• 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

七条融合原则:对26种分子净原子电荷分配方法进行标准化统计分析的案例研究

Seven confluence principles: a case study of standardized statistical analysis for 26 methods that assign net atomic charges in molecules.

作者信息

Manz Thomas A

机构信息

Chemical & Materials Engineering, New Mexico State University Las Cruces New Mexico 88003-3805 USA

出版信息

RSC Adv. 2020 Dec 15;10(72):44121-44148. doi: 10.1039/d0ra06392d. eCollection 2020 Dec 9.

DOI:10.1039/d0ra06392d
PMID:35517149
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9058476/
Abstract

This article studies two kinds of information extracted from statistical correlations between methods for assigning net atomic charges (NACs) in molecules. First, relative charge transfer magnitudes are quantified by performing instant least squares fitting (ILSF) on the NACs reported by Cho (, 2020, , 688-696) across 26 methods applied to ∼2000 molecules. The Hirshfeld and Voronoi deformation density (VDD) methods had the smallest charge transfer magnitudes, while the quantum theory of atoms in molecules (QTAIM) method had the largest charge transfer magnitude. Methods optimized to reproduce the molecular dipole moment (, ACP, ADCH, CM5) have smaller charge transfer magnitudes than methods optimized to reproduce the molecular electrostatic potential (, CHELPG, HLY, MK, RESP). Several methods had charge transfer magnitudes even larger than the electrostatic potential fitting group. Second, confluence between different charge assignment methods is quantified to identify which charge assignment method produces the best NAC values for predicting linear correlations the results of 20 charge assignment methods having a complete basis set limit across the dataset of ∼2000 molecules. The DDEC6 NACs were the best such predictor of the entire dataset. Seven confluence principles are introduced explaining why confluent quantitative descriptors offer predictive advantages for modeling a broad range of physical properties and target applications. These confluence principles can be applied in various fields of scientific inquiry. A theory is derived showing confluence is better revealed by standardized statistical analysis (, principal components analysis of the correlation matrix and standardized reversible linear regression) than by unstandardized statistical analysis. These confluence principles were used together with other key principles and the scientific method to make assigning atom-in-material properties non-arbitrary. The N@C system provides an unambiguous and non-arbitrary falsifiable test of atomic population analysis methods. The HLY, ISA, MK, and RESP methods failed for this material.

摘要

本文研究了从分子中净原子电荷(NAC)分配方法之间的统计相关性中提取的两类信息。首先,通过对Cho(2020年,第688 - 696页)报道的应用于约2000个分子的26种方法所得到的NAC进行即时最小二乘法拟合(ILSF),来量化相对电荷转移量。Hirshfeld方法和Voronoi变形密度(VDD)方法的电荷转移量最小,而分子中的原子量子理论(QTAIM)方法的电荷转移量最大。为重现分子偶极矩而优化的方法(如ACP、ADCH、CM5)的电荷转移量比为重现分子静电势而优化的方法(如CHELPG、HLY、MK、RESP)要小。有几种方法的电荷转移量甚至比静电势拟合组的还要大。其次,对不同电荷分配方法之间的融合程度进行量化,以确定哪种电荷分配方法能产生最佳的NAC值,用于预测约2000个分子数据集上20种具有完整基组极限的电荷分配方法的线性相关结果。DDEC6 NAC是整个数据集的最佳此类预测指标。引入了七条融合原则,解释了为什么融合定量描述符在对广泛的物理性质和目标应用进行建模时具有预测优势。这些融合原则可应用于科学探究的各个领域。推导了一种理论,表明通过标准化统计分析(如相关矩阵的主成分分析和标准化可逆线性回归)比通过非标准化统计分析能更好地揭示融合。这些融合原则与其他关键原则及科学方法一起使用,使得材料中原子性质的分配不再是任意的。N@C系统为原子布居分析方法提供了一个明确且非任意的可证伪测试。HLY、ISA、MK和RESP方法对这种材料不适用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5110/9058476/f56b5f04c8a4/d0ra06392d-f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5110/9058476/c1e31c547806/d0ra06392d-f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5110/9058476/2bf623b13224/d0ra06392d-f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5110/9058476/f56b5f04c8a4/d0ra06392d-f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5110/9058476/c1e31c547806/d0ra06392d-f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5110/9058476/2bf623b13224/d0ra06392d-f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5110/9058476/f56b5f04c8a4/d0ra06392d-f3.jpg

