Sourav Ranjan Ghosh, Sasthi Charan Halder, Atish Dipankar Jana
{"title":"Evolution of B13n (n = + 3 to − 3) wheel with electron injection/abstraction: an insight from electronic structure analysis","authors":"Sourav Ranjan Ghosh, Sasthi Charan Halder, Atish Dipankar Jana","doi":"10.1007/s00894-025-06375-y","DOIUrl":null,"url":null,"abstract":"<div><h3>Context</h3><p>The planar B<sub>13</sub><sup>+1</sup> cluster, a prototypical molecular ‘Wankel motor’, has captivated the scientific community with its exceptional stability as well as rotor action. The present study is an exploration of how incremental electron injection/abstraction influences the electronic structure of B<sub>13</sub> clusters with B<sub>13</sub><sup>+1</sup> as a reference one. It has been found that seven different charge states (from + 3 to − 3) of B<sub>13</sub> cluster are possible, among which B<sub>13</sub><sup>−1</sup> triplet is the lowest energy cluster. For B<sub>13</sub><sup><i>n</i></sup> clusters, <i>n</i> = + 3 to − 2, the clusters are planar and possess C<sub>2v</sub> symmetry and their relative atomic arrangement is similar to B<sub>13</sub><sup>+1</sup> ground state (GS) structure in which a triangular boron core is encircled by ten peripheral boron atoms. B<sub>13</sub><sup>−3</sup> cluster has a different geometric arrangement of atoms like that of the B<sub>13</sub><sup>+1</sup> transition state (TS) structure; remains planar, possesses C<sub>2v</sub> symmetry. The different atomic arrangement of B<sub>13</sub><sup>−3</sup> can be assigned to the electronic structural relaxation to reduce the electronic stress arising from high negative charge. B<sub>13</sub><sup>+1</sup> cluster is characterized by a unique electron density distribution in the cluster plane which is analogous to a ‘tri-spoke wheel’ configuration. In it, three spokes of electron dense lines connect the triangular core to the nearly circular periphery. The present study unveils how the injection or abstraction of electrons modifies the electronic topology in the cluster plane and how the spoke-wheel geometry evolves. It has been found that, in the + 3 and + 2 charge states, the wheel consists of four and five spokes respectively. On the other hand, for all other clusters, the overall electronic topology resembles that of the tri-spoke wheel-like B<sub>13</sub><sup>+1</sup> cluster. AIM analysis helped to trace out and characterize the evolution of the spoke-wheel topology with electron density at ring critical points and the bond paths.</p><h3>Methods</h3><p>Density Functional Theory (DFT), utilizing the 6–311 + G(d) basis set and the PBE1PBE hybrid density functional, has been employed to determine the minimum energy structures of B<sub>13</sub> clusters with different charged states. The calculations have been performed using a superfine integration grid and very tight optimization settings, as implemented in GAUSSIAN 09 Revision D.01. To address potential instabilities in SCF calculations, wavefunction stability has been thoroughly analysed. AIM analysis and various real-space functions, including electron density, Localized Orbital Locator (LOL), Phase-Space defined Fisher Information Density (PS-FID), and Electron Localization Function (ELF), have been investigated. Multiwfn 3.8 was utilized for plotting these functions.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 5","pages":""},"PeriodicalIF":2.1000,"publicationDate":"2025-04-29","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/s00894-025-06375-y","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
The planar B13+1 cluster, a prototypical molecular ‘Wankel motor’, has captivated the scientific community with its exceptional stability as well as rotor action. The present study is an exploration of how incremental electron injection/abstraction influences the electronic structure of B13 clusters with B13+1 as a reference one. It has been found that seven different charge states (from + 3 to − 3) of B13 cluster are possible, among which B13−1 triplet is the lowest energy cluster. For B13n clusters, n = + 3 to − 2, the clusters are planar and possess C2v symmetry and their relative atomic arrangement is similar to B13+1 ground state (GS) structure in which a triangular boron core is encircled by ten peripheral boron atoms. B13−3 cluster has a different geometric arrangement of atoms like that of the B13+1 transition state (TS) structure; remains planar, possesses C2v symmetry. The different atomic arrangement of B13−3 can be assigned to the electronic structural relaxation to reduce the electronic stress arising from high negative charge. B13+1 cluster is characterized by a unique electron density distribution in the cluster plane which is analogous to a ‘tri-spoke wheel’ configuration. In it, three spokes of electron dense lines connect the triangular core to the nearly circular periphery. The present study unveils how the injection or abstraction of electrons modifies the electronic topology in the cluster plane and how the spoke-wheel geometry evolves. It has been found that, in the + 3 and + 2 charge states, the wheel consists of four and five spokes respectively. On the other hand, for all other clusters, the overall electronic topology resembles that of the tri-spoke wheel-like B13+1 cluster. AIM analysis helped to trace out and characterize the evolution of the spoke-wheel topology with electron density at ring critical points and the bond paths.
Methods
Density Functional Theory (DFT), utilizing the 6–311 + G(d) basis set and the PBE1PBE hybrid density functional, has been employed to determine the minimum energy structures of B13 clusters with different charged states. The calculations have been performed using a superfine integration grid and very tight optimization settings, as implemented in GAUSSIAN 09 Revision D.01. To address potential instabilities in SCF calculations, wavefunction stability has been thoroughly analysed. AIM analysis and various real-space functions, including electron density, Localized Orbital Locator (LOL), Phase-Space defined Fisher Information Density (PS-FID), and Electron Localization Function (ELF), have been investigated. Multiwfn 3.8 was utilized for plotting these functions.
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.