Description of changes in chemical bonding along the pathways of chemical reactions by deformation of the molecular electrostatic potential

2025
journal article
article
dc.abstract.enContext : The analysis of the changes in the electronic structure along intrinsic reaction coordinate (IRC) paths for model reactions: (i) ethylene + butadiene cycloaddition, (ii) prototype SN2 reaction $Cl^{-}$ + CH3Cl, (iii) HCN/CNH isomerization assisted by water, (iv) CO + HF → C(O)HF was performed, in terms of changes in the deformation density (Δr) and the deformation of MEP (ΔMEP). The main goal was to further examine the utility of the ΔMEP as a descriptor of chemical bonding, and to compare the pictures resulting from Δr and ΔMEP. Both approaches clearly show that the main changes in the electronic structure occur in the TS region. The ΔMEP picture is fully consistent with that based on Δρ for the reactions of the neutral species leading to the neutral products without large charge transfer between the fragments. In the case of reactions with large electron density displacements, the ΔMEP picture is dominated by charge transfer leading to more clear indication of charge shifts than the analysis of Δr. Methods: All the calculations were performed using the ADF package. The Becke–Perdew exchange–correlation functional was used with the Grimme’s dispersion correction (D3 version) with Becke-Johnson damping. The Slater TZP basis sets defned within the ADF program were applied. For the analysed reactions, the stationary points were determined and veri fed by frequency calculations, and the IRC was determined. Further analysis was performed for the structures of reactants, TS, products, and the points corresponding to the minimum and maximum of the reaction force. For each point, two frag ments, A and B, corresponding to the reactants were considered. The deformation density was calculated as the diference between the electron density of the system AB and the sum of densities of A and B, Δp(r) = $p^{AB}$(r) − $p^{A}$(r)− $p^{B}$(r), with the same fragment defnition as in the ETS-NOCV method. Correspondingly, deformation in MEP was determined as ΔV(r) = $V^{AB}$(r) −$V^{A}$(r)−$V^{B}$(r)
dc.affiliationSzkoła Doktorska Nauk Ścisłych i Przyrodniczych
dc.affiliationWydział Chemii : Zakład Chemii Teoretycznej im. Kazimierza Gumińskiego
dc.contributor.authorŻurowska, Olga - 401128
dc.contributor.authorMichalak, Artur - 101384
dc.date.accession2025-02-12
dc.date.accessioned2025-02-12T12:57:47Z
dc.date.available2025-02-12T12:57:47Z
dc.date.createdat2025-01-23T17:40:51Zen
dc.date.issued2025
dc.date.openaccess0
dc.description.accesstimew momencie opublikowania
dc.description.number1
dc.description.versionostateczna wersja wydawcy
dc.description.volume31
dc.identifier.articleid33
dc.identifier.doi10.1007/s00894-024-06239-x
dc.identifier.eissn0948-5023
dc.identifier.issn1610-2940
dc.identifier.urihttps://ruj.uj.edu.pl/handle/item/548166
dc.identifier.weblinkhttps://link.springer.com/article/10.1007/s00894-024-06239-x
dc.languageeng
dc.language.containereng
dc.rightsUdzielam licencji. Uznanie autorstwa 4.0 Międzynarodowa
dc.rights.licenceCC-BY
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/legalcode.pl
dc.share.typeinne
dc.subject.endeformation of molecular electrostatic potential
dc.subject.endeformation density
dc.subject.enchemical reactivity
dc.subject.enchemical bonding
dc.subject.encycloaddition reaction
dc.subject.enSN2 reaction
dc.subject.enHCN/CNH isomerization assisted by water
dc.subject.enCO+HF reaction
dc.subtypeArticle
dc.titleDescription of changes in chemical bonding along the pathways of chemical reactions by deformation of the molecular electrostatic potential
dc.title.journalJournal of Molecular Modeling
dc.typeJournalArticle