相似文献

1
Seven confluence principles: a case study of standardized statistical analysis for 26 methods that assign net atomic charges in molecules.七条融合原则:对26种分子净原子电荷分配方法进行标准化统计分析的案例研究
RSC Adv. 2020 Dec 15;10(72):44121-44148. doi: 10.1039/d0ra06392d. eCollection 2020 Dec 9.
2
Apples to apples comparison of standardized to unstandardized principal component analysis of methods that assign partial atomic charges in molecules.对分子中分配部分原子电荷的方法进行标准化主成分分析与非标准化主成分分析的同类比较。
RSC Adv. 2022 Nov 3;12(49):31617-31628. doi: 10.1039/d2ra06349b.
3
The Atomic Partial Charges Arboretum: Trying to See the Forest for the Trees.原子部分电荷植物园:试图见树木更见森林。
Chemphyschem. 2020 Apr 20;21(8):688-696. doi: 10.1002/cphc.202000040. Epub 2020 Mar 23.
4
Determining Partial Atomic Charges for Liquid Water: Assessing Electronic Structure and Charge Models.确定液态水中的部分原子电荷:评估电子结构和电荷模型。
J Chem Theory Comput. 2021 Feb 9;17(2):889-901. doi: 10.1021/acs.jctc.0c01102. Epub 2021 Jan 6.
5
Unavoidable failure of point charge descriptions of electronic density changes for out-of-plane distortions.面外变形时,点电荷描述电子密度变化不可避免地失败。
Spectrochim Acta A Mol Biomol Spectrosc. 2022 Apr 15;271:120891. doi: 10.1016/j.saa.2022.120891. Epub 2022 Jan 15.
6
Charge Model 5: An Extension of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions in Gaseous and Condensed Phases.电荷模型 5:希夫菲尔德布居分析的扩展,用于准确描述气相和凝聚相中的分子相互作用。
J Chem Theory Comput. 2012 Feb 14;8(2):527-41. doi: 10.1021/ct200866d. Epub 2012 Feb 3.
7
Partial Atomic Charges and Screened Charge Models of the Electrostatic Potential.静电势的部分原子电荷与屏蔽电荷模型
J Chem Theory Comput. 2012 Jun 12;8(6):1989-98. doi: 10.1021/ct2009285. Epub 2012 May 7.
8
Tuned and Balanced Redistributed Charge Scheme for Combined Quantum Mechanical and Molecular Mechanical (QM/MM) Methods and Fragment Methods: Tuning Based on the CM5 Charge Model.用于组合量子力学和分子力学(QM/MM)方法及片段方法的调谐与平衡再分布电荷方案:基于CM5电荷模型的调谐
J Chem Theory Comput. 2013 Feb 12;9(2):1036-42. doi: 10.1021/ct300935m. Epub 2013 Jan 11.
9
Atoms-in-molecules study of the genetically encoded amino acids. III. Bond and atomic properties and their correlations with experiment including mutation-induced changes in protein stability and genetic coding.遗传编码氨基酸的分子内原子研究。III. 键和原子性质及其与实验的相关性,包括突变诱导的蛋白质稳定性变化和遗传编码。
Proteins. 2003 Aug 15;52(3):360-99. doi: 10.1002/prot.10414.
10
Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis.沃罗诺伊变形密度(VDD)电荷:对穆利肯、巴德、赫希菲尔德、温霍尔德和VDD电荷分析方法的评估。
J Comput Chem. 2004 Jan 30;25(2):189-210. doi: 10.1002/jcc.10351.

引用本文的文献

1
How well do various QM-derived net atomic charges reproduce the electrostatic potential surrounding a material across multiple geometric conformations?各种源自量子力学的净原子电荷在多个几何构象中对材料周围静电势的再现程度如何?
RSC Adv. 2025 Jul 7;15(29):23223-23265. doi: 10.1039/d4ra07900k. eCollection 2025 Jul 4.
2
A formally exact theory to construct nonreactive forcefields using linear regression to optimize bonded parameters.一种使用线性回归优化成键参数来构建非反应性力场的形式上精确的理论。
RSC Adv. 2024 Oct 22;14(45):33345-33383. doi: 10.1039/d4ra01861c. eCollection 2024 Oct 17.
3
An automated protocol to construct flexibility parameters for classical forcefields: applications to metal-organic frameworks.

