Σ-hole Bond Research Articles

Utilization of σ-Holes on Sulfur and Halogen Atoms for Supramolecular Cation···Anion Interactions in Bilayer Ni(dmit)2 Anion Radical Salts

We prepared novel Ni(dmit)2 anion radical salts with ethyl-4-halothiazolium cations (Et-4XT, with X denoting the halogen: I, Br, or Cl), (Et-4IT)[Ni(dmit)2]2 (1), (Et-4BrT)[Ni(dmit)2]2 (2), and (Et-4ClT)2[Ni(dmit)2]5 (3). Single-crystal X-ray diffraction analysis of 1–3 indicates that, unlike the halogen atoms that have only one σ-hole each, the cations’ sulfur atoms each have two σ-holes that lie approximately along the extensions of the C–S bonds. The presence of the σ-holes is supported by electrostatic potential of the cations calculated based on the density functional theory method. In the crystals of 1–3, these σ-holes interact with lone pairs on the terminal thioketone moieties in the Ni(dmit)2 anion radicals to form electrostatic σ-hole bonds (halogen bonds and chalcogen bonds). This results in supramolecular cation···anion networks. Crystal and electronic structure analyses, and electrical and magnetic measurements reveal that the salts 1 and 2 are isostructural bilayer Mott systems, in which two...

σ‐Hole Bond Versus Hydrogen Bond: From Tetravalent to Pentavalent N, P, and As Atoms

Ab initio calculations were performed on complexes of ZH4 (+) (Z=N, P, As) and their fluoro derivatives, ZFH3 (+) and ZF4 (+) , with a HCN (or LiCN) molecule acting as the Lewis base through the nitrogen electronegative center. It was found that the complexes are linked by the ZH⋅⋅⋅N hydrogen bond or another type of noncovalent interaction in which the tetravalent heavy atom of the cation acts as the Lewis acid center, that is, when the Z⋅⋅⋅N link exists, which may be classified as the σ-hole bond. The formation of the latter interaction is usually preferable to the formation of the corresponding hydrogen bond. The Z⋅⋅⋅N interaction may be also considered as the preliminary stage of the SN 2 reaction. This is supported by the observation that for a short Z⋅⋅⋅N contact, the corresponding complex geometry coincides with the trigonal-bipyramidal geometry typical for the transition state of the SN 2 reaction. The Z⋅⋅⋅N interaction for some of complexes analyzed here possesses characteristics typical for covalent bonds. Numerous interrelations between geometrical, topological and energetic parameters are discussed. The natural bond orbital method as well as the Quantum Theory of "Atoms in Molecules" is applied to characterize interactions in the analyzed complexes. The experimental evidences of the existence of these interactions, based on the Cambridge Structure Database search, are also presented. In addition, it is justified that mechanisms of the formation of the Z⋅⋅⋅N interactions are similar to the processes occurring for the other noncovalent links. The formation of Z⋅⋅⋅N interaction as well as of other interactions may be explained with the use of the σ-hole concept.

Halogen bonding and other σ-hole interactions: a perspective

A σ-hole bond is a noncovalent interaction between a covalently-bonded atom of Groups IV-VII and a negative site, e.g. a lone pair of a Lewis base or an anion. It involves a region of positive electrostatic potential, labeled a σ-hole, on the extension of one of the covalent bonds to the atom. The σ-hole is due to the anisotropy of the atom's charge distribution. Halogen bonding is a subset of σ-hole interactions. Their features and properties can be fully explained in terms of electrostatics and polarization plus dispersion. The strengths of the interactions generally correlate well with the magnitudes of the positive and negative electrostatic potentials of the σ-hole and the negative site. In certain instances, however, polarizabilities must be taken into account explicitly, as the polarization of the negative site reaches a level that can be viewed as a degree of dative sharing (coordinate covalence). In the gas phase, σ-hole interactions with neutral bases are often thermodynamically unfavorable due to the relatively large entropy loss upon complex formation.

