Structure-directing sulfur...metal noncovalent semicoordination bonding

Abstract

The abundance and geometric features of nonbonding contacts between metal centers and 'soft' sulfur atoms bound to a non-metal substituent R were analyzed by processing data from the Cambridge Structural Database. The angular arrangement of M, S and R atoms with /(R-SÁ Á ÁM) down to 150 was a common feature of the late transition metal complexes exhibiting shortened R-SÁ Á ÁM contacts. Several model nickel(II), palladium(II), platinum(II) and gold(I) complexes were chosen for a theoretical analysis of R-SÁ Á ÁM interactions using the DFT method applied to (equilibrium) isolated systems. A combination of the real-space approaches, such as Quantum Theory of Atoms in Molecules (QTAIM), noncovalent interaction index (NCI), electron localization function (ELF) and Interacting Quantum Atoms (IQA), and orbital (Natural Bond Orbitals, NBO) methods was used to provide insights into the nature and energetics of R-SÁ Á ÁM interactions with respect to the metal atom identity and its coordination environment. The explored features of the R-SÁ Á ÁM interactions support the trends observed by inspecting the CSD statistics, and indicate a predominant contribution of semicoordination bonds between nucleophilic sites of the sulfur atom and electrophilic sites of the metal. A contribution of chalcogen bonding (that is formally opposite to semicoordination) was also recognized, although it was significantly smaller in magnitude. The analysis of R-SÁ Á ÁM interaction strengths was performed and the structure-directing role of the intramolecular R-SÁ Á ÁM interactions in stabilizing certain conformations of metal complexes was revealed. research papers Acta Cryst. (2020). B76, 436-449 Ananyev et al. Structure-directing SÁ Á ÁM noncovalent semicoordination bonding 437 Figure 1Electrophilic (two -holes in blue) and nucleophilic sites (two LPs in red) in ChR 2 ; formation of a noncovalent contact (SB or HB) with an electrophile and noncovalent contact (ChB) with a nucleophile. The idealized angles are shown for both types of contacts.

Crystalline Peroxosolvates: Nature of the Coformer, Hydrogen-Bonded Networks and Clusters, Intermolecular Interactions

“…(Calculation of the electron density characteristics in plane wave basis is not trivial due to the use of pseudopotentials [133].) The approaches indicated above are often used to assess intermolecular interactions of various natures in various crystals [134][135][136], which gives rise to well-founded criticism [137,138].…”

Metal-Involving Chalcogen Bond. The Case of Platinum(II) Interaction with Se/Te-Based σ-Hole Donors

“…All our previous attempts to design a system that would include a ChB with nucleophilic metals as ChB accepting centers (to give σh-Ch••• metal d-orbital structure-directing interactions) were unsuccessful; the only identified contacts between metal and chalcogen centers were of semicoordinative M δ+ •••Ch δ− origin. 41 To continue our studies focused on the search for a metalbased ChB, we considered that the switch of the nature of the interaction between M and Ch centers from semicoordination (M δ+ •••Ch δ− ) to a ChB (σh-Ch•••d z 2 -M) can be achieved by the targeted selection of ChB donors and acceptors: (i) The strength of a ChB should increase in the order of S < Se < Te, with stronger EWGs of R EWG 2 Ch and with sterically unhindered Ch. For these reasons, as ChB donors, we addressed (4-NC 5 F 4 ) 2 Se 42 and (4-NC 5 F 4 ) 2 Te.…”

“…In contrast to the achieved progress in the understanding and utilization of metal-involving halogen bonding, ChB with a metal has not yet been discovered. All our previous attempts to design a system that would include a ChB with nucleophilic metals as ChB accepting centers (to give σh-Ch···metal d -orbital structure-directing interactions) were unsuccessful; the only identified contacts between metal and chalcogen centers were of semicoordinative M δ+ ···Ch δ− origin …”

Theoretical Characterization of the Hydrogen Bonding Interaction Sites of Mycolactone C Using the ONIOM Method

“…There is, however, very little work devoted to the study of competition between different sites within a single molecular structure. Etter and Reutzel 11 have been among the first research teams to classify the acceptor power of H binding (ALH) of different organic functionalities. More recently, some works were focused on the competition between nitrogen and oxygen atoms [12][13][14][15][16] or between amino and nitrile nitrogen atoms 17 in different structural units.…”