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使用 SM8、SM8AD 和 SMD 溶剂化模型预测 SAMPL2 水溶剂化自由能和互变异构体比例。

Prediction of SAMPL2 aqueous solvation free energies and tautomeric ratios using the SM8, SM8AD, and SMD solvation models.

机构信息

Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455-0431, USA.

出版信息

J Comput Aided Mol Des. 2010 Apr;24(4):317-33. doi: 10.1007/s10822-010-9333-9. Epub 2010 Apr 1.

Abstract

We applied the solvation models SM8, SM8AD, and SMD in combination with the Minnesota M06-2X density functional to predict vacuum-water transfer free energies (Task 1) and tautomeric ratios in aqueous solution (Task 2) for the SAMPL2 test set. The bulk-electrostatic contribution to the free energy of solvation is treated as follows: SM8 employs the generalized Born model with the Coulomb field approximation, SM8AD employs the generalized Born approximation with asymmetric descreening, and SMD solves the nonhomogeneous Poisson equation. The non-bulk-electrostatic contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell is treated as a sum of terms that are products of geometry-dependent atomic surface tensions and solvent-accessible surface areas of the individual atoms of the solute. On average, three models tested in the present work perform similarly. In particular, we achieved mean unsigned errors of 1.3 (SM8), 2.0 (SM8AD), and 2.6 kcal/mol (SMD) for the aqueous free energies of 30 out of 31 compounds with known reference data involved in Task 1 and mean unsigned errors of 2.7 (SM8), 1.8 (SM8AD), and 2.4 kcal/mol (SMD) in the free energy differences (tautomeric ratios) for 21 tautomeric pairs in aqueous solution involved in Task 2.

摘要

我们应用溶剂化模型 SM8、SM8AD 和 SMD 结合 Minnesota M06-2X 密度泛函来预测 SAMPL2 测试集中的真空-水转移自由能(任务 1)和水溶液中的互变异构体比例(任务 2)。溶剂化自由能的体静电贡献如下处理:SM8 采用具有库仑场近似的广义 Born 模型,SM8AD 采用具有不对称去屏蔽的广义 Born 近似,SMD 求解非均匀泊松方程。第一个溶剂化壳层中溶质和溶剂分子之间的短程相互作用产生的非体静电贡献被处理为项的总和,这些项是溶质各个原子的几何相关原子表面张力和溶剂可及表面积的乘积。平均而言,本工作中测试的三个模型表现相似。特别是,我们在任务 1 中涉及的 31 种已知参考数据的 30 种化合物的水溶液自由能中获得了 1.3(SM8)、2.0(SM8AD)和 2.6 kcal/mol(SMD)的平均无偏差误差,在任务 2 中涉及的 21 种互变异构对在水溶液中的自由能差异(互变异构体比例)中获得了 2.7(SM8)、1.8(SM8AD)和 2.4 kcal/mol(SMD)的平均无偏差误差。

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