Does Oxygen Feature Chalcogen Bonding?

Abstract

Using the second-order Møller–Plesset perturbation theory (MP2), together with Dunning’s all-electron correlation consistent basis set aug-cc-pVTZ, we show that the covalently bound oxygen atom present in a series of 21 prototypical monomer molecules examined does conceive a positive (or a negative) σ-hole. A σ-hole, in general, is an electron density-deficient region on a bound atom M along the outer extension of the R–M covalent bond, where R is the reminder part of the molecule, and M is the main group atom covalently bonded to R. We have also examined some exemplar 1:1 binary complexes that are formed between five randomly chosen monomers of the above series and the nitrogen- and oxygen-containing Lewis bases in N2, PN, NH3, and OH2. We show that the O-centered positive σ-hole in the selected monomers has the ability to form the chalcogen bonding interaction, and this is when the σ-hole on O is placed in the close proximity of the negative site in the partner molecule. Although the interaction energy and the various other 12 characteristics revealed from this study indicate the presence of any weakly bound interaction between the monomers in the six complexes, our result is strongly inconsistent with the general view that oxygen does not form a chalcogen-bonded interaction.

Nature of halogen‐centered intermolecular interactions in crystal growth and design: Fluorine‐centered interactions in dimers in crystalline hexafluoropropylene as a prototype

“…[31] We have also stressed in that study that the use of a 0.001 au isodensity envelope can be misleading especially when the V s,max associated with the local region is weakly positive or weakly negative, as this isodensity envelope is arbitrary. [33,35,61] In such a case, a 0.0015 au (or even higher) isodensity mapped electrostatic surface does reasonably recover what might be expected intuitively, and does explain why the F and Cl atoms in CF 4 and CH 3 Cl are capable of attracting a negative site, a view that is in line with rationalizations made by others. [62] We suggested that while a 0.001 au isodensity surface may be good for some systems, this should not be regarded as a universal isodensity envelope for mapping the electrostatic potential.…”

“…By contrast, and as mentioned above, the equatorial sites of the halogen derivative, which are generally occupied by lone pairs, are usually negative, but there are occasions when they can be positive (e.g., the fluorine in FCN and FCCCN). [33][34][35] These (generally) negative lateral sites enable the covalently bound halogen to act both as a hydrogen-and halogen-bond (and/or σ-hole bond) acceptor. [8][9][10][11][12][13][14]36] Provided the V s,max on the outer portion of the axial site is positive, it can serve as a halogen bond donor.…”

“…This is the case, for example, with the negative σ-hole in CH 3 F, C 6 H 5 F, and C 6 F 5 , which are not visible along the outer portion of the C F bond extensions. [33][34][35] It is thus recommended that the evaluation of the signs and magnitudes of local minima and maxima of electrostatic potential, simultaneously with the color-coded molecular surface of electrostatic potential, is an essential step in providing a definitive view of whether or not a specific site of an atom on a molecular surface does conceive a positive or a negative σ-hole, and whether it is able to sustain an attractive engagement with a negative site to form an NCI. [66] IUPAC recommendation of characterization An IUPAC task group [67] has defined halogen bonding with a specific set of characteristics and properties, which are valid only when the bound halogen has a positive axial site (i.e., a positive σ-hole).…”

“…Even so, halogen bonding should always be viewed as the attractive engagement between the positive outer region on the halogen and a negative site (a halogen bond acceptor), which is consistent with others. [33,35,68] This is a very broad view, and is applicable to many kinds of intermolecular interactions formed between two entities of opposite polarity. For instance, it is applicable regardless of whether the intramolecular and/or intermolecular interaction refers to pnictogen bonding, [69][70][71] chalcogen bonding, [69] dihydrogen [72] and hydrogen-hydrogen bonding, [73] σ-hole bonding, [8][9][10][11] and hydrogen bonding, [14,22] or similar interactions (all involve at least one positive site).…”

“…However, this kind of attraction between negative and positive sites cannot always explain the underlying chemistry of a lump-hole or type-III interaction, [33] as emanates between interacting sites of unequal electron density of identical polarity that are in close proximity. For instance, the intermolecular interaction persisting between fluorine atoms in numerous fluorinated systems following the type-I (and sometimes type-II) bonding topology might be grouped into this latter category, yet they do not comprise any requirement of involvement of a positive or a negative site [33,35] (further discussion is provided below with examples).…”