Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Eliseeva AA

PROVIDER: S-EPMC8395620 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Eliseeva Anastasiya A AA Ivanov Daniil M DM Rozhkov Anton V AV Ananyev Ivan V IV Frontera Antonio A Kukushkin Vadim Yu VY

JACS Au 20210219 3

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. ...[more]

PMID: 34467299

Similar Datasets

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

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

Halogen Bonding Involving Isomeric Isocyanide/Nitrile Groups.

Project description:2,3,5,6-Tetramethyl-1,4-diisocyanobenzene (1), 1,4-diisocyanobenzene (2), and 1,4-dicyanobenzene (3) were co-crystallized with 1,3,5-triiodotrifluorobenzene (1,3,5-FIB) to give three cocrystals, 1·1,3,5-FIB, 2·2(1,3,5-FIB), and 3·2(1,3,5-FIB), which were studied by X-ray diffraction. A common feature of the three structures is the presence of I···Cisocyanide or I···Nnitrile halogen bonds (HaBs), which occurs between an iodine σ-hole and the isocyanide C-(or the nitrile N-) atom. The diisocyanide and dinitrile cocrystals 2·2(1,3,5-FIB) and 3·2(1,3,5-FIB) are isostructural, thus providing a basis for accurate comparison of the two types of noncovalent linkages of C≡N/N≡C groups in the composition of structurally similar entities and in one crystal environment. The bonding situation was studied by a set of theoretical methods. Diisocyanides are more nucleophilic than the dinitrile and they exhibit stronger binding to 1,3,5-FIB. In all structures, the HaBs are mostly determined by the electrostatic interactions, but the dispersion and induction components also provide a noticeable contribution and make the HaBs attractive. Charge transfer has a small contribution (<5%) to the HaB and it is higher for the diisocyanide than for the dinitrile systems. At the same time, diisocyanide and dinitrile structures exhibit typical electron-donor and π-acceptor properties in relation to the HaB donor.

| S-EPMC10487382 | biostudies-literature

Structurally Optimized Potent Dual-Targeting NBTI Antibacterials with an Enhanced Bifurcated Halogen-Bonding Propensity.

Project description:We designed and synthesized an optimized library of novel bacterial topoisomerase inhibitors with p-halogenated phenyl right-hand side fragments and significantly enhanced and balanced dual-targeted DNA gyrase and topoisomerase IV activities of Staphylococcus aureus and Escherichia coli. By increasing the electron-withdrawing properties of the p-halogenated phenyl right-hand side fragment and maintaining a similar lipophilicity and size, an increased potency was achieved, indicating that the antibacterial activities of this series of novel bacterial topoisomerase inhibitors against all target enzymes are determined by halogen-bonding rather than van der Waals interactions. They show nanomolar enzyme inhibitory and whole-cell antibacterial activities against S. aureus and methicillin-resistant S. aureus (MRSA) strains. However, due to the relatively high substrate specificity for the bacterial efflux pumps, they tend to be less potent against E. coli and other Gram-negative pathogens.

| S-EPMC8436411 | biostudies-literature

Exploring Orthogonality between Halogen and Hydrogen Bonding Involving Benzene.

Project description:The concept of orthogonality between halogen and hydrogen bonding, brought out by Ho and coworkers some years ago, has become a widely accepted idea within the chemists' community. While the original work was based on a common carbonyl oxygen as acceptor for both interactions, we explore here, by means of M06-2X, M11, ωB97X, and ωB97XD/aug-cc-PVTZ DFT calculations, the interdependence of halogen and hydrogen bonding with a shared π-electron system of benzene. The donor groups (specifically NCBr and H2O) were placed on either or the same side of the ring, according to a double T-shaped or a perpendicular geometry, respectively. The results demonstrate that the two interactions with benzene are not strictly independent on each other, therefore outlining that the orthogonality between halogen and hydrogen bonding, intended as energetical independence between the two interactions, should be carefully evaluated according to the specific acceptor group.

| S-EPMC8659280 | biostudies-literature

The Origin of the σ-Hole in Halogen Atoms: a Valence Bond Perspective.

Project description:A detailed Valence Bond-Spin Coupled analysis of a series of halogenated molecules is here reported, allowing to get a rigorous ab initio demonstration of the qualitative models previously proposed to explain the origin of halogen bonding. The concepts of σ-hole and negative belt observed around the halogen atoms in the electrostatic potential maps are here interpreted by analysis of the relevant Spin Coupled orbitals.

| S-EPMC7136650 | biostudies-literature

Metal Centers as Nucleophiles: Oxymoron of Halogen Bond-Involving Crystal Engineering.

