x射线电子密度的总能量?

IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
Lou Massa, Chérif F. Matta
{"title":"x射线电子密度的总能量?","authors":"Lou Massa,&nbsp;Chérif F. Matta","doi":"10.1007/s00894-024-06224-4","DOIUrl":null,"url":null,"abstract":"<div><h3>Context</h3><p>This approach to quantum crystallography ensures the satisfaction of three quantum conditions, namely, idempotency, hermiticity, and normalization of the one-body density matrix, simultaneously as the X-ray diffraction problem is solved to reproduce the observed structure factors. The variational theorem used to optimize energy will only hold true if the density matrices used for such purpose are <i>N</i>-representable. The point of <i>N</i>-representability is to ensure the mapping of a density matrix to an <i>N</i>-body antisymmetric wavefunction. The antisymmetry is consistent with the experimental indistinguishability of fermions. This article develops a procedure for the fast and accurate application of quantum crystallography to large systems while guaranteeing that the results are <i>N</i>-representable.</p><h3>Methods</h3><p>For large molecules, it is advantageous to have the one-body density matrix assembled from sub-matrices of fragments within a scheme known as the kernel energy method (KEM). KEM accounts for up to two-body interactions between all fragments and ignores higher order interactions, an approximation that proved accurate through extensive past numerical testing. Since this approach to quantum crystallography rests on a single-determinant description, an explicit form of the corresponding <i>N</i>-representable two-body density matrix, which is determined by its one-body counterpart, is also given along with its use to calculate the total energy. This approach can be applied to extract conceptual density functional theory properties, quantum theory of atoms in molecules (QTAIM) properties, etc. from experimental structure factors.</p><h3>Graphical Abstract</h3>\n<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1000,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"The total energy from X-ray electron density?\",\"authors\":\"Lou Massa,&nbsp;Chérif F. Matta\",\"doi\":\"10.1007/s00894-024-06224-4\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Context</h3><p>This approach to quantum crystallography ensures the satisfaction of three quantum conditions, namely, idempotency, hermiticity, and normalization of the one-body density matrix, simultaneously as the X-ray diffraction problem is solved to reproduce the observed structure factors. The variational theorem used to optimize energy will only hold true if the density matrices used for such purpose are <i>N</i>-representable. The point of <i>N</i>-representability is to ensure the mapping of a density matrix to an <i>N</i>-body antisymmetric wavefunction. The antisymmetry is consistent with the experimental indistinguishability of fermions. This article develops a procedure for the fast and accurate application of quantum crystallography to large systems while guaranteeing that the results are <i>N</i>-representable.</p><h3>Methods</h3><p>For large molecules, it is advantageous to have the one-body density matrix assembled from sub-matrices of fragments within a scheme known as the kernel energy method (KEM). KEM accounts for up to two-body interactions between all fragments and ignores higher order interactions, an approximation that proved accurate through extensive past numerical testing. Since this approach to quantum crystallography rests on a single-determinant description, an explicit form of the corresponding <i>N</i>-representable two-body density matrix, which is determined by its one-body counterpart, is also given along with its use to calculate the total energy. This approach can be applied to extract conceptual density functional theory properties, quantum theory of atoms in molecules (QTAIM) properties, etc. from experimental structure factors.</p><h3>Graphical Abstract</h3>\\n<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>\",\"PeriodicalId\":651,\"journal\":{\"name\":\"Journal of Molecular Modeling\",\"volume\":\"31 3\",\"pages\":\"\"},\"PeriodicalIF\":2.1000,\"publicationDate\":\"2025-02-06\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Molecular Modeling\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://link.springer.com/article/10.1007/s00894-024-06224-4\",\"RegionNum\":4,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Molecular Modeling","FirstCategoryId":"92","ListUrlMain":"https://link.springer.com/article/10.1007/s00894-024-06224-4","RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

背景:这种量子晶体学方法在解决x射线衍射问题再现观察到的结构因素的同时,保证了三个量子条件的满足,即单体密度矩阵的幂等性、厄米性和规格化。用于优化能量的变分定理只有在用于此目的的密度矩阵是n可表示的情况下才成立。n可表示性的意义在于保证密度矩阵到n体反对称波函数的映射。这种反对称性与实验中费米子的不可区分性是一致的。本文开发了一种快速准确地将量子晶体学应用于大型系统的程序,同时保证结果是n可表示的。方法:对于大分子,在核能法(KEM)的方案中,由碎片的子矩阵组装成一个体密度矩阵是有利的。KEM解释了所有碎片之间的两体相互作用,忽略了高阶相互作用,这一近似通过大量的过去数值测试证明是准确的。由于量子晶体学的这种方法依赖于单行列式描述,因此也给出了相应的n可表示的两体密度矩阵的显式形式,该矩阵由其单体对应矩阵决定,并使用它来计算总能量。该方法可用于从实验结构因素中提取概念密度泛函理论性质、分子中原子量子理论(QTAIM)性质等。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
The total energy from X-ray electron density?

Context

This approach to quantum crystallography ensures the satisfaction of three quantum conditions, namely, idempotency, hermiticity, and normalization of the one-body density matrix, simultaneously as the X-ray diffraction problem is solved to reproduce the observed structure factors. The variational theorem used to optimize energy will only hold true if the density matrices used for such purpose are N-representable. The point of N-representability is to ensure the mapping of a density matrix to an N-body antisymmetric wavefunction. The antisymmetry is consistent with the experimental indistinguishability of fermions. This article develops a procedure for the fast and accurate application of quantum crystallography to large systems while guaranteeing that the results are N-representable.

Methods

For large molecules, it is advantageous to have the one-body density matrix assembled from sub-matrices of fragments within a scheme known as the kernel energy method (KEM). KEM accounts for up to two-body interactions between all fragments and ignores higher order interactions, an approximation that proved accurate through extensive past numerical testing. Since this approach to quantum crystallography rests on a single-determinant description, an explicit form of the corresponding N-representable two-body density matrix, which is determined by its one-body counterpart, is also given along with its use to calculate the total energy. This approach can be applied to extract conceptual density functional theory properties, quantum theory of atoms in molecules (QTAIM) properties, etc. from experimental structure factors.

Graphical Abstract

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Journal of Molecular Modeling
Journal of Molecular Modeling 化学-化学综合
CiteScore
3.50
自引率
4.50%
发文量
362
审稿时长
2.9 months
期刊介绍: The Journal of Molecular Modeling focuses on "hardcore" modeling, publishing high-quality research and reports. Founded in 1995 as a purely electronic journal, it has adapted its format to include a full-color print edition, and adjusted its aims and scope fit the fast-changing field of molecular modeling, with a particular focus on three-dimensional modeling. Today, the journal covers all aspects of molecular modeling including life science modeling; materials modeling; new methods; and computational chemistry. Topics include computer-aided molecular design; rational drug design, de novo ligand design, receptor modeling and docking; cheminformatics, data analysis, visualization and mining; computational medicinal chemistry; homology modeling; simulation of peptides, DNA and other biopolymers; quantitative structure-activity relationships (QSAR) and ADME-modeling; modeling of biological reaction mechanisms; and combined experimental and computational studies in which calculations play a major role.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信