂性质的线性展开系数中。G-SFED 在各种溶剂中对大小和极性范围广泛的溶质分子都适用良好，这可以通过一组 5753 种不同溶剂和 890 种溶质的溶剂化自由能来证明。用 G-SFED 计算了小分子有机化合物和肽的辛醇-水分配系数，每组的精度在 0.4 对数单位以内。G-SFED 的计算时间与分子中的非氢原子数（n）呈线性关系，即 O(n)。
