Computational Insight into the Nature and Strength of the π-Hole Type Chalcogen∙∙∙Chalcogen Interactions in the XO2∙∙∙CH3YCH3 Complexes (X = S, Se, Te; Y = O, S, Se, Te)
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ABSTRACT:
SUBMITTER: Lei F
PROVIDER: S-EPMC10671658 | biostudies-literature | 2023 Nov
REPOSITORIES: biostudies-literature
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Project description:MP2/aug-cc-pVTZ calculations have been performed on π-hole triel- and chalcogen-bonded complexes involving a heteroaromatic compound. These complexes are very stable with large interaction energy up to -47 kcal mol-1. The sp2-hybridized nitrogen atom engages in a stronger π-hole bond than the sp-hybridized species although the former has smaller negative electrostatic potential. The sp2-hybridized oxygen atom in 1,4-benzoquinone is a weaker electron donor in the π-hole bond than the sp2-hybridized nitrogen atom. The π-hole triel bond is stronger than the π-hole chalcogen bond. A clear structural deformation is found for the triel or chalcogen donor molecule in these π-hole-bonded complexes. The triel bond exhibits partially covalent interaction, whereas the chalcogen bond exhibits covalent interaction in the SO3 complexes of pyrazine and pyridine derivatives with a sp2-hybridized nitrogen atom. Intermolecular charge transfer (>0.2e) occurs to a considerable extent in these complexes. In ternary complexes involving an aromatic compound, wherein a triel bond and a chalcogen bond coexist, both the interactions are weakened or strengthened when the central aromatic molecule acts as a double Lewis base or plays a dual role of both a base and an acid. Both electrostatic and charge transfer effects have important contributions toward changes in the strength of both interactions.
| S-EPMC9083131 | biostudies-literature
Project description:The pnicogen, chalcogen, and halogen bonds between 6-OXF2-fulvene (X = As, Sb, Se, Te, Br, and I) and three nitrogen-containing bases (FCN, HCN, and NH3) are compared. For each nitrogen base, the halogen bond is strongest, followed by the pnicogen bond, and the chalcogen bond is weakest. For each type of bond, the binding increases in the FCN < HCN < NH3 pattern. Both FCN and HCN engage in a bond with comparable strengths and the interaction energies of most bonds are < -6 kcal/mol. However, the strongest base NH3 forms a much more stable complex, particularly for the halogen bond with the interaction energy going up to -18 kcal/mol. For the same type of interaction, its strength increases as the mass of the central X atom increases. These bonds are different in strength, but all of them are dominated by the electrostatic interaction, with the polarization contribution important for the stronger interaction. The presence of these bonds changes the geometries of 6-OXF2-fulvene, particularly for the halogen bond formed by NH3, where the F-X-F arrangement is almost vertical to the fulvene ring.
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Project description:Herein, the potential of ZO3 and ZF2 aerogen-comprising molecules (where Z = Ar, Kr, and Xe) to engage in σ-, lp-, and π-hole site-based interactions was comparatively studied using various ab initio computations. For the first time, a premier in-depth elucidation of the external electric field (EEF) influence on the strength of the σ-, lp-, and π-hole site-based interactions within the ZO3/ZF2⋯NH3 and ⋯NCH complexes was addressed using oriented EEF with disparate magnitude. Upon the energetic features, σ-hole site-based interactions were noticed with the most prominent preferability in comparison to lp- and π-hole analogs. This finding was ensured by the negative interaction energy values of -11.65, -3.50, and -2.74 kcal mol-1 in the case of σ-, lp-, and π-hole site-based interactions within the XeO3⋯ and XeF2⋯NH3 complexes, respectively. Detailedly, the strength of the σ- and lp-hole site-based interactions directly correlated with the atomic size of the aerogen atoms and the magnitude of the positively oriented EEF. Unexpectedly, an irregular correlation was noticed for the interaction energies of the π-hole site-based interactions with the size of the π-hole. Interestingly, the π-hole site-based interactions within Kr-comprising complexes exhibited higher negative interaction energies than the Ar- and Xe-comprising counterparts. Notwithstanding, a direct proportion between the interaction energies of the π-hole site-based interactions and π-hole size was obtained by employing EEF along the positive orientation with high strength. The present outcomes would be a fundamental basis for forthcoming progress in studying the σ-, lp-, and π-hole site-based interactions within aerogen-comprising complexes and their pertinent applications in materials science and crystal engineering.
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Project description:Chalcogen bonds are σ hole interactions and have been used in recent years as an alternative to hydrogen bonds. In general, the electrostatic potential at the chalcogen atom and orbital delocalization effects are made responsible for the orientation of the chalcogen bond. Here, we were able to show by means of SAPT calculations that neither the induction (orbital delocalization effects) nor the electrostatic term is causing the spatial orientation of strong chalcogen bonds in tellurium-containing aromatics. Instead, steric interactions (Pauli repulsion) are responsible for the orientation. Against chemical intuition the dispersion energies of the examined tellurium-containing aromatics are far less important for the net attractive forces compared to the energies in the corresponding sulfur and selenium compounds. Our results underline the importance of often overlooked steric interactions (Pauli repulsion) in conformational control of σ hole interactions.
