HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.
Chalcogen
bonding has been investigated in terms of the electron
density distribution ρ(r) around chalcogen atoms.
The evolution of ρ(r) along the series of chalcogen
atoms is shown based on ab initio calculations on chalcogenophthalic
anhydrides C8O2H4Chal (Chal = O,
S, Se, and Te), where the Chal atom is in its sp
3 hybridization. From a detailed analysis of the experimental
and theoretical electron density and the L(r) = −∇2ρ(r) function
in the crystal phase of C8O2H4Se,
we characterize directionality and strength of chalcogen bonding (Se···O
and Se···Se) and hydrogen bonding (Se···H)
interactions. In addition, several isolated dimers and a trimer of
C8O2H4Se have been also studied at
the X-ray geometry in order to compare interaction energies with those
estimated from the measured electron density. Similarly to halogen
atoms in halogen bonding interactions, the anisotropic distribution
of ρ(r) around the Chal atoms was found to be at
the origin of chalcogen bonding. Therefore, the concepts, developed
earlier for halogen bonding, are extended here to chalcogen bonding
interactions. From the results of this work, the L(r) function proves to be more precise than the σ-hole
concept to identify electrophilic sites of Se-atoms in sp
3 hybridization.
The structure of a crystal of Sr0.61Ba0.39Nb2O6 has been solved and refined as an incommensurate structure in five-dimensional superspace. The structure is tetragonal, superspace group P4bm(\,pp1/2,p - p1/2), unit-cell parameters a = 12.4566 (9), c = 7.8698 (6) Å, modulation vectors q
1 = 0.3075 (6) (a* + b*), q
2 = 0.3075 (6) (a* − b*). The data collection was performed on a KUMA-CCD diffractometer and allowed the integration of weak first-order satellite reflections. The structure was refined from 2569 reflections to a final value of R = 0.0479. The modulation affects mainly the positions of the O atoms, which are displaced by as much as 0.5 Å, and the site 4c that is occupied by Sr and Ba atoms. Only a simplified model, in which this atomic position is occupied by an effective atom Sr/Ba, could be refined from the data set. The modulation of displacement parameters has been used to account for the modulated distribution of Sr and Ba. The whole refinement uses only first-order modulation waves, but there are strong indications that for a complete solution the use of higher-order satellites and a more complicated model is necessary.
Trimers based on intermolecular halogen-bonding interactions (Hal 3 -synthons) have been studied in hexachlorobenzene, hexabromobenzene, pentachlorophenol, and pentabromophenol. Attention is paid to the comparison of Cl 3 -and Br 3 -synthons and to their competition with hydrogen bonds (HBs), based on the experimental and theoretical charge density analyses in crystal and gas phases. The main differences between Cl 3 -and Br 3 -synthons are established coming from the particular structure of the valence shell charge concentration region in Cl and Br atoms. Electrophilic−nucleophilic interactions take place within the intermolecular regions of Hal 3 -synthons by putting face-to-face charge depletion (CD) and charge concentration (CC) regions belonging to the valence shell of the halogen atoms. The electrostatic interaction follows the electrophilic and nucleophilic power of these regions and is monitored by the negative Laplacian values normalized to charge density unit (L/ρ) at the corresponding topological critical points (CPs) of the L(r) = −∇ 2 ρ(r) function. According to the topological and energetic properties at CPs of ρ(r) and L(r), it is observed that Hal 3 -synthons can successfully compete with intermolecular HBs in the analyzed structures. On the basis of the estimated interaction energy and the electrostatic descriptor Δ(L/ρ) = (L/ρ) CC − (L/ρ) CD , we conclude that a strong dispersion contribution assists Hal3-synthons in this competition.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.