• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法,用中文像聊天一样搜索,搜遍4000万医学文献。AI智能推荐,让科研检索更轻松。

立即免费搜索

文件翻译

保留排版,准确专业,支持PDF/Word/PPT等文件格式,支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述,25分钟生成高质量综述,智能提取关键信息,辅助科研写作。

立即免费体验

应用于有机体系的电负性均衡方法与分割电荷平衡:参数化、验证及比较

The electronegativity equalization method and the split charge equilibration applied to organic systems: parametrization, validation, and comparison.

作者信息

Verstraelen Toon, Van Speybroeck Veronique, Waroquier Michel

机构信息

Center for Molecular Modeling, Ghent University, 9000 Ghent, Belgium.

出版信息

J Chem Phys. 2009 Jul 28;131(4):044127. doi: 10.1063/1.3187034.

DOI:10.1063/1.3187034
PMID:19655857
Abstract

An extensive benchmark of the electronegativity equalization method (EEM) and the split charge equilibration (SQE) model on a very diverse set of organic molecules is presented. These models efficiently compute atomic partial charges and are used in the development of polarizable force fields. The predicted partial charges that depend on empirical parameters are calibrated to reproduce results from quantum mechanical calculations. Recently, SQE is presented as an extension of the EEM to obtain the correct size dependence of the molecular polarizability. In this work, 12 parametrization protocols are applied to each model and the optimal parameters are benchmarked systematically. The training data for the empirical parameters comprise of MP2/Aug-CC-pVDZ calculations on 500 organic molecules containing the elements H, C, N, O, F, S, Cl, and Br. These molecules have been selected by an ingenious and autonomous protocol from an initial set of almost 500,000 small organic molecules. It is clear that the SQE model outperforms the EEM in all benchmark assessments. When using Hirshfeld-I charges for the calibration, the SQE model optimally reproduces the molecular electrostatic potential from the ab initio calculations. Applications on chain molecules, i.e., alkanes, alkenes, and alpha alanine helices, confirm that the EEM gives rise to a divergent behavior for the polarizability, while the SQE model shows the correct trends. We conclude that the SQE model is an essential component of a polarizable force field, showing several advantages over the original EEM.

摘要

本文给出了对电负性均衡方法(EEM)和分裂电荷平衡(SQE)模型在一组非常多样的有机分子上的广泛基准测试。这些模型能有效地计算原子部分电荷,并用于可极化力场的开发。依赖于经验参数预测的部分电荷经过校准以重现量子力学计算的结果。最近,SQE作为EEM的扩展被提出,以获得分子极化率正确的尺寸依赖性。在这项工作中,对每个模型应用了12种参数化协议,并对最优参数进行了系统的基准测试。经验参数的训练数据包括对500个含有H、C、N、O、F、S、Cl和Br元素的有机分子进行的MP2/aug-cc-pVDZ计算。这些分子是通过一种巧妙的自主协议从最初近50万个小有机分子集合中挑选出来的。显然,在所有基准评估中,SQE模型都优于EEM。当使用Hirshfeld-I电荷进行校准时,SQE模型能最优地重现从头算计算得到的分子静电势。在链状分子(即烷烃、烯烃和α-丙氨酸螺旋)上的应用证实,EEM在极化率方面会产生发散行为,而SQE模型显示出正确的趋势。我们得出结论,SQE模型是可极化力场的一个重要组成部分,与原始的EEM相比具有几个优点。

