Solving the enigma of weak fluorine contacts in the solid state: a periodic DFT study of fluorinated organic crystals

Abstract

The nature and strength of weak interactions with organic fluorine in the solid state are revealed by periodic density functional theory (periodic DFT) calculations coupled with experimental data on the structure and sublimation thermodynamics of crystalline organofluorine compounds. To minimize other intermolecular interactions, several sets of crystals of perfluorinated and partially fluorinated organic molecules are considered. This allows us to establish the theoretical levels providing an adequate description of the metric and electron-density parameters of the C-F⋯F-C interactions and the sublimation enthalpy of crystalline perfluorinated compounds. A detailed comparison of the C-F⋯F-C and C-H⋯F-C interactions is performed using the relaxed molecular geometry in the studied crystals. The change in the crystalline packing of aromatic compounds during their partial fluorination points to the structure-directing role of C-H⋯F-C interactions due to the dominant electrostatic contribution to these contacts. C-H⋯F-C and C-H⋯O interactions are found to be identical in nature and comparable in energy. The factors that determine the contribution of these interactions to the crystal packing are revealed. The reliability of the results is confirmed by considering the superposition of the electrostatic potential and electron density gradient fields in the area of the investigated intermolecular interactions.

Scheme 1. The molecular structures of the single-component crystals under study, divided into three classes by the type of predominant non-covalent interactions. Refcodes of the crystals are given in parentheses.

Fig. 1. C–H⋯F–C synthons referred to in this study. C–H⋯F dimer motif in the o-C₆H₂F₄ crystal (synthon A) and C–H⋯F–C dimer motif in the cocrystal of C₆F₆ and anthracene (synthon D). Spatial orientation of molecules in the C₆F₆ – anthracene dimer, obtained as a result of optimization at the PBE/6-31(F+)G** approximation (lower panel). H⋯F interactions are denoted by dotted lines.

Fig. 2. The deviations of experimental F⋯F distances ΔR(F⋯F) in crystalline CF₄, C₆F₆, C₅NF₅, C₅NHF₄ (black circles) and C₆F₅COOH (red triangles) from theoretical F⋯F distances R(F⋯F) computed at the PBE-D3/6-31+(F)G** level. The horizontal dotted line corresponds to zero deviation. The vertical dotted line is a sum of van der Waals radii for fluorine atoms (∼2.94 Å (ref. 94 and 95)).

Fig. 3. Fragments of crystalline C₄HF₅ (upper panel), m-C₆H₂F₄ (middle panel) and o-C₆H₂F₄ (lower panel). The C–H⋯F–C and C–F⋯F–C interactions are denoted by dotted lines. Two types of C–F⋯F–C contacts occur in C₄HF₅ crystal, namely, intra- and interlayer ones. The latter are shown with red dotted lines.

Fig. 4. Superposition of gradient fields of the electrostatic potential (pink) and the electron density (blue) in crystalline C₄HF₅: in the plane of the H1⋯(BCP) ⋯F9 interaction (left), in the plane of the inter-layer F5⋯(BCP)⋯F5 interaction (lower right), in the plane of the intra-layer F1⋯(BCP)⋯F9 (middle right) and the inter-layer F9⋯(BCP)⋯F13 (upper right) interactions. Bond paths are given by black lines. The nuclei positions are given by red circles.

Fig. 5. Electrostatic potential in the C₄HF₅ molecule, panels (a) and (b), and the molecule removed from the C₄HF₅ crystal, panels (c) and (d) projected onto surface of constant electron density. The latter value is 0.011 a.u. on panels (a) and (c) and 0.007 a.u. on panel (b) and (d). These values correspond to the electron density at the BCPs for the C9–H1⋯F9 and C1–F5⋯F5 interactions (Table 2). Bond paths are marked with yellow lines. The grey, light grey and yellow circles represent the carbon, hydrogen and fluorine atoms, respectively.

Fig. 6. Transformation of packing type in the row benzene – partially fluorinated benzenes – hexafluorobenzene. Refcodes of the crystals are given in parentheses. The C–H⋯F–C interactions are denoted by dotted lines.

Fig. 7. CSD-based estimation of the probability density function (PDF) of the C_ArH⋯X distance (a) and C_Ar–H⋯X angle (b) distribution, where X = O, F. The C–H bond lengths were normalized to the neutron-diffraction value (1.089 Å); the cone correction was also considered.

Fig. 8. Left panel: superposition of gradient fields of the electrostatic potential (pink) and the electron density (blue) for the KEGWEZ crystal. The bond paths are given by black lines. The nuclei positions are given by red circles. Right panel: the fragment of the KEGWEZ crystal. Atoms forming the C–H⋯F–C, C–F⋯F–C, C–H⋯O interactions are labeled.

Fig. 9. Deformation density maps for the C7–H2⋯O2 contact (left) and C8–H3⋯F1 contact (right) in the KEGWEZ crystal. The solid red lines represent positive contours and the broken blue lines represent negative contours. The values of charge depletion on the hydrogen atoms are given. All the contour lines are drawn at the intervals of ± 0.1 eÅ⁻³, except the additional contours with a step width of 0.01 eÅ⁻³ at the values close to those given on the map (0.03–0.1 eÅ⁻³). For atomic labels see Fig. 8.

Fig. 10. Superposition of gradient fields of the electrostatic potential (pink) and the electron density (blue) for the TISQER crystal. The bond paths are given by black lines. The nuclei positions are given by red circles. For atomic labels see Fig. S6.

Fig. 11. Deformation density maps for the C8–H3⋯F1 interaction (left) and O1–H8⋯O5 H-bond (right) in the TISQER crystal. The solid red lines represent positive contours and the broken blue lines represent negative contours. The values of charge depletion on the hydrogen atoms are given. The contours are drawn at the intervals of ± 0.05 eÅ⁻³. For atomic labels see Fig. S6.