{"title":"Local potential energy density – A DFT analysis and the local binding energy in complexes with multiple interactions","authors":"Caio L. Firme","doi":"10.1016/j.jmgm.2024.108879","DOIUrl":null,"url":null,"abstract":"<div><div>A recently developed method, so-called local potential energy density, LPED, provides the binding energy density of intra/intermolecular interactions. The LPED cannot directly give the binding energy of intra/intermolecular interactions. However, it can indirectly give the binding energy through the linear equation between LPED and supramolecular binding energy, SME. In addition, the LPED can be used to obtain the SME of local or individual interactions indirectly for the case of complexes with multiple interactions, which cannot be obtained for any other method to our knowledge. The calculation of the LPED was evaluated with three different levels of theory using density functional methods. The linearity of LPED and SME between the reference level of theory (ωB97X-D/aug-cc-pVTZ) and the other levels of theory are similar among the studied levels of theory. In addition, LPED was used indirectly to obtain the local binding energy of intermolecular interactions of complexes with multiple interactions, such as the EDTA-Ca<sup>+2</sup> and the fosfomycin-Ca<sup>+2</sup>.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108879"},"PeriodicalIF":2.7000,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of molecular graphics & modelling","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1093326324001797","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
Abstract
A recently developed method, so-called local potential energy density, LPED, provides the binding energy density of intra/intermolecular interactions. The LPED cannot directly give the binding energy of intra/intermolecular interactions. However, it can indirectly give the binding energy through the linear equation between LPED and supramolecular binding energy, SME. In addition, the LPED can be used to obtain the SME of local or individual interactions indirectly for the case of complexes with multiple interactions, which cannot be obtained for any other method to our knowledge. The calculation of the LPED was evaluated with three different levels of theory using density functional methods. The linearity of LPED and SME between the reference level of theory (ωB97X-D/aug-cc-pVTZ) and the other levels of theory are similar among the studied levels of theory. In addition, LPED was used indirectly to obtain the local binding energy of intermolecular interactions of complexes with multiple interactions, such as the EDTA-Ca+2 and the fosfomycin-Ca+2.
期刊介绍:
The Journal of Molecular Graphics and Modelling is devoted to the publication of papers on the uses of computers in theoretical investigations of molecular structure, function, interaction, and design. The scope of the journal includes all aspects of molecular modeling and computational chemistry, including, for instance, the study of molecular shape and properties, molecular simulations, protein and polymer engineering, drug design, materials design, structure-activity and structure-property relationships, database mining, and compound library design.
As a primary research journal, JMGM seeks to bring new knowledge to the attention of our readers. As such, submissions to the journal need to not only report results, but must draw conclusions and explore implications of the work presented. Authors are strongly encouraged to bear this in mind when preparing manuscripts. Routine applications of standard modelling approaches, providing only very limited new scientific insight, will not meet our criteria for publication. Reproducibility of reported calculations is an important issue. Wherever possible, we urge authors to enhance their papers with Supplementary Data, for example, in QSAR studies machine-readable versions of molecular datasets or in the development of new force-field parameters versions of the topology and force field parameter files. Routine applications of existing methods that do not lead to genuinely new insight will not be considered.