{"title":"Towards a unified fold-cusp model for bond polarity scaling: electron rearrangements in the pyrolytic isomerization of cubane to cyclooctatetraene","authors":"Leandro Ayarde-Henríquez, Cristian Guerra, Patricia Pérez, Eduardo Chamorro","doi":"10.1007/s00894-024-06229-z","DOIUrl":null,"url":null,"abstract":"<div><h3>Context</h3><p>This study meticulously examines the criteria for assigning electron rearrangements along the intrinsic reaction coordinate (IRC) leading to bond formation and breaking processes during the pyrolytic isomerization of cubane (CUB) to 1,3,5,7-cyclooctatetraene (COT) from both thermochemical and bonding perspectives. Notably, no cusp-type function was detected in the initial thermal conversion step of CUB to bicyclo[4.2.0]octa-2,4,7-triene (BOT). Contrary to previous reports, all relevant fluxes of the pairing density must be described in terms of fold unfolding. The transannular ring opening in the second step highlights characteristics indicative of a cusp-type catastrophe, facilitating a direct comparison with fold features. This fact underscores the critical role of density symmetry persistence near topographical events in determining the type of bifurcation. A fold-cusp unified model for scaling the polarity of chemical bonds is proposed, integrating ubiquitous reaction classes such as isomerization, bimolecular nucleophilic substitution, and cycloaddition. The analysis reveals that bond polarity index (BPI) values within the [0, 10<sup>−5</sup>] au interval correlate with cusp unfolding, whereas fold spans over a broader [10<sup>−3</sup>, ∞) au spectrum. These insights emphasize that the cusp polynomial is suitable for describing chemical processes involving symmetric electron density distributions, particularly those involving homolytic bond cleavages; in contrast, fold characterizes most chemical events.</p><h3>Methods</h3><p>Geometry optimization and frequency calculations were conducted using various DFT functionals. In line with recent findings concerning the rigorous application of BET, the characterization of bond formations and scissions via unfoldings was carried out by carefully monitoring the determinant of the Hessian matrix at all potentially degenerate CPs and their relative distance. The computed gas-phase activation enthalpies strongly align with experimental values, stressing the adequacy of the chosen levels of theory in describing the ELF topography along the IRC. The BPI was determined using the methodology proposed by Allen and collaborators.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1000,"publicationDate":"2025-01-13","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/s00894-024-06229-z","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
This study meticulously examines the criteria for assigning electron rearrangements along the intrinsic reaction coordinate (IRC) leading to bond formation and breaking processes during the pyrolytic isomerization of cubane (CUB) to 1,3,5,7-cyclooctatetraene (COT) from both thermochemical and bonding perspectives. Notably, no cusp-type function was detected in the initial thermal conversion step of CUB to bicyclo[4.2.0]octa-2,4,7-triene (BOT). Contrary to previous reports, all relevant fluxes of the pairing density must be described in terms of fold unfolding. The transannular ring opening in the second step highlights characteristics indicative of a cusp-type catastrophe, facilitating a direct comparison with fold features. This fact underscores the critical role of density symmetry persistence near topographical events in determining the type of bifurcation. A fold-cusp unified model for scaling the polarity of chemical bonds is proposed, integrating ubiquitous reaction classes such as isomerization, bimolecular nucleophilic substitution, and cycloaddition. The analysis reveals that bond polarity index (BPI) values within the [0, 10−5] au interval correlate with cusp unfolding, whereas fold spans over a broader [10−3, ∞) au spectrum. These insights emphasize that the cusp polynomial is suitable for describing chemical processes involving symmetric electron density distributions, particularly those involving homolytic bond cleavages; in contrast, fold characterizes most chemical events.
Methods
Geometry optimization and frequency calculations were conducted using various DFT functionals. In line with recent findings concerning the rigorous application of BET, the characterization of bond formations and scissions via unfoldings was carried out by carefully monitoring the determinant of the Hessian matrix at all potentially degenerate CPs and their relative distance. The computed gas-phase activation enthalpies strongly align with experimental values, stressing the adequacy of the chosen levels of theory in describing the ELF topography along the IRC. The BPI was determined using the methodology proposed by Allen and collaborators.
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.