Characterization of fluorine-centred `F...O' σ-hole interactions in the solid state

Abstract

In the current study, the crystal structure of 1-(3-nitrophenyl)-2,2,2-trifluoroethanone (A1) and (E)-4-((4-fluorophenyl) diazenyl)phenol (A2) has been analyzed for the characterization of the presence of a `unique' and `rare' intermolecular C(sp/sp)-F...O contact, which has been observed to play a significant role in the crystal packing. Theoretical charge-density calculations have been performed to study the nature and strength associated with the existence of this intermolecular F...O contact, wherein the F atom is attached to an sp-hybridized C atom in the case of A1 and to an sp hybridized carbon in the case of A2. The crystal packing of the former contains two `electronically different' Csp-F...O contacts which are present across and in between the layers of molecules. In the latter case, it is characterized by the presence of a very `short' (2.708 Å) and `highly directional' (168° at ∠C4-F1...O1 and 174° at ∠C10-O1...F1) Csp-F...O contact. According to the Cambridge Structural Database (CSD) study, it is a rare example in molecular crystals. Topological features of F...O contacts in the solid state were compared with the gas-phase models. The two-dimensional and three-dimensional static deformation density obtained from theoretical multipole modeling confirm the presence of a charge depleted region on the F atoms. Minimization of the electrostatic repulsion between like charges are observed through subtle arrangements in the electronic environment in two of the short intermolecular F...O contacts. These contacts were investigated using inputs from pair energy decomposition analysis, Bader's quantum theory of atoms in molecules (QTAIM), Hirshfeld surface analysis, delocalization index, reduced density gradient (RDG) plot, electrostatic potential surface and distributed atomic polarizability. The intermolecular energy decomposition (PIXEL) and RDG-NCI (non-covalent interaction) analysis of the F...O contacts establish the interaction to be dispersive in nature. The mutual polarization of an O atom by fluorine and vice versa provides real physical insights into the role of atomic polarizability in interacting atoms in molecules in crystals.

Revealing Factors Influencing the Fluorine‐Centered Non‐Covalent Interactions in Some Fluorine‐Substituted Molecular Complexes: Insights from First‐Principles Studies

“…A similar view has been presented by Koohi and coworkers . Several studies have suggested the possibility of positive σ‐hole regions on covalently bound fluorine in molecules, enabling a fundamental understanding of the way fluorine in molecules interact with the negative sites to form fluorine‐centered non‐covalent interactions …”

“…[27] Several studies have suggested the possibility of positive s-hole regions on covalently bound fluorine in molecules, enabling a fundamental understanding of the way fluorine in molecules interact with the negative sites to form fluorine-centered non-covalent interactions. [45][46][47] The traditional "R d + ÀF dÀ " picture of fluorine suggests that it can only interact with electrophilic centers such as backbonecarbonyl carbon atoms or hydrogen-bond donors in proteins, but it has been asserted that this view, which neglects polarization, is incomplete and the trifluoromethyl groups in molecules can act both as electrophiles and nucleophiles to form non-covalent interactions. [48] A survey of the Protein Databank has revealed more than 600 weak interactions involving a trifluorotoluene moiety.…”

On the Interplay between Charge‐Shift Bonding and Halogen Bonding

“…Considered as a measure of the sharing of electron-pairs between atoms, [63,65] δ is found in the literature to have a value approaching to zero for the so-called non-bonding or weak interactions, meanwhile it shows values approaching to the formal bond order for covalent and CS bonds. [66] For instance, these δ values significantly differ from those obtained from crystal structures of exceptionally short O···F XBs, between 0.02 and 0.05, [67] and those corresponding to characteristic XB interactions in complexes between diiodine and substituted pyridines, between 0.27 and 0.41; [68] all these values being obtained at an analogous level of theory (B3LYP/6-311G**). Consequently, such δ(At, Cl) values in Y 3 CÀ At···Cl À systems indicate an important degree of exchanged electrons between At and Cl atoms, associated to a covalent and/or CS component.…”

SBA15–Fluconazole as a Protective Approach Against Mild Steel Corrosion: Synthesis, Characterization, and Computational Studies

“…These interactions were classified into two groups: F⋅⋅⋅O, O⋅⋅⋅O, N⋅⋅⋅⋅O, and C⋅⋅⋅O, belonging to non‐canonical weak interactions; and O−H⋅⋅⋅O, O−H⋅⋅⋅N, and O−H⋅⋅⋅F, categorized as hydrogen bonds. Although it is not clear that the four contacts of the former group could be in the bond categories of halogen, chalcogen, pnicogen, or tetrel, which have been explained mainly in electrostatic terms because of the presence of sigma holes, it is recognized that these contribute to the stability of molecular clusters and crystals and, therefore, must have an attractive nature. C−H⋅⋅⋅O can be considered a hydrogen bond, albeit a weaker and non‐classical type .…”

“…These interactions were classified into two groups:F ···O, O···O, N····O, and C···O, belonging to non-canonical weaki nteractions;a nd OÀH···O, OÀH···N, and OÀH···F,c ategorized as hydrogen bonds. Althoughi ti sn ot clear that the four contacts of the former group could be in the bond categories of halogen, chalcogen, pnicogen, or tetrel, [65][66][67][68][69][70][71][72][73] which have been explained mainly in electrostatic terms because of the presence of sigma holes, [74] it is recognized that thesec ontributet ot he stabilityo fm olecular clusters andc rystalsa nd, therefore, must have an attractive nature.C ÀH···O can be considered ah ydrogen bond, [72] albeit aw eaker and non-classical type. [75] For both groups of interactions, low values of the electron density were searched, with the Laplacian (positive in each case) and the virial field at the bond critical points (BCPs).…”