Introducing Charge Hydration Asymmetry into the Generalized Born Model.
Introducing Charge Hydration Asymmetry into the Generalized Born Model.
复制标题
将电荷水合不对称引入广义诞生模型。
DOI：
10.1021/ct4010917
复制
发表时间：
2014-04-08
影响因子：
5.5
通讯作者：
Onufriev, Alexey V.
中科院分区：
文献类型：
--
作者：
Mukhopadhyay, Abhishek;Aguilar, Boris H.;Tolokh, Igor S.;Onufriev, Alexey V.
电荷水化不对称性(CHA)--溶剂化自由能不变对溶质电荷反转的影响--在标准的线性响应连续静电学中被忽略了。提出的电荷水化不对称广义Born(CHA-GB)近似将这一效应引入到流行的广义Born(GB)模型中。通过分析修正将CHA添加到GB方程中，该分析修正量化了给定水模型的CHA的具体倾向；后者由水模型中的电荷分布确定。在显式水(TIP3P、TIP4P-Ew和TIP5P-E)自由能计算中，CHA的显著变化由CHA-GB紧密复制，其精度类似于SEA和3D-RISM等模型，超出了线性响应。与参考显式(TIP3P)静电溶剂化自由能相比，CHA-GB在精度上比标准GB提高了约40%，对248个刚性小中性分子(CHA-GB的均方根误差为0.88千卡/摩尔，国标为1.24千卡/摩尔)和48个氨基酸类似物的构象(RMSE=0.81千卡/摩尔比1.26千卡/摩尔)进行了测试。CHA-GB采用了一种新的介电边界定义，该定义没有将CHA效应包含在固有原子半径中。该策略导致找到一组新的针对CHA-GB优化的固有原子半径；与针对GB优化的半径集相比，这些半径显示出随原子类型的物理意义的变化。与原GB模型中常用的几种半径集相比，新的半径集在不同类别的分子间表现出更好的可转换性。
The effect of charge hydration asymmetry (CHA)—non-invariance of solvation free energy upon solute charge inversion—is missing from the standard linear response continuum electrostatics. The proposed charge hydration asymmetric–generalized Born (CHA–GB) approximation introduces this effect into the popular generalized Born (GB) model. The CHA is added to the GB equation via an analytical correction that quantifies the specific propensity of CHA of a given water model; the latter is determined by the charge distribution within the water model. Significant variations in CHA seen in explicit water (TIP3P, TIP4P-Ew, and TIP5P-E) free energy calculations on charge-inverted “molecular bracelets” are closely reproduced by CHA–GB, with the accuracy similar to models such as SEA and 3D-RISM that go beyond the linear response. Compared against reference explicit (TIP3P) electrostatic solvation free energies, CHA–GB shows about a 40% improvement in accuracy over the canonical GB, tested on a diverse set of 248 rigid small neutral molecules (root mean square error, rmse = 0.88 kcal/mol for CHA–GB vs 1.24 kcal/mol for GB) and 48 conformations of amino acid analogs (rmse = 0.81 kcal/mol vs 1.26 kcal/mol). CHA–GB employs a novel definition of the dielectric boundary that does not subsume the CHA effects into the intrinsic atomic radii. The strategy leads to finding a new set of intrinsic atomic radii optimized for CHA–GB; these radii show physically meaningful variation with the atom type, in contrast to the radii set optimized for GB. Compared to several popular radii sets used with the original GB model, the new radii set shows better transferability between different classes of molecules.
登录
查看更多内容
影响因子：
2.7
作者：
De Castro, LFP;Zacharias, M
通讯作者：
Zacharias, M
影响因子：
15
作者：
Amaro RE;Cheng X;Ivanov I;Xu D;McCammon JA
通讯作者：
McCammon JA
影响因子：
5.5
作者：
Felts, Anthony K.;Gallicchio, Emilio;Levy, Ronald M.
通讯作者：
Levy, Ronald M.
影响因子：
3
作者：
Feig, M;Onufriev, A;Brooks, CL
通讯作者：
Brooks, CL
影响因子：
4.4
作者：
Dzubiella, J;Hansen, JP
通讯作者：
Hansen, JP