Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization.
Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization.
复制标题
DOI：
10.1021/ct200142z
复制
发表时间：
2011-07-12
影响因子：
5.5
通讯作者：
Hou, Tingjun
中科院分区：
文献类型：
--
作者：
Wang, Junmei;Hou, Tingjun
分子力学力场（FF）方法是研究凝聚相性质的有效方法。它们是实验的补充，并且常常可以在原子细节上超越实验。即使FF专门用于研究生物分子的结构、动力学和功能，FF准确再现代表生物分子化学部分的小分子的实验液体性质仍然很重要。否则，力场可能无法正确描述水溶液中大分子的结构和能量。在这项工作中，我们进行了系统的研究，以评估一般琥珀力场（GAFF）在研究密度和蒸发热的一个大的有机分子，涵盖了最常见的化学官能团。最新的技术，如粒子网格Ewald（PME）计算静电能，和朗之万动力学标度温度，已被应用在分子动力学（MD）模拟。对于密度，71种有机化合物的平均百分误差（APE）为4.43%时，与实验值相比。更值得注意的是，在排除两个异常值和四个其他化合物后，APE下降到3.43%，这些化合物的实验密度是在高于1.0 atm的压力下测量的。对于汽化热，已经研究了几种方案，最好的一种是P4/ntt 0，其平均无符号误差（AUE）和均方根误差（RMSE）分别为0.93和1.20 kcal/mol。讨论了如何通过适当的货车德瓦耳斯（vdW）参数化来减小预报误差。一个令人鼓舞的发现，在vdW参数化的密度和汽化热接近其“理想”值在一个同步的方式时，vdW参数进行调整。以下使用热力学积分的水合自由能计算进一步证明了vdW细化。我们得出结论，简单的vdW参数化可以显着减少预测误差。我们相信，GAFF可以大大提高其性能，在预测有机分子的液体性质后，一个系统的vdW参数化，这将在一个单独的文件。
Molecular mechanical force field (FF) methods are useful in studying condensed phase properties. They are complementary to experiment and can often go beyond experiment in atomic details. Even a FF is specific for studying structures, dynamics and functions of biomolecules, it is still important for the FF to accurately reproduce the experimental liquid properties of small molecules that represent the chemical moieties of biomolecules. Otherwise, the force field may not describe the structures and energies of macromolecules in aqueous solutions properly. In this work, we have carried out a systematic study to evaluate the General AMBER Force Field (GAFF) in studying densities and heats of vaporization for a large set of organic molecules that covers the most common chemical functional groups. The latest techniques, such as the particle mesh Ewald (PME) for calculating electrostatic energies, and Langevin dynamics for scaling temperatures, have been applied in the molecular dynamics (MD) simulations. For density, the average percent error (APE) of 71 organic compounds is 4.43% when compared to the experimental values. More encouragingly, the APE drops to 3.43% after the exclusion of two outliers and four other compounds for which the experimental densities have been measured with pressures higher than 1.0 atm. For heat of vaporization, several protocols have been investigated and the best one, P4/ntt0, achieves an average unsigned error (AUE) and a root-mean-square error (RMSE) of 0.93 and 1.20 kcal/mol, respectively. How to reduce the prediction errors through proper van der Waals (vdW) parameterization has been discussed. An encouraging finding in vdW parameterization is that both densities and heats of vaporization approach their “ideal” values in a synchronous fashion when vdW parameters are tuned. The following hydration free energy calculation using thermodynamic integration further justifies the vdW refinement. We conclude that simple vdW parameterization can significantly reduce the prediction errors. We believe that GAFF can greatly improve its performance in predicting liquid properties of organic molecules after a systematic vdW parameterization, which will be reported in a separate paper.
登录
查看更多内容
DOI：
10.1016/s0166-1280(97)00237-6
发表时间：
1998-02-09
期刊：
THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE
影响因子：
--
作者：
Jorgensen, WL;McDonald, NA
通讯作者：
McDonald, NA
影响因子：
4.4
作者：
Horn, HW;Swope, WC;Head-Gordon, T
通讯作者：
Head-Gordon, T
影响因子：
4.4
作者：
ESSMANN, U;PERERA, L;PEDERSEN, LG
通讯作者：
PEDERSEN, LG
影响因子：
4.4
作者：
Izaguirre, JA;Catarello, DP;Skeel, RD
通讯作者：
Skeel, RD
影响因子：
4.4
作者：
BILLETER, SR;KING, PM;VANGUNSTEREN, WF
通讯作者：
VANGUNSTEREN, WF