Browse
Submit Data
Databases
API
Help

Dataset Information

47 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Anion-Anion Interactions in Aerogen-Bonded Complexes. Influence of Solvent Environment.

ABSTRACT: Ab initio calculations are applied to the question as to whether a AeX5- anion (Ae = Kr, Xe) can engage in a stable complex with another anion: F-, Cl-, or CN-. The latter approaches the central Ae atom from above the molecular plane, along its C5 axis. While the electrostatic repulsion between the two anions prevents their association in the gas phase, immersion of the system in a polar medium allows dimerization to proceed. The aerogen bond is a weak one, with binding energies less than 2 kcal/mol, even in highly polar aqueous solvent. The complexes are metastable in the less polar solvents THF and DMF, with dissociation opposed by a small energy barrier.

SUBMITTER: Grabarz A

PROVIDER: S-EPMC8067769 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Anion-Anion Interactions in Aerogen-Bonded Complexes. Influence of Solvent Environment.

Grabarz Anna A Michalczyk Mariusz M Zierkiewicz Wiktor W Scheiner Steve S

Molecules (Basel, Switzerland) 20210407 8

Ab initio calculations are applied to the question as to whether a AeX5- anion (Ae = Kr, Xe) can engage in a stable complex with another anion: F-, Cl-, or CN-. The latter approaches the central Ae atom from above the molecular plane, along its C5 axis. While the electrostatic repulsion between the two anions prevents their association in the gas phase, immersion of the system in a polar medium allows dimerization to proceed. The ...[more]

PMID: 33917030

Similar Datasets

Hydrogen-Bonded and Halogen-Bonded: Orthogonal Interactions for the Chloride Anion of a Pyrazolium Salt.

Project description:In the hydrochloride of a pyrazolyl-substituted acetylacetone, the chloride anion is hydrogen-bonded to the protonated pyrazolyl moiety. Equimolar co-crystallization with tetrafluorodiiodobenzene (TFDIB) leads to a supramolecular aggregate in which TFDIB is situated on a crystallographic center of inversion. The iodine atom in the asymmetric unit acts as halogen bond donor, and the chloride acceptor approaches the σ-hole of this TFDIB iodine subtending an almost linear halogen bond, with Cl···I = 3.1653(11) Å and Cl···I-C = 179.32(6)°. This contact is roughly orthogonal to the N-H···Cl hydrogen bond. An analysis of the electron density according to Bader's Quantum Theory of Atoms in Molecules confirms bond critical points (bcps) for both short contacts, with ρbcp = 0.129 for the halogen and 0.321eÅ-3 for the hydrogen bond. Our halogen-bonded adduct represents the prototype for a future class of co-crystals with tunable electron density distribution about the σ-hole contact.

| S-EPMC8272125 | biostudies-literature

Anion-π interactions influence pK(a) values.

Project description:Five 8-(4-R-phenyl)-1-naphthol derivatives were prepared by PdCl(2)-catalysed electrophilic aromatic substitution. The pK(a)' values for these 1,8-disubstituted arene naphthols have been measured in acetonitrile/water (R = NO(2), 8.42; R = Cl, 8.52; R = H, 8.56; R = Me 8.68; and R = OMe, 8.71) and indicate a correlation with the electronic nature of the arene substituent, as determined through LFER analysis. Contributions to the relative pK(a)' values have been interpreted, using M06-2X DFT calculations, as consisting of two components: A small contribution from initial OH-π bonding in the starting materials and a larger contribution from anion-π interactions in the products. Such effects have implications for a range of other systems.

| S-EPMC3079108 | biostudies-literature

Comparison between Tetrel Bonded Complexes Stabilized by σ and π Hole Interactions.

