Browse
Submit Data
Databases
API
Help

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

On the reciprocal relationship between σ-hole bonding and (anti)aromaticity gain in ketocyclopolyenes.

ABSTRACT: σ-Hole bonding interactions (e.g., tetrel, pnictogen, chalcogen, and halogen bonding) can polarize π-electrons to enhance cyclic [4n] π-electron delocalization (i.e., antiaromaticity gain) or cyclic [4n + 2] π-electron delocalization (i.e., aromaticity gain). Examples based on the ketocyclopolyenes: cyclopentadienone, tropone, and planar cyclononatetraenone are presented. Recognizing this relationship has implications, for example, for tuning the electronic properties of fulvene-based π-conjugated systems such as 9-fluorenone.

SUBMITTER: Paudel HR

PROVIDER: S-EPMC7376970 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Magnesium-halobenzene bonding: mapping the halogen sigma-hole with a Lewis-acidic complex.

Project description:Complexes of the Lewis base-free cations (MeBDI)Mg+ and ( tBuBDI)Mg+ with Ph-X ligands (X = F, Cl, Br, I) have been studied (MeBDI = HC[C(Me)N-DIPP]2 and tBuBDI = HC[C(tBu)N-DIPP]2; DIPP = 2,6-diisopropylphenyl). For the smaller β-diketiminate ligand (MeBDI) only complexes with PhF could be isolated. Heavier Ph-X ligands could not compete with bonding of Mg to the weakly coordinating anion B(C6F5)4 -. For the cations with the bulkier tBuBDI ligand, the full series of halobenzene complexes was structurally characterized. Crystal structures show that the Mg⋯X-Ph angle strongly decreases with the size of X: F 139.1°, Cl 101.4°, Br 97.7°, I 95.1°. This trend, which is supported by DFT calculations, can be explained with the σ-hole which increases from F to I. Charge calculation and Atoms-In-Molecules analyses show that Mg⋯F-Ph bonding originates from electrostatic attraction between Mg2+ and the very polar C δ+-F δ- bond. For the heavier halobenzenes, polarization of the halogen atom becomes increasingly important (Cl < Br < I). Complexation with Mg leads in all cases to significant Ph-X bond activation and elongation. This unusual coordination of halogenated species to early main group metals is therefore relevant to C-X bond breaking.

| S-EPMC8179342 | biostudies-literature

Bifurcated Halogen Bonding Involving Two Rhodium(I) Centers as an Integrated σ-Hole Acceptor.

Project description:The complexes [RhX(COD)]2 (X = Cl, Br; COD = 1,5-cyclooctadiene) form cocrystals with σ-hole iodine donors. X-ray diffraction studies and extensive theoretical considerations indicate that the d z 2-orbitals of two positively charged rhodium(I) centers provide sufficient nucleophilicity to form a three-center halogen bond (XB) with the σ-hole donors. The two metal centers function as an integrated XB acceptor, providing assembly via a metal-involving XB.

| S-EPMC8395620 | biostudies-literature

Anti-Electrostatic Pi-Hole Bonding: How Covalency Conquers Coulombics.

Project description:Intermolecular bonding attraction at π-bonded centers is often described as "electrostatically driven" and given quasi-classical rationalization in terms of a "pi hole" depletion region in the electrostatic potential. However, we demonstrate here that such bonding attraction also occurs between closed-shell ions of like charge, thereby yielding locally stable complexes that sharply violate classical electrostatic expectations. Standard DFT and MP2 computational methods are employed to investigate complexation of simple pi-bonded diatomic anions (BO-, CN-) with simple atomic anions (H-, F-) or with one another. Such "anti-electrostatic" anion-anion attractions are shown to lead to robust metastable binding wells (ranging up to 20-30 kcal/mol at DFT level, or still deeper at dynamically correlated MP2 level) that are shielded by broad predissociation barriers (ranging up to 1.5 Å width) from long-range ionic dissociation. Like-charge attraction at pi-centers thereby provides additional evidence for the dominance of 3-center/4-electron (3c/4e) nD-π*AX interactions that are fully analogous to the nD-σ*AH interactions of H-bonding. Using standard keyword options of natural bond orbital (NBO) analysis, we demonstrate that both n-σ* (sigma hole) and n-π* (pi hole) interactions represent simple variants of the essential resonance-type donor-acceptor (Bürgi-Dunitz-type) attraction that apparently underlies all intermolecular association phenomena of chemical interest. We further demonstrate that "deletion" of such π*-based donor-acceptor interaction obliterates the characteristic Bürgi-Dunitz signatures of pi-hole interactions, thereby establishing the unique cause/effect relationship to short-range covalency ("charge transfer") rather than envisioned Coulombic properties of unperturbed monomers.

| S-EPMC8780338 | biostudies-literature

Substituted adenine quartets: interplay between substituent effect, hydrogen bonding, and aromaticity.

Project description:Adenine, one of the components of DNA/RNA helices, has the ability to form self-organizing structures with cyclic hydrogen bonds (A4), similar to guanine quartets. Here, we report a computational investigation of the effect of substituents (X = NO2, Cl, F, H, Me, and NH2) on the electronic structure of 9H-adenine and its quartets (A4-N1, A4-N3, and A4-N7). DFT calculations were used to show the relationships between the electronic nature of the substituents, strength of H-bonds in the quartets, and aromaticity of five- and six-membered rings of adenine. We demonstrated how the remote substituent X modifies the proton-donating properties of the NH2 group involved in the H-bonds within quartets and how the position of the substituent and its electronic nature affect the stability of the quartets. We also showed the possible changes in electronic properties of the substituent and aromaticity of adenine rings caused by tetramer formation. The results indicate that the observed relationships depend on the A4 type. Moreover, the same substituent can both strengthen and weaken intermolecular interactions, depending on the substitution position.

| S-EPMC9054646 | biostudies-literature

Unconventional Type III Halogen···Halogen Interactions: A Quantum Mechanical Elucidation of σ-Hole···σ-Hole and Di-σ-Hole Interactions.

