Duan Yong, Wang Junmei, Cieplak Piotr, Luo Ray
UC Davis Genome Center and Department of Biomedical Engineering, University of California, Davis, One Shields Avenue, Davis, California 95616, United States.
Department of Pharmaceutical Sciences, University of Pittsburgh, 3501 Terrace Street, Pittsburgh, Pennsylvania 15261, United States.
J Chem Inf Model. 2025 Feb 10;65(3):1428-1440. doi: 10.1021/acs.jcim.4c02175. Epub 2025 Jan 26.
Atomic polarizabilities are considered to be fundamental parameters in polarizable molecular mechanical force fields that play pivotal roles in determining model transferability across different electrostatic environments. In an earlier work, the atomic polarizabilities were obtained by fitting them to the B3LYP/aug-cc-pvtz molecular polarizability tensors of mainly small molecules. Taking advantage of the recent PCMRESPPOL method, we refine the atomic polarizabilities for condensed-phase simulations using a polarizable Gaussian Multipole (pGM) force field. Departing from earlier works, in this work, we incorporated polarizability tensors of a large number of dimers and electrostatic potentials (ESPs) in multiple solvents. We calculated 1565 × 4 ESPs of small molecule monomers and dimers of noble gas and small molecules and 4742 × 4 ESPs of small molecule dimers in four solvents (diethyl ether, ε = 4.24, dichloroethane, ε = 10.13, acetone, ε = 20.49, and water, ε = 78.36). For the gas-phase polarizability tensors, we supplemented the molecule set that was used in our earlier work by adding both the 4252 monomer and dimer sets studied by Shaw and co-workers and the 7211 small molecule monomers listed in the QM7b database to a combined total of 13,523 molecular polarizability tensors of monomers and dimers. The QM7b polarizability set was obtained from quantum-machine.org and was calculated at the LR-CCSD/d-aug-cc-pVDZ level of theory. All other polarizability tensors and all ESPs were calculated at the ωB97X-D/aug-cc-pVTZ level of theory. The atomic polarizabilities were developed using all polarizability tensors and the 1565 × 4 ESPs of small molecule monomers and were then assessed by comparing them to the 4742 × 4 ab initio ESPs of small molecule dimers. The predicted dimer ESPs had an average relative root-mean-square error (RRMSE) of 9.30%, which was only slightly larger than the average fitting RRMSE of 9.15% of the monomer ESPs. The transferability of the polarizability set was further evaluated by comparing the ESPs calculated using parameters developed in another dielectric environment for both tetrapeptide and DES monomer data sets. It was observed that the polarizabilities of this work retained or slightly improved the transferability over the one discussed in earlier work even though the number of parameters in the present set is about half of that in the earlier set. Excluding the gas-phase data, for the DES monomer set, the average transfer RRMSEs were 16.25% and 10.83% for pGM-ind and pGM-perm methods, respectively, comparable to the average fitting RRMSEs of 16.03% and 10.54%; for tetrapeptides, the average transfer RRMSEs were 5.62% and 3.95% for pGM-ind and pGM-perm methods, respectively, slightly larger than 5.41% and 3.61% of the fitting RRMSEs. Therefore, we conclude that the pGM methods with updated polarizabilities achieved remarkable transferability from monomer to dimer and from one solvent to another.
原子极化率被认为是可极化分子力学力场中的基本参数,在决定模型在不同静电环境下的可转移性方面起着关键作用。在早期的一项工作中,通过将原子极化率拟合到主要是小分子的B3LYP/aug-cc-pvtz分子极化率张量来获得原子极化率。利用最近的PCMRESPPOL方法,我们使用可极化高斯多极子(pGM)力场对用于凝聚相模拟的原子极化率进行了优化。与早期工作不同的是,在这项工作中,我们纳入了大量二聚体的极化率张量以及多种溶剂中的静电势(ESP)。我们计算了稀有气体小分子单体和二聚体的1565×4个ESP以及四种溶剂(乙醚,ε = 4.24,二氯乙烷,ε = 10.13,丙酮,ε = 20.49,水,ε = 78.36)中小分子二聚体的4742×4个ESP。对于气相极化率张量,我们通过将Shaw及其同事研究的4252个单体和二聚体集以及QM7b数据库中列出的7211个小分子单体添加到总共13523个单体和二聚体的分子极化率张量中,对我们早期工作中使用的分子集进行了补充。QM7b极化率集来自quantum-machine.org,并在LR-CCSD/d-aug-cc-pVDZ理论水平上计算。所有其他极化率张量和所有ESP均在ωB97X-D/aug-cc-pVTZ理论水平上计算。使用所有极化率张量和小分子单体的1565×4个ESP来开发原子极化率,然后通过将它们与小分子二聚体的4742×4个从头算ESP进行比较来评估。预测的二聚体ESP的平均相对均方根误差(RRMSE)为9.30%,仅略大于单体ESP的平均拟合RRMSE的9.15%。通过比较使用在另一种介电环境中开发的参数计算的四肽和DES单体数据集的ESP,进一步评估了极化率集的可转移性。结果发现,尽管本集中的参数数量约为早期集的一半,但这项工作中的极化率在可转移性方面相对于早期工作中讨论的极化率有所保留或略有提高。不包括气相数据,对于DES单体集,pGM-ind和pGM-perm方法的平均转移RRMSE分别为16.25%和10.83%,与平均拟合RRMSE的16.03%和10.54%相当;对于四肽,pGM-ind和pGM-perm方法的平均转移RRMSE分别为5.62%和3.95%,略大于拟合RRMSE的5.41%和3.61%。因此,我们得出结论,具有更新极化率的pGM方法在从单体到二聚体以及从一种溶剂到另一种溶剂方面实现了显著的可转移性。