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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
Project description:Organic molecules with heavy main-group elements frequently form supramolecular links to electron-rich centres. One particular case of such interactions is halogen bonding. Most studies of this phenomenon have been concerned with either dimers or infinitely extended structures (polymers and lattices) but well-defined cyclic structures remain elusive. Here we present oligomeric aggregates of heterocycles that are linked by chalcogen-centered interactions and behave as genuine macrocyclic species. The molecules of 3-methyl-5-phenyl-1,2-tellurazole 2-oxide assemble a variety of supramolecular aggregates that includes cyclic tetramers and hexamers, as well as a helical polymer. In all these aggregates, the building blocks are connected by Te(…)O-N bridges. Nuclear magnetic resonance spectroscopic experiments demonstrate that the two types of annular aggregates are persistent in solution. These self-assembled structures form coordination complexes with transition-metal ions, act as fullerene receptors and host small molecules in a crystal.
| S-EPMC4838886 | biostudies-literature
Project description:Organic molecules with heavy main-group elements frequently form supramolecular links to electron-rich centres. One particular case of such interactions is halogen bonding. Most studies of this phenomenon have been concerned with either dimers or infinitely extended structures (polymers and lattices) but well-defined cyclic structures remain elusive. Here we present oligomeric aggregates of heterocycles that are linked by chalcogen-centered interactions and behave as genuine macrocyclic species. The molecules of 3-methyl-5-phenyl-1,2-tellurazole 2-oxide assemble a variety of supramolecular aggregates that includes cyclic tetramers and hexamers, as well as a helical polymer. In all these aggregates, the building blocks are connected by Te(…)O-N bridges. Nuclear magnetic resonance spectroscopic experiments demonstrate that the two types of annular aggregates are persistent in solution. These self-assembled structures form coordination complexes with transition-metal ions, act as fullerene receptors and host small molecules in a crystal.
| S-EPMC4838886 | biostudies-literature
Project description:The investigated co-crystal of 3-chloro-N-methylpyridinium iodide with tetrabromoquinone (3-Cl-N-MePy·I·Br4Q) reveals a π-hole interaction between an iodide anion and a quinoid ring involving an n → π* charge transfer. The quinoid ring has a partial negative charge (estimated to be in the range 0.08-0.11e) and a partial radical character, which is related to the black colour of the crystals (crystals of neutral tetrabromoquinone are yellow). A detailed X-ray charge density study revealed two symmetry-independent bond critical points between the iodide anions and carbon atoms of the ring. Their maximum electron density of 0.065 e Å-3 was reproduced by quantum chemical modelling. The energy of the interaction is estimated to be -11.16 kcal mol-1, which is comparable to the strength of moderate hydrogen bonding (about -10 kcal mol-1); it is dominantly electrostatic in nature, with a considerable dispersion component.
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Project description:Trichloro niobium(V) complexes 3 and 4 with the sulfur- or selenium-bridged [OEO]-type bis(phenolate) ligands (E = S, Se) were synthesized and fully characterized on the basis of their NMR spectroscopic data and X-ray crystallographic analysis. In the crystalline state of 4, the [OSeO]-core of the ligand was coordinated to the niobium center in a fac-fashion. The corresponding tribenzyl niobium(V) complexes 5 and 6 were also prepared by the reactions of 3 and 4 with 3 equivalents of PhCH2MgCl in toluene. The X-ray diffraction analysis of 6 revealed that the distorted six-coordinated niobium center incorporated in the [OSeO]-type ligand took a mer-fashion, and one benzyl ligand was coordinated to the niobium center by η2-fashion. Complexes 5 and 6 were tested for the phenylacetylene polymerization that produced poly(phenylacetylene)s (PPAs), oligomers, and triphenylbenzenes (TPBs) depending on the chalcogen atom in the [OEO]-type ligand.
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Project description:Gold(I) metal complexes are finding increasing applications as therapeutic agents against a variety of diseases. As their potential use as effective metallodrugs is continuously confirmed, the issue of their administration, distribution and delivery to desired biological targets emerges. Graphene and its derivatives possess attractive properties in terms of high affinity and low toxicity, suggesting that they can efficaciously be used as drug nanocarriers. In the present study, we computationally address the adsorption of a gold(I) N-heterocyclic monocarbene, namely, IMeAuCl (where IMe = 1,3-dimethylimidazol-2-ylidene), on graphene. The Au(I) N-heterocyclic carbene family has indeed shown promising anticancer activity and the N-heterocyclic ring could easily interact with planar graphene nanostructures. By means of high-level electronic structure approaches, we investigated the strength and nature of the involved interaction using small graphene prototypes, which allow us to benchmark the best-performing DFT functionals as well as assess the role of the different contributions to total interaction energies. Moreover, realistic adsorption enthalpies and free energy values are obtained by exploiting the optimal DFT method to describe the drug adsorption on larger graphene models. Such values (ΔHads = -18.4 kcal/mol and ΔGads= -7.20 kcal/mol for the largest C150H30 model) indicate a very favorable adsorption, mainly arising from the dispersion component of the interaction, with the electrostatic attraction also playing a non-negligible role.
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