相似文献

1
The electronegativity equalization method and the split charge equilibration applied to organic systems: parametrization, validation, and comparison.应用于有机体系的电负性均衡方法与分割电荷平衡:参数化、验证及比较
J Chem Phys. 2009 Jul 28;131(4):044127. doi: 10.1063/1.3187034.
2
Electronegativity equalization method: parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme.电负性均衡方法:使用默茨-科尔曼-辛格电荷分布方案对有机分子进行参数化和验证
J Comput Chem. 2009 May;30(7):1174-8. doi: 10.1002/jcc.21142.
3
Assessment of Atomic Charge Models for Gas-Phase Computations on Polypeptides.评估多肽气相计算中原子电荷模型。
J Chem Theory Comput. 2012 Feb 14;8(2):661-76. doi: 10.1021/ct200512e. Epub 2012 Jan 17.
4
Nonmetallic electronegativity equalization and point-dipole interaction model including exchange interactions for molecular dipole moments and polarizabilities.用于分子偶极矩和极化率的包含交换相互作用的非金属电负性均衡和点偶极相互作用模型。
J Chem Phys. 2009 Jul 28;131(4):044101. doi: 10.1063/1.3166142.
5
A new force field (ECEPP-05) for peptides, proteins, and organic molecules.一种用于肽、蛋白质和有机分子的新力场(ECEPP - 05)。
J Phys Chem B. 2006 Mar 16;110(10):5025-44. doi: 10.1021/jp054994x.
6
The Significance of Parameters in Charge Equilibration Models.电荷平衡模型中参数的意义。
J Chem Theory Comput. 2011 Jun 14;7(6):1750-64. doi: 10.1021/ct200006e. Epub 2011 May 2.
7
A modified electronegativity equalization method for fast and accurate calculation of atomic charges in large biological molecules.一种用于快速准确计算大型生物分子中原子电荷的改进型电负性均衡方法。
Phys Chem Chem Phys. 2009 Aug 7;11(29):6082-9. doi: 10.1039/b821696g. Epub 2009 May 26.
8
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.快速、高效地生成高质量的原子电荷。AM1-BCC模型:II. 参数化与验证。
J Comput Chem. 2002 Dec;23(16):1623-41. doi: 10.1002/jcc.10128.
9
Toward an alternative hardness kernel matrix structure in the Electronegativity Equalization Method (EEM).
J Chem Inf Model. 2006 Jul-Aug;46(4):1657-65. doi: 10.1021/ci050505e.
10
Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery.高通量计算药物发现中依赖构象的精确分子静电势。
J Comput Chem. 2010 Jun;31(8):1722-32. doi: 10.1002/jcc.21460.

引用本文的文献

1
Influence of the Lennard-Jones Combination Rules on the Simulated Properties of Organic Liquids at Optimal Force-Field Parametrization.最优化力场参数化条件下 Lennard-Jones 组合规则对有机液体模拟性质的影响。
J Chem Theory Comput. 2023 Apr 11;19(7):2048-2063. doi: 10.1021/acs.jctc.2c01170. Epub 2023 Mar 15.
2
Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set.基于针对相同实验数据集优化的两种凝聚相力场的(卤代)烷烃的联合和全原子表示的比较。
J Chem Theory Comput. 2022 Nov 8;18(11):6757-6778. doi: 10.1021/acs.jctc.2c00524. Epub 2022 Oct 3.
3
Molecular Interactions From the Density Functional Theory for Chemical Reactivity: The Interaction Energy Between Two-Reagents.
基于密度泛函理论的化学反应性分子相互作用:两种反应物之间的相互作用能
Front Chem. 2022 Jun 13;10:906674. doi: 10.3389/fchem.2022.906674. eCollection 2022.
4
Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds.针对考虑大型化合物家族的实验纯液体性质,基于片段的力场的系统优化:应用于氧和氮化合物。
Phys Chem Chem Phys. 2021 Sep 7;23(33):17774-17793. doi: 10.1039/d1cp02001c. Epub 2021 Aug 5.
5
Minimally Empirical Double-Hybrid Functionals Trained against the GMTKN55 Database: revDSD-PBEP86-D4, revDOD-PBE-D4, and DOD-SCAN-D4.针对GMTKN55数据库训练的最小经验双杂化泛函:revDSD-PBEP86-D4、revDOD-PBE-D4和DOD-SCAN-D4。
J Phys Chem A. 2019 Jun 20;123(24):5129-5143. doi: 10.1021/acs.jpca.9b03157. Epub 2019 Jun 12.
6
Evaluating Charge Equilibration Methods To Generate Electrostatic Fields in Nanoporous Materials.评估用于在纳米多孔材料中生成静电场的电荷平衡方法。
J Chem Theory Comput. 2019 Jan 8;15(1):382-401. doi: 10.1021/acs.jctc.8b00669. Epub 2018 Dec 4.
7
Fractional nuclear charge approach to isolated anion densities for Hirshfeld partitioning methods.用于 Hirshfeld 划分方法的孤立阴离子密度的分数核电荷方法。
J Mol Model. 2017 Nov 21;23(12):348. doi: 10.1007/s00894-017-3514-6.
8
Metal Ion Modeling Using Classical Mechanics.使用经典力学的金属离子建模
Chem Rev. 2017 Feb 8;117(3):1564-1686. doi: 10.1021/acs.chemrev.6b00440. Epub 2017 Jan 3.
9
Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald.可极化分子动力学中极化能及相关作用力的可扩展评估:II. 迈向使用光滑粒子网格埃瓦尔德方法的大规模并行计算
J Chem Theory Comput. 2014 Feb 28;10(4):1638-1651. doi: 10.1021/ct401096t.
10
AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules.原子电荷计算器:用于交互式基于网络计算大型生物分子复合物和类药物分子中的原子电荷。
J Cheminform. 2015 Oct 22;7:50. doi: 10.1186/s13321-015-0099-x. eCollection 2015.