{"title":"B-N体系的分子模拟:硼球烯-吡啶杂化物的相互作用和性质","authors":"Ling Pei, Li-Juan Zhang, Hai-Bo Yao","doi":"10.1007/s00894-025-06513-6","DOIUrl":null,"url":null,"abstract":"<div><h3>Context</h3><p>Borospherene (B₄₀), an all-boron fullerene analogue, exhibits Lewis acidity at its boron sites, while pyridine, a common organic ligand, acts as a Lewis base. Despite extensive research on B₄₀ interactions with metals and small inorganic molecules, the potential for functionalization with organic ligands like pyridine to form novel hybrid materials, such as borospherene–organic frameworks (BOFs), remains largely unexplored. This study investigates the structure, stability, and nature of interactions in B₄₀-pyridine (B₄₀-Py) complexes. Structural searches identified 18 isomers, with detailed analysis revealing that the most stable complexes form through direct B–N interactions. The B–N bonding exhibits a synergistic combination of covalent and ionic character, as evidenced by multiple computational analyses. The most stable isomer (involving B(4) site) provides crucial insights for designing B–N functional molecules and BOFs based on borospherene.</p><h3>Methods</h3><p>Density functional theory (DFT) calculations were performed using Gaussian 16. Initial structural searches employed the Molclus program coupled with xTB pre-optimization. Geometry optimizations and frequency calculations (confirming no imaginary frequencies) for isomers were carried out at the M062X/6-311G(d), PBE0-D3/6-311G(d), and B3LYP-D3/6-311G(d) levels, incorporating Grimme's D3 dispersion correction. Basis-set superposition error (BSSE) corrections were applied using the counterpoise method. Subsequent analyses for the six lowest-energy isomers included: electrostatic potential (ESP) mapping, quantum theory of atoms in molecules (AIM) analysis, charge-density difference analysis, and visualization of non-covalent interactions using the independent gradient model based on Hirshfeld partition (IGMH) and the interaction region indicator (IRI). These analyses utilized the Multiwfn 3.8 software package.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 11","pages":""},"PeriodicalIF":2.5000,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Molecular simulation of B-N systems: insights into the interactions and properties of borospherene–pyridine hybrids\",\"authors\":\"Ling Pei, Li-Juan Zhang, Hai-Bo Yao\",\"doi\":\"10.1007/s00894-025-06513-6\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Context</h3><p>Borospherene (B₄₀), an all-boron fullerene analogue, exhibits Lewis acidity at its boron sites, while pyridine, a common organic ligand, acts as a Lewis base. Despite extensive research on B₄₀ interactions with metals and small inorganic molecules, the potential for functionalization with organic ligands like pyridine to form novel hybrid materials, such as borospherene–organic frameworks (BOFs), remains largely unexplored. This study investigates the structure, stability, and nature of interactions in B₄₀-pyridine (B₄₀-Py) complexes. Structural searches identified 18 isomers, with detailed analysis revealing that the most stable complexes form through direct B–N interactions. The B–N bonding exhibits a synergistic combination of covalent and ionic character, as evidenced by multiple computational analyses. The most stable isomer (involving B(4) site) provides crucial insights for designing B–N functional molecules and BOFs based on borospherene.</p><h3>Methods</h3><p>Density functional theory (DFT) calculations were performed using Gaussian 16. Initial structural searches employed the Molclus program coupled with xTB pre-optimization. Geometry optimizations and frequency calculations (confirming no imaginary frequencies) for isomers were carried out at the M062X/6-311G(d), PBE0-D3/6-311G(d), and B3LYP-D3/6-311G(d) levels, incorporating Grimme's D3 dispersion correction. Basis-set superposition error (BSSE) corrections were applied using the counterpoise method. Subsequent analyses for the six lowest-energy isomers included: electrostatic potential (ESP) mapping, quantum theory of atoms in molecules (AIM) analysis, charge-density difference analysis, and visualization of non-covalent interactions using the independent gradient model based on Hirshfeld partition (IGMH) and the interaction region indicator (IRI). These analyses utilized the Multiwfn 3.8 software package.</p></div>\",\"PeriodicalId\":651,\"journal\":{\"name\":\"Journal of Molecular Modeling\",\"volume\":\"31 11\",\"pages\":\"\"},\"PeriodicalIF\":2.5000,\"publicationDate\":\"2025-10-10\",\"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/s00894-025-06513-6\",\"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/s00894-025-06513-6","RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
Molecular simulation of B-N systems: insights into the interactions and properties of borospherene–pyridine hybrids
Context
Borospherene (B₄₀), an all-boron fullerene analogue, exhibits Lewis acidity at its boron sites, while pyridine, a common organic ligand, acts as a Lewis base. Despite extensive research on B₄₀ interactions with metals and small inorganic molecules, the potential for functionalization with organic ligands like pyridine to form novel hybrid materials, such as borospherene–organic frameworks (BOFs), remains largely unexplored. This study investigates the structure, stability, and nature of interactions in B₄₀-pyridine (B₄₀-Py) complexes. Structural searches identified 18 isomers, with detailed analysis revealing that the most stable complexes form through direct B–N interactions. The B–N bonding exhibits a synergistic combination of covalent and ionic character, as evidenced by multiple computational analyses. The most stable isomer (involving B(4) site) provides crucial insights for designing B–N functional molecules and BOFs based on borospherene.
Methods
Density functional theory (DFT) calculations were performed using Gaussian 16. Initial structural searches employed the Molclus program coupled with xTB pre-optimization. Geometry optimizations and frequency calculations (confirming no imaginary frequencies) for isomers were carried out at the M062X/6-311G(d), PBE0-D3/6-311G(d), and B3LYP-D3/6-311G(d) levels, incorporating Grimme's D3 dispersion correction. Basis-set superposition error (BSSE) corrections were applied using the counterpoise method. Subsequent analyses for the six lowest-energy isomers included: electrostatic potential (ESP) mapping, quantum theory of atoms in molecules (AIM) analysis, charge-density difference analysis, and visualization of non-covalent interactions using the independent gradient model based on Hirshfeld partition (IGMH) and the interaction region indicator (IRI). These analyses utilized the Multiwfn 3.8 software package.
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.