{"title":"Theoretical characterizations on three oxygen-containing polyatomic anion binding of the single/double pincer-like receptors","authors":"Pei Zhao, Qingqing Yao, Yue Li, Wenbo Zhang, Yanzhi Liu, Zhi-Feng Li, Kun Yuan","doi":"10.1007/s00894-026-06964-5","DOIUrl":null,"url":null,"abstract":"<div><h3>Context</h3><p>In this paper, density functional theory calculations were used to systematically characterize the binding behavior of the two types of pincer-like receptors with different configurations (E-type and Z-type) to three oxygen-containing polyatomic anions (SO<sub>4</sub><sup>2−</sup>, C<sub>2</sub>O<sub>4</sub><sup>2−</sup> and NO<sub>3</sub><sup>−</sup>). The E-type receptor (2ENH<sub>2</sub>) shows slightly preferential binding of SO<sub>4</sub><sup>2−</sup>. Independent gradient model based on Hirshfeld partition (IGMH) analysis characterized the non-covalent interaction patterns between the receptor and anion. Meanwhile, molecular electrostatic potential (ESP) analysis revealed changes in charge distribution upon anion binding. UV–Vis spectra and <sup>1</sup>H NMR calculations provided complementary information on the electronic and structural changes induced by complexation between anion and receptor. In addition, ab initio molecular dynamics (AIMD) simulations were used to examine the structural persistence of representative host–guest complexes. Overall, the results clarify how receptor configuration, hydrogen-bonding topology, anion properties, and solvent environment collectively influence anion recognition.</p><h3>Methods</h3><p>All geometries were optimized at the B3LYP-D3BJ/def2-SVP level of theory without any symmetry constraints. The host–guest binding energies (Δ<i>E</i><sub>b</sub><sup>cp</sup>) were corrected for basis set superposition error (BSSE). Additional calculations using B3LYP-D3BJ/def2-TZVP with counterpoise correction were performed for selected complexes to assess the robustness of the binding energies. Wave function analyses were performed using the Multiwfn program. AIMD simulations were using the ORCA 5.0 program with the composite method of B97-3c developed by Grimme and coworkers. All other calculations were performed using the Gaussian 16 program.</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":"32 10","pages":""},"PeriodicalIF":2.9000,"publicationDate":"2026-09-24","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/s00894-026-06964-5","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
Abstract
Context
In this paper, density functional theory calculations were used to systematically characterize the binding behavior of the two types of pincer-like receptors with different configurations (E-type and Z-type) to three oxygen-containing polyatomic anions (SO42−, C2O42− and NO3−). The E-type receptor (2ENH2) shows slightly preferential binding of SO42−. Independent gradient model based on Hirshfeld partition (IGMH) analysis characterized the non-covalent interaction patterns between the receptor and anion. Meanwhile, molecular electrostatic potential (ESP) analysis revealed changes in charge distribution upon anion binding. UV–Vis spectra and 1H NMR calculations provided complementary information on the electronic and structural changes induced by complexation between anion and receptor. In addition, ab initio molecular dynamics (AIMD) simulations were used to examine the structural persistence of representative host–guest complexes. Overall, the results clarify how receptor configuration, hydrogen-bonding topology, anion properties, and solvent environment collectively influence anion recognition.
Methods
All geometries were optimized at the B3LYP-D3BJ/def2-SVP level of theory without any symmetry constraints. The host–guest binding energies (ΔEbcp) were corrected for basis set superposition error (BSSE). Additional calculations using B3LYP-D3BJ/def2-TZVP with counterpoise correction were performed for selected complexes to assess the robustness of the binding energies. Wave function analyses were performed using the Multiwfn program. AIMD simulations were using the ORCA 5.0 program with the composite method of B97-3c developed by Grimme and coworkers. All other calculations were performed using the Gaussian 16 program.
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.