本文引用的文献

1
Correction: Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology.勘误:介绍DDEC6原子布居分析:第1部分。电荷划分理论与方法。
RSC Adv. 2022 May 12;12(23):14384. doi: 10.1039/d2ra90050e.
2
Introducing DDEC6 atomic population analysis: part 4. Efficient parallel computation of net atomic charges, atomic spin moments, bond orders, and more.介绍DDEC6原子布居分析:第4部分。净原子电荷、原子自旋矩、键级等的高效并行计算。
RSC Adv. 2018 Jan 11;8(5):2678-2707. doi: 10.1039/c7ra11829e. eCollection 2018 Jan 9.
3
A collection of forcefield precursors for metal-organic frameworks.
一种用于构建经典力场柔性参数的自动化协议:在金属有机框架中的应用。
RSC Adv. 2024 Jul 19;14(31):22714-22762. doi: 10.1039/d4ra01859a. eCollection 2024 Jul 12.
4
Energy Electronegativity and Chemical Bonding.能量电负性与化学键。
Molecules. 2022 Nov 25;27(23):8215. doi: 10.3390/molecules27238215.
5
Apples to apples comparison of standardized to unstandardized principal component analysis of methods that assign partial atomic charges in molecules.对分子中分配部分原子电荷的方法进行标准化主成分分析与非标准化主成分分析的同类比较。
RSC Adv. 2022 Nov 3;12(49):31617-31628. doi: 10.1039/d2ra06349b.
6
Are "GAPT Charges" Really Just Charges?“GAPT 费用”真的只是费用吗?
J Chem Inf Model. 2021 Aug 23;61(8):3881-3890. doi: 10.1021/acs.jcim.1c00165. Epub 2021 Jul 29.
金属有机框架的力场前体集合。
RSC Adv. 2019 Nov 13;9(63):36492-36507. doi: 10.1039/c9ra07327b. eCollection 2019 Nov 11.
4
New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 2. Linear-scaling computational algorithms and parallelization.用于计算材料中原子极化率和色散系数的新标度关系:第2部分。线性标度计算算法与并行化
RSC Adv. 2019 Oct 17;9(57):33310-33336. doi: 10.1039/c9ra01983a. eCollection 2019 Oct 15.
5
Bond orders of the diatomic molecules.双原子分子的键级。
RSC Adv. 2019 May 31;9(30):17072-17092. doi: 10.1039/c9ra00974d. eCollection 2019 May 29.
6
New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 1. Theory and accuracy.用于计算材料中原子极化率和色散系数的新标度关系:第1部分。理论与精度。
RSC Adv. 2019 Jun 19;9(34):19297-19324. doi: 10.1039/c9ra03003d.
7
Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges.原子电荷计算器 II:用于计算部分原子电荷的网络工具。
Nucleic Acids Res. 2020 Jul 2;48(W1):W591-W596. doi: 10.1093/nar/gkaa367.
8
The Atomic Partial Charges Arboretum: Trying to See the Forest for the Trees.原子部分电荷植物园:试图见树木更见森林。
Chemphyschem. 2020 Apr 20;21(8):688-696. doi: 10.1002/cphc.202000040. Epub 2020 Mar 23.
9
Revisiting OPLS-AA Force Field for the Simulation of Anionic Surfactants in Concentrated Electrolyte Solutions.重新考察 OPLS-AA 力场用于模拟离子型表面活性剂在浓电解质溶液中的行为。
J Chem Theory Comput. 2020 Feb 11;16(2):1136-1145. doi: 10.1021/acs.jctc.9b00947. Epub 2020 Jan 27.
10
Olefin Metathesis in Confined Geometries: A Biomimetic Approach toward Selective Macrocyclization.受限几何中的烯烃复分解反应:一种对选择性大环化的仿生方法。
J Am Chem Soc. 2019 Dec 4;141(48):19014-19022. doi: 10.1021/jacs.9b08776. Epub 2019 Nov 18.