Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability.
Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability.
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DOI：
10.1021/jp112133g
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发表时间：
2011-03-31
影响因子：
3.3
通讯作者：
Duan, Yong
中科院分区：
文献类型：
--
作者：
Wang, Junmei;Cieplak, Piotr;Li, Jie;Hou, Tingjun;Luo, Ray;Duan, Yong
在这项工作中，四种类型的极化模型已被开发用于计算原子电荷和诱导点偶极子之间的相互作用。这些模型包括Applequist模型、Thole线性模型、Thole指数模型和Thole Tinker-like模型。极化率模型已被优化，以重现实验的静态分子极化率从分子折射测量上的一组420个分子的Bosque和销售报告。我们根据相互作用类型将模型分为五组，即形成键的两个原子的相互作用，键角和二面角是否被关闭或缩小。当1-2（键合），1-3（由两个键分开）相互作用关闭和/或1-4（由三个键分开）相互作用按比例缩小时，包括Applequist模型在内的所有模型都实现了类似的性能：平均百分比误差（APE）范围为1.15%至1.23%，平均无符号误差（AUE）范围为0.143至0.158 μ 3。当考虑短程1-2、1-3和全1-4项时（D组模型），三个Thole模型的APE范围为1.30%至1.58%，而Applequist模型（DA）的APE显著更大（3.82%）。三个Thole模型的AUE范围从0.166到0.196 3，而Applequist模型的AUE为0.446 3。使用70-分子货车Duijnen和Swart数据集的进一步评估清楚地表明，开发的模型是准确的和高度可转移的，并且实际上比使用该特定数据集开发的模型（集合E模型）更准确。A、B和C模型组明显比D和E模型组更准确的事实强烈地表明，包括1-2和1-3相互作用降低了可转移性和准确性。
In this work, four types of polarizable models have been developed for calculating interactions between atomic charges and induced point dipoles. These include the Applequist, Thole linear, Thole exponential model, and the Thole Tinker-like. The polarizability models have been optimized to reproduce the experimental static molecular polarizabilities obtained from the molecular refraction measurements on a set of 420 molecules reported by Bosque and Sales. We grouped the models into five sets depending on the interaction types, i.e. whether the interactions of two atoms that form bond, bond angle and dihedral angle are turned off or scaled down. When 1-2 (bonded), 1-3 (separated by two bonds) interactions are turned off and/or 1-4 (separated by three bonds) interactions are scaled down, all the models including the Applequist model achieved similar performance: the average percentage errors (APE) ranges from 1.15% to 1.23%, and The average unsigned errors (AUE) ranges from 0.143 to 0.158 Å3. When the short-range 1-2, 1-3 and full 1-4 terms are taken into account (Set D models), the APE ranges from 1.30% to 1.58% for the three Thole models whereas the Applequist model (DA) has a significantly larger APE (3.82%). The AUE ranges from 0.166 to 0.196 Å3 for the three Thole models, compared to 0.446 Å3 for the Applequist model. Further assessement using the 70-molecule van Duijnen and Swart data set clearly showed that the developed models are both accurate and highly transferable and are in fact more accurate than the models developed using this particular data set (Set E models). The fact that A, B, and C model sets are notably more accurate than both D and E model sets strongly suggests that the inclusion of 1-2 and 1-3 interactions reduces the transferability and accuracy.
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影响因子：
3
作者：
Cieplak, P;Caldwell, J;Kollman, P
通讯作者：
Kollman, P
影响因子：
3
作者：
BROOKS, BR;BRUCCOLERI, RE;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
15
作者：
APPLEQUIST, J;CARL, JR;FUNG, KK
通讯作者：
FUNG, KK
DOI：
10.1073/pnas.91.10.4436
发表时间：
1994-05-10
影响因子：
11.1
作者：
BOWIE, JU;EISENBERG, D
通讯作者：
EISENBERG, D
影响因子：
2.9
作者：
Kaminski, GA;Stern, HA;Friesner, RA
通讯作者：
Friesner, RA