Project description:Herein, two unconventional type III halogen···halogen interactions, namely, σ-hole···σ-hole and di-σ-hole interactions, were reported in a series of halogenated complexes. In type III, the A-halogen···halogen angles are typically equal to 180°, and the occurrence of σ-hole on halogen atoms is mandatory. Using diverse quantum mechanical calculations, it was demonstrated that the occurrence of such interactions with binding energies varied from -0.35 to -1.30 kcal/mol. Symmetry-adapted perturbation theory-based energy decomposition analysis (SAPT-EDA) revealed that type III interactions are dominated by dispersion forces, while electrostatic forces are unfavorable. Cambridge Structure Database (CSD) survey unveiled the experimental evidence for the manifestation of σ-hole···σ-hole interactions in crystal structures. This work might be deemed as a foundation for a vast number of forthcoming crystal engineering and materials science studies.

| S-EPMC7469378 | biostudies-literature

Multiple local σ-aromaticity of nonagermanide clusters.

Project description:Nonagermanide clusters are widely used in inorganic synthesis and are actively studied by experimentalists and theoreticians. However, chemical bonding of such versatile species is still not completely understood. In our work we deciphered a bonding pattern for various experimentally obtained nonagermanide species. We localized the electron density via the AdNDP algorithm for the model structures ([Ge9]4-, [Ge9{P(NH2)2}3]-, Cu[Ge9{P(NH2)2}3] and Cu(NHC)[Ge9{P(NH2)2}3]) and obtained a simple and chemically intuitive bonding pattern which can explain the variety of active sites and the existence of both D 3h and C 4v geometries for such clusters. Moreover, the [Ge9]4- core is found to be a unique example of an inorganic Zintl cluster with multiple local σ-aromaticity.

| S-EPMC6568043 | biostudies-literature

Stabilizing σ-hole Dimethyl Interactions.

Project description:Methyl groups bound to electronegative atoms, such as N or O, are recognized to participate in tetrel bonding as Lewis acids. On the other hand, the capability of methyl groups bound to electropositive atoms, such as B or Al, to act as Lewis bases has been recently reported. Herein, we analyze the combination of these two behaviors to establish attractive methyl···methyl interactions. We have explored the Cambridge Structural Database to find experimental examples of these dimethyl-bound systems, finding a significant degree of directionality in the relative disposition of the two methyl groups. Moreover, we have carried out a comprehensive computational analysis at the DFT level of the dimethyl interactions, including the natural bond orbital, energy decomposition analysis, and topological analysis of the electron density (QTAIM and NCI). The dimethyl interaction is characterized as weak yet attractive and based on electrostatics, with a non-negligible contribution from orbital charge transfer and polarization.

| S-EPMC10327473 | biostudies-literature

σ-Aromaticity in planar pentacoordinate aluminium and gallium clusters.

Project description:Planar hypercoordinate structures are gaining immense attention due to the shift from common paradigm. Herein, our high level ab initio calculations predict that planar pentacoordinate aluminium and gallium centres in Cu5Al2+ and Cu5Ga2+ clusters are global minima in their singlet ground states. These clusters are thermodynamically and kinetically very stable. Detailed electronic structure analyses reveal the presence of σ-aromaticity which is the driving force for the stability of the planar form.

| S-EPMC9203769 | biostudies-literature

Revisiting Aromaticity and Chemical Bonding of Fluorinated Benzene Derivatives.

Project description:The electron delocalization of benzene (C6H6) and hexafluorobenzene (C6F6) was analyzed in terms of the induced magnetic field, nucleus-independent chemical shift (NICS), and ring current strength (RCS). The computed out-of-plane component of the induced magnetic field at a distance (r) greater than or equal to 1.0 Å above the ring center correlates well (R (2)>0.99) with the RCS value. According to these criteria, fluorination has two effects on the C6 skeleton; concomitantly, the resonant effects diminish the π electron delocalization and the inductive effects decrease the charge density at the ring center and therefore reduce the magnitude of the paratropic current generated in this region. The equilibrium between both effects decreases aromaticity in the fluorinated benzene derivatives. These results can be extrapolated to determine the aromaticity of any derivative within the series of fluorinated benzene derivatives (C6H(6-n)F n , where n=1-5).

| S-EPMC4522180 | biostudies-literature

Exploring the simultaneous σ-hole/π-hole bonding characteristics of a Br⋯π interaction in an ebselen derivative <i>via</i> experimental and theoretical electron-density analysis.

Project description:In this study, the nature and characteristics of a short Br⋯π interaction observed in an ebselen derivative, 2-(2-bromophenyl)benzo[d][1,2]selenazol-3(2H)-one, has been explored. The electronic nature of this Br⋯π interaction was investigated via high-resolution X-ray diffraction and periodic density functional theory calculations using atoms-in-molecules (AIM) analysis. This study unravels the simultaneous presence of σ-hole and π-hole bonding characteristics in the same interaction. The dual characteristics of this unique Br⋯π interaction are further established via molecular electrostatic potentials (MESPs) and natural bond orbitals (NBOs).

| S-EPMC6126650 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data