Project description:The σ-hole tetrel bonds formed by a tetravalent molecule are compared with those involving a π-hole above the tetrel atom in a trivalent bonding situation. The former are modeled by TH₄, TH₃F, and TH₂F₂ (T = Si, Ge, Sn) and the latter by TH₂=CH₂, THF=CH₂, and TF₂=CH₂, all paired with NH₃ as Lewis base. The latter π-bonded complexes are considerably more strongly bound, despite the near equivalence of the σ and π-hole intensities. The larger binding energies of the π-dimers are attributed to greater electrostatic attraction and orbital interaction. Each progressive replacement of H by F increases the strength of the tetrel bond, whether σ or π. The magnitudes of the maxima of the molecular electrostatic potential in the two types of systems are not good indicators of either the interaction energy or even the full Coulombic energy. The geometry of the Lewis acid is significantly distorted by the formation of the dimer, more so in the case of the σ-bonded complexes, and this deformation intensifies the σ and π holes.

| S-EPMC6100375 | biostudies-literature

Anion mediated, tunable isoguanosine self-assemblies: decoding the conformation influence and solvent effects.

Project description:Systematic investigations were performed with various substituted groups at C8 purine and ribose. A series of isoG analogs, C8-phenyl substituted isoG were synthesized and applied for Cs+ coordination. The structural proximity between purine and ribose limited pentaplex formation for C8-phenyl substituted isoG derivatives. Based on this observation, deoxy isoG derivative with modification on ribose (tert-butyldimethylsilyl ether) was applied to assemble with the Cs+ cation. Critical solvent (CDCl3 and CD3CN) and anion (BPh4 -, BARF-, and PF6 -) effects were revealed, leading to the controllable formation of various stable isoG pentaplexes, including singly charged decamer, doubly charged decamer, and 15-mer, etc. Finally, the X-ray crystal structure of [isoG20Cs3]3+(BARF-)3 was successfully obtained, which is the first example of multiple-layer deoxy isoG binding with the Cs+ cation, providing solid evidence of this new isoG ionophore beyond two-layer sandwich self-assembly.

| S-EPMC8171338 | biostudies-literature

Striking Impact of Solvent Polarity on the Strength of Hydrogen-Bonded Complexes: A Nexus Between Theory and Experiment.

Project description:The binding free energy of hydrogen-bonded complexes is generally inversely proportional to the solvent dielectric constant. This occurs because the solvent-accessible surface area of the complex is always smaller than that of the individual subsystems, leading to a reduction in solvation energy. The present study explores the potential for stabilizing hydrogen-bonded complexes in a solvent with higher polarity. Contrary to the established understanding, we have demonstrated that the hydrogen-bonded complex (CH3CH2COOH⋅⋅⋅2,4,6-trimethylpyridine) can be better stabilized in a solvent with higher polarity. In this case, a significant charge transfer between the subsystems results in an increased dipole moment of the complex, leading to its stabilization in a more polar solvent. The expected inverse relationship between binding free energy and solvent dielectric constant is observed when the charge transfer between the subsystems is low. Thus, the magnitude of the charge transfer between subsystems is possibly the key factor in determining the stabilization or destabilization of H-bonded complexes in different solvents. Here, we present a comprehensive study that combines experimental and theoretical approaches, including nuclear magnetic resonance (NMR), infrared (IR) spectroscopies and quantum chemical calculations to validate the findings.

| S-EPMC11914941 | biostudies-literature

Hydrogen-bonded nickel(I) complexes.

Project description:A series of nickel(ii) tris(2-pyridylmethyl)amine (TPA) complexes featuring appended hydrogen bonds (H-bonds) to halides (F, Cl, Br) was synthesized and charcterized. Reduction to the nickel(i) state provided access to an unusual nickel(i) fluoride complex stabilized by H-bonds, enabling structural and spectroscopic characterization.

| S-EPMC7931650 | biostudies-literature

Beyond Size Complementary Factors in Anion-Tetralactam Macrocycle Complexes: From Intrinsic Gas-Phase to Solvent-Predicted Stabilities.

