{"title":"x射线电子密度的总能量?","authors":"Lou Massa, 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, 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}
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.
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.