New solvation free energy function comprising intermolecular solvation and intramolecular self-solvation terms.
New solvation free energy function comprising intermolecular solvation and intramolecular self-solvation terms.
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DOI：
10.1186/1758-2946-5-8
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发表时间：
2013-02-04
影响因子：
8.6
通讯作者：
Park H
中科院分区：
文献类型：
--
作者：
Choi H;Kang H;Park H
溶剂化自由能是估算分子的各种物理化学性质及其与大分子受体结合所需的解溶成本的一个基本热力学参数。本文通过对溶剂-接触模型的改进，提出了一个新的溶剂化自由能函数，并测试了它在估算不同尺寸和形状有机分子的溶剂化自由能中的适用性。这个新的溶剂化自由能函数是通过将现有的溶质-溶剂相互作用项与反映分子内相互作用对溶剂化影响的自溶剂化项相结合而构造的。在该溶剂化模型中需要确定四种原子参数：原子碎裂体积、原子最大占有率、原子溶剂化和原子自溶剂化参数。用标准遗传算法对共37种原子的所有这些参数进行了优化，使362个有机分子的实验溶剂化自由能与由溶剂化自由能函数计算的自由能之差最小。由新的溶剂化模型计算的溶剂化自由能与实验结果吻合较好，训练集和测试集的相关系数平方分别为0.88和0.85。因此，本溶剂化模型有望用于估算有机分子的溶剂化自由能。
Solvation free energy is a fundamental thermodynamic quantity that should be determined to estimate various physicochemical properties of a molecule and the desolvation cost for its binding to macromolecular receptors. Here, we propose a new solvation free energy function through the improvement of the solvent-contact model, and test its applicability in estimating the solvation free energies of organic molecules with varying sizes and shapes. This new solvation free energy function is constructed by combining the existing solute-solvent interaction term with the self-solvation term that reflects the effects of intramolecular interactions on solvation. Four kinds of atomic parameters should be determined in this solvation model: atomic fragmental volume, maximum atomic occupancy, atomic solvation, and atomic self-solvation parameters. All of these parameters for total 37 atom types are optimized by the operation of a standard genetic algorithm in such a way to minimize the difference between the experimental solvation free energies and those calculated by the solvation free energy function for 362 organic molecules. The solvation free energies estimated from the new solvation model compare well with the experimental results with the associated squared correlation coefficients of 0.88 and 0.85 for training and test sets, respectively. The present solvation model is thus expected to be useful for estimating the solvation free energies of organic molecules.
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DOI：
10.1093/protein/4.8.903
发表时间：
1991-12-01
期刊：
PROTEIN ENGINEERING
影响因子：
--
作者：
MEHLER, EL;SOLMAJER, T
通讯作者：
SOLMAJER, T
影响因子：
5.5
作者：
Corbeil, Christopher R.;Sulea, Traian;Purisima, Enrico O.
通讯作者：
Purisima, Enrico O.
影响因子：
15
作者：
Genheden, Samuel;Mikulskis, Paulius;Ryde, Ulf
通讯作者：
Ryde, Ulf
影响因子：
4.4
作者：
JORGENSEN, WL;CHANDRASEKHAR, J;KLEIN, ML
通讯作者：
KLEIN, ML
影响因子：
3.3
作者：
Chang, Jaeeon;Lenhoff, Abraham M.;Sandler, Stanley I.
通讯作者：
Sandler, Stanley I.