同时考虑分子极化性张量和溶液内静电势的可极化高斯多极力场原子极化性的完善。

IF 5.3 2区 化学 Q1 CHEMISTRY, MEDICINAL
Yong Duan, Junmei Wang, Piotr Cieplak, Ray Luo
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引用次数: 0

摘要

原子极化率被认为是可极化分子力学力场的基本参数,在决定模型在不同静电环境中的可转移性方面起着关键作用。在早期的工作中,原子极化率是通过拟合主要小分子的B3LYP/ augc -cc-pvtz分子极化率张量得到的。利用最近的PCMRESPPOL方法,我们使用可极化的高斯多极(pGM)力场来改进凝聚相模拟的原子极化率。从早期的工作出发,在这项工作中,我们纳入了大量二聚体的极化张量和多种溶剂中的静电电位(esp)。在四种溶剂(乙醚,ε = 4.24,二氯乙烷,ε = 10.13,丙酮,ε = 20.49,水,ε = 78.36)中,稀有气体和小分子的小分子单体和二聚体的ESPs分别为1565 × 4,小分子二聚体的ESPs为4742 × 4。对于气相极化张量,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13523个单体和二聚体的分子极化张量中,从而补充了我们早期工作中使用的分子集。QM7b极化集从quantummachine.org上获得,并在理论的LR-CCSD/d-aug-cc-pVDZ水平上进行了计算。所有其他极化张量和所有esp均在理论的ωB97X-D/aug-cc-pVTZ水平上计算。利用所有的极化张量和小分子单体的1565 × 4电导率建立了原子极化率,并将其与小分子二聚体的4742 × 4电导率进行了比较。预测的二聚体电位的平均相对均方根误差(RRMSE)为9.30%,仅略大于单体电位的平均拟合RRMSE(9.15%)。通过比较在另一介质环境中为四肽和DES单体数据集开发的参数计算的esp,进一步评估极化集的可转移性。可以观察到,尽管本集的参数数量约为先前集的一半,但本工作的极化率与先前讨论的工作相比保留或略微提高了可转移性。除去气相数据,对于DES单体集,pGM-ind和pGM-perm方法的平均迁移rrmse分别为16.25%和10.83%,而pGM-perm方法的平均迁移rrmse分别为16.03%和10.54%;对于四肽,pGM-ind法和pGM-perm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,具有更新极性的pGM方法实现了从单体到二聚体以及从一种溶剂到另一种溶剂的显著转移。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials.

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.

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来源期刊
CiteScore
9.80
自引率
10.70%
发文量
529
审稿时长
1.4 months
期刊介绍: The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery. Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field. As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.
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