Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules.
Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules.
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DOI：
10.1021/ct200304d
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发表时间：
2011-10-11
影响因子：
5.5
通讯作者：
Ponder, Jay W.
中科院分区：
文献类型：
--
作者：
Ren, Pengyu;Wu, Chuanjie;Ponder, Jay W.
基于永久原子多极和原子诱导偶极子的经验势被报道用于烷烃、醇、胺、硫化物、醛、羧酸、酰胺、芳烃和其它小有机分子。从气相从头算分子轨道计算得到了原子的永久多极矩到四极矩。货车德瓦尔斯参数通过拟合气相同二聚体QM的能量和结构，以及纯液体的实验密度和汽化热得到。作为验证，与水的气相异二聚体的氢键能和结构的评估使用所得的潜力。对于32个同二聚体和异二聚体，缔合能与从头计算结果一致，在0.4千卡/摩尔。氢键距离与QM优化几何构型的均方根偏差小于0.06 μ m。此外，分子动力学模拟计算的液体自扩散和静态介电常数与实验值一致。力场也被用来计算溶剂化自由能的27个化合物不包括在参数化过程中，与RMS误差为0.69千卡/摩尔。研究结果表明，AMOEBA力场在不同的环境和阶段都表现良好。在静电模型和开发参数的协议所涉及的关键算法进行了详细说明，以方便扩展到其他分子系统。
An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.
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影响因子：
4.1
作者：
BENNETT, CH
通讯作者：
BENNETT, CH
影响因子：
15
作者：
Aston, JG;Siller, CW;Messerly, GH
通讯作者：
Messerly, GH
影响因子：
2.8
作者：
BARTHEL, J;BACHHUBER, K;HETZENAUER, H
通讯作者：
HETZENAUER, H
影响因子：
15
作者：
APPLEQUIST, J;CARL, JR;FUNG, KK
通讯作者：
FUNG, KK
影响因子：
1.7
作者：
Brdarski, S;Åstrand, PO;Karlström, G
通讯作者：
Karlström, G