dspace.entity.typePublicationen
dc.abstract.en
Context : The analysis of the changes in the electronic structure along intrinsic reaction coordinate (IRC) paths for model reactions: (i) ethylene + butadiene cycloaddition, (ii) prototype SN2 reaction $Cl^{-}$ + CH3Cl, (iii) HCN/CNH isomerization assisted by water, (iv) CO + HF → C(O)HF was performed, in terms of changes in the deformation density (Δr) and the deformation of MEP (ΔMEP). The main goal was to further examine the utility of the ΔMEP as a descriptor of chemical bonding, and to compare the pictures resulting from Δr and ΔMEP. Both approaches clearly show that the main changes in the electronic structure occur in the TS region. The ΔMEP picture is fully consistent with that based on Δρ for the reactions of the neutral species leading to the neutral products without large charge transfer between the fragments. In the case of reactions with large electron density displacements, the ΔMEP picture is dominated by charge transfer leading to more clear indication of charge shifts than the analysis of Δr. Methods: All the calculations were performed using the ADF package. The Becke–Perdew exchange–correlation functional was used with the Grimme’s dispersion correction (D3 version) with Becke-Johnson damping. The Slater TZP basis sets defned within the ADF program were applied. For the analysed reactions, the stationary points were determined and veri fed by frequency calculations, and the IRC was determined. Further analysis was performed for the structures of reactants, TS, products, and the points corresponding to the minimum and maximum of the reaction force. For each point, two frag ments, A and B, corresponding to the reactants were considered. The deformation density was calculated as the diference between the electron density of the system AB and the sum of densities of A and B, Δp(r) = $p^{AB}$(r) − $p^{A}$(r)− $p^{B}$(r), with the same fragment defnition as in the ETS-NOCV method. Correspondingly, deformation in MEP was determined as ΔV(r) = $V^{AB}$(r) −$V^{A}$(r)−$V^{B}$(r)
dc.affiliation
Szkoła Doktorska Nauk Ścisłych i Przyrodniczych
dc.affiliation
Wydział Chemii : Zakład Chemii Teoretycznej im. Kazimierza Gumińskiego
dc.contributor.author
Żurowska, Olga - 401128
dc.contributor.author
Michalak, Artur - 101384
dc.date.accession
2025-02-12
dc.date.accessioned
2025-02-12T12:57:47Z
dc.date.available
2025-02-12T12:57:47Z
dc.date.createdaten
2025-01-23T17:40:51Z
dc.date.issued
2025
dc.date.openaccess
0
dc.description.accesstime
w momencie opublikowania
dc.description.number
1
dc.description.version
ostateczna wersja wydawcy
dc.description.volume
31
dc.identifier.articleid
33
dc.identifier.doi
10.1007/s00894-024-06239-x
dc.identifier.eissn
0948-5023
dc.identifier.issn
1610-2940
dc.identifier.uri
https://ruj.uj.edu.pl/handle/item/548166
dc.identifier.weblink
https://link.springer.com/article/10.1007/s00894-024-06239-x
dc.language
eng
dc.language.container
eng
dc.rights
Udzielam licencji. Uznanie autorstwa 4.0 Międzynarodowa
dc.rights.licence
CC-BY
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/legalcode.pl
dc.share.type
inne
dc.subject.en
deformation of molecular electrostatic potential
dc.subject.en
deformation density
dc.subject.en
chemical reactivity
dc.subject.en
chemical bonding
dc.subject.en
cycloaddition reaction
dc.subject.en
SN2 reaction
dc.subject.en
HCN/CNH isomerization assisted by water
dc.subject.en
CO+HF reaction
dc.subtype
Article
dc.title
Description of changes in chemical bonding along the pathways of chemical reactions by deformation of the molecular electrostatic potential
dc.title.journal
Journal of Molecular Modeling
dc.type
JournalArticle
dspace.entity.typeen
Publication
Affiliations

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