Project description:The gas-phase affinities of different types of anions X- (halogen anions, oxoanions, and hydrogenated anions) toward a model tetralactam-based macrocycle receptor (1), defined in terms of stability of an anion-receptor complex (1 + X-) against its disintegration, were evaluated by dissociation studies using a mass spectrometry-based methodology and supported by theoretical calculations (density functional theory-PBE0). The gas-phase complex with Cl- was found to be tailor-made for the macrocycle 1, while 1 + SA- (SA- = salicylate anion) and 1 + HSO4- were the weakest ones. Other complexes displayed a relatively low-stability dispersion (<1.2 kcal·mol-1). The 1/εr approach of the electrostatic contribution scaling method was used to predict the stability trends in a dimethyl sulfoxide solvent from the gas-phase binding energy partition using the symmetry-adapted perturbation theory. High deformation energy and differences in solvation energies were suggested to be the main sources of inconsistency in the predicted and experimental stabilities of 1 + F- and 1 + H2PO4- complexes.

| S-EPMC7590939 | biostudies-literature

Stabilizing Halogen-Bonded Complex between Metallic Anion and Iodide.

Project description:Halogen bonds (XBs) between metal anions and halides have seldom been reported because metal anions are reactive for XB donors. The pyramidal-shaped Mn(CO)5- anion is a candidate metallic XB acceptor with a ligand-protected metal core that maintains the negative charge and an open site to accept XB donors. Herein, Mn(CO)5- is prepared by electrospray ionization, and its reaction with CH3I in gas phase is studied using mass spectrometry and density functional theory (DFT) calculation. The product observed experimentally at m/z = 337 is assigned as [IMn(CO)4(OCCH3)]-, which is formed by successive nucleophilic substitution and reductive elimination, instead of the halogen-bonded complex (XC) CH3-I···Mn(CO)5-, because the I···Mn interaction is weak within XC and it could be a transient species. Inspiringly, DFT calculations predict that replacing CH3I with CF3I can strengthen the halogen bonding within the XC due to the electro-withdrawing ability of F. More importantly, in so doing, the nucleophilic substitution barrier can be raised significantly, ~30 kcal/mol, thus leaving the system trapping within the XC region. In brief, the combination of a passivating metal core and the introduction of an electro-withdrawing group to the halide can enable strong halogen bonding between metallic anion and iodide.

| S-EPMC9692347 | biostudies-literature

Side-On Bonded Beryllium Dinitrogen Complexes.

Project description:The preparation and spectroscopic identification of the complexes NNBe(η2 -N2 ) and (NN)2 Be(η2 -N2 ) and the energetically higher lying isomers Be(NN)2 and Be(NN)3 are reported. NNBe(η2 -N2 ) and (NN)2 Be(η2 -N2 ) are the first examples of covalently side-on bonded N2 adducts of a main-group element. The analysis of the electronic structure using modern methods of quantum chemistry suggests that NNBe(η2 -N2 ) and (NN)2 Be(η2 -N2 ) should be classified as π complexes rather than metalladiazirines.

| S-EPMC7317369 | biostudies-literature

Probing Solute-Solvent Interactions of Transition Metal Complexes Using L-Edge Absorption Spectroscopy.

Project description:In order to tailor solution-phase chemical reactions involving transition metal complexes, it is critical to understand how their valence electronic charge distributions are affected by the solution environment. Here, solute-solvent interactions of a solvatochromic mixed-ligand iron complex were investigated using X-ray absorption spectroscopy at the transition metal L2,3-edge. Due to the selectivity of the corresponding core excitations to the iron 3d orbitals, the method grants direct access to the valence electronic structure around the iron center and its response to interactions with the solvent environment. A linear increase of the total L2,3-edge absorption cross section as a function of the solvent Lewis acidity is revealed. The effect is caused by relative changes in different metal-ligand-bonding channels, which preserve local charge densities while increasing the density of unoccupied states around the iron center. These conclusions are corroborated by a combination of molecular dynamics and spectrum simulations based on time-dependent density functional theory. The simulations reproduce the spectral trends observed in the X-ray but also optical absorption experiments. Our results underscore the importance of solute-solvent interactions when aiming for an accurate description of the valence electronic structure of solvated transition metal complexes and demonstrate how L2,3-edge absorption spectroscopy can aid in understanding the impact of the solution environment on intramolecular covalency and the electronic charge distribution.

| S-EPMC7357850 | 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