Project description:This review highlights recent studies discovering unconventional halogen bonding (HaB) that involves positively charged metal centers. These centers provide their filled d-orbitals for HaB, and thus behave as nucleophilic components toward the noncovalent interaction. This role of some electron-rich transition metal centers can be considered an oxymoron in the sense that the metal is, in most cases, formally cationic; consequently, its electron donor function is unexpected. The importance of Ha⋅⋅⋅d-[M] (Ha=halogen; M is Group 9 (Rh, Ir), 10 (Ni, Pd, Pt), or 11 (Cu, Au)) interactions in crystal engineering is emphasized by showing remarkable examples (reported and uncovered by our processing of the Cambridge Structural Database), where this Ha⋅⋅⋅d-[M] directional interaction guides the formation of solid supramolecular assemblies of different dimensionalities.

| S-EPMC9298210 | biostudies-literature

Nitropyridine-1-Oxides as Excellent π-Hole Donors: Interplay between σ-Hole (Halogen, Hydrogen, Triel, and Coordination Bonds) and π-Hole Interactions.

Project description:In this manuscript, we use the primary source of geometrical information, i.e., Cambridge Structural Database (CSD), combined with density functional theory (DFT) calculations (PBE0-D3/def2-TZVP level of theory) to demonstrate the relevance of π-hole interactions in para-nitro substituted pyridine-1-oxides. More importantly, we show that the molecular electrostatic potential (MEP) value above and below the π-hole of the nitro group is largely influenced by the participation of the N-oxide group in several interactions like hydrogen-bonding (HB) halogen-bonding (XB), triel bonding (TrB), and finally, coordination-bonding (CB) (N+-O- coordinated to a transition metal). The CSD search discloses that p-nitro-pyridine-1-oxide derivatives have a strong propensity to participate in π-hole interactions via the nitro group and, concurrently, N-oxide group participates in a series of interactions as electron donor. Remarkably, the DFT calculations show from strong to moderate cooperativity effects between π-hole and HB/XB/TrB/CB interactions (σ-bonding). The synergistic effects between π-hole and σ-hole bonding interactions are studied in terms of cooperativity energies, using MEP surface analysis and the Bader's quantum theory of atoms in molecules (QTAIM).

| S-EPMC6678756 | biostudies-literature

Halogen Bonding Involving CO and CS with Carbon as the Electron Donor.

Project description:MP2/aug'-cc-pVTZ calculations have been carried out to investigate the halogen-bonded complexes formed when CO and CS act as electron-pair donors through C to ClF, ClNC, ClCl, ClOH, ClCN, ClCCH, and ClNH₂. CO forms only complexes stabilized by traditional halogen bonds, and all ClY molecules form traditional halogen-bonded complexes with SC, except ClF which forms only an ion-pair complex. Ion-pair complexes are also found on the SC:ClNC and SC:ClCl surfaces. SC:ClY complexes stabilized by traditional halogen bonds have greater binding energies than the corresponding OC:ClY complexes. The largest binding energies are found for the ion-pair SC-Cl⁺:-Y complexes. The transition structures which connect the complex and the ion pair on SC:ClNC and SC:ClCl potential surfaces provide the barriers for inter-converting these structures. Charge-transfer from the lone pair on C to the σ-hole on Cl is the primary charge-transfer interaction stabilizing OC:ClY and SC:ClY complexes with traditional halogen bonds. A secondary charge-transfer occurs from the lone pairs on Cl to the in-plane and out-of-plane π antibonding orbitals of ClY. This secondary interaction assumes increased importance in the SC:ClNH₂ complex, and is a factor leading to its unusual structure. C-O and C-S stretching frequencies and 13C chemical shieldings increase upon complex formation with ClY molecules. These two spectroscopic properties clearly differentiate between SC:ClY complexes and SC-Cl⁺:-Y ion pairs. Spin-spin coupling constants 1xJ(C-Cl) for OC:ClY complexes increase with decreasing distance. As a function of the C-Cl distance, 1xJ(C-Cl) and ¹J(C-Cl) provide a fingerprint of the evolution of the halogen bond from a traditional halogen bond in the complexes, to a chlorine-shared halogen bond in the transition structures, to a covalent bond in the ion pairs.

| S-EPMC6150174 | biostudies-literature

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

Project description: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.

| S-EPMC7376970 | 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