Polarization-induced σ-holes and hydrogen bonding

The strong collinear polarizability of the A-H bond in A-H···B hydrogen bonds is shown to lead to an enhanced σ-hole on the donor hydrogen atom and hence to stronger hydrogen bonding. This effect helps to explain the directionality of hydrogen bonds, the well known cooperative effect in hydrogen bonding, and the occurrence of blue-shifting. The latter results when significant additional electron density is shifted into the A-H bonding region by the polarization effect. The shift in the A-H stretching frequency is shown to depend essentially linearly on the calculated atomic charge on the donor hydrogen for all donors in which A belongs to the same row of the periodic table. A further result of the polarization effect, which is also expected for other σ-hole bonds, is that the strength of the non-covalent interaction depends strongly on external electric fields.

Cooperative and Diminutive Unusual Weak Bonding In F3CX···HMgH···Y and F3CX···Y···HMgH Trimers (X = Cl, Br; Y = HCN, and HNC)

MP2 calculations with cc-pVTZ basis set were used to analyze intermolecular interactions in F(3)CX···HMgH···Y and F(3)CX···Y···HMgH triads (X = Cl, Br; Y = HCN, and HNC) which are connecting with three kinds of unusual weak interactions, namely halogen-hydride, dihydrogen, and σ-hole. To understand the properties of the systems better, the corresponding dyads are also studied. Molecular geometries, binding energies, and infrared spectra of monomers, dyads, and triads were investigated at the MP2/cc-pVTZ computational level. Particular attention is given to parameters such as cooperative energies, cooperative dipole moments, and many-body interaction energies. Those complexes with simultaneous presence of a σ-hole bond and a dihydrogen bond show cooperativity energy ranging between -1.02 and -2.31 kJ mol(-1), whereas those with a halogen-hydride bond and a dihydrogen bond are diminutive, with this energetic effect between 0.1 and 0.63 kJ mol(-1). The electronic properties of the complexes have been analyzed using the molecular electrostatic potential (MEP), the electron density shift maps, and the parameters derived from the atoms in molecules (AIM) methodology.

Intramolecular S···O chalcogen bond in thioindirubin

Results of X-ray diffraction study and quantum-chemical calculations revealed that molecular conformation of thioindirubin molecule creates suitable conditions for formation of intramolecular C–H···O and S···O interactions. Analysis of molecular electrostatic potential (MEP) demonstrates existence of two areas of positive MEP (σ-holes) in the outermost part of the sulfur atom on the continuation of the lines of the C–S bonds. One of these σ-holes is oriented toward region of negative MEP around the oxygen atom of carbonyl group. Such situation corresponds to formation of σ-hole or chalcogen bond. Existence of both types of bonding interactions is confirmed by topological analysis of electron density distribution using “Atoms in Molecules” (AIM) theory. Energies of the C–H···O hydrogen bond and the S···O σ-hole bond derived from AIM and NBO theories are very close.

Competition and cooperativity between hydrogen bond and σ-hole bond in SCS–(HF) n ( n = 1 and 2) systems

Quantum chemical calculations have been performed for 1:1 and 1:2 systems of SCS and HF at the MP2/aug-cc-pVTZ level. There are two isomers for SCS–HF dimer. One is combined through a hydrogen bond with SCS as the electron donor; the other is formed by a σ-hole bond with SCS as the electron acceptor. Although the σ-hole bond is weaker than the hydrogen bond, the former is still competitive with the latter in this system. For comparison, the OCO–HF, SeCSe–HF, and SCS–HCl systems have also been analyzed. The most stable structure is the trimer where there are a FH⋯S hydrogen bond and a direct HF–HF contact simultaneously. It is shown that there is a cooperative effect between the hydrogen bond and the σ-hole bond. The band of 3843 cm −1 is assigned to the H–F stretch vibration in the σ-hole-bonded dimer. The natural bond orbital (NBO) and atoms in molecules (AIM) analyses have been performed for a better understanding the interactions.