Bruno Landeros-Rivera,
Rafael Moreno-Esparza and
Jesús Hernández-Trujillo*
Facultad de Química, UNAM, Mexico City, 04510, Mexico. E-mail: jesusht@unam.mx
First published on 11th August 2016
The effect of halogen substitution on the intermolecular interactions and crystal packing of arene–perhaloarene adducts was studied by means of theoretical methods. Solid state density functional theory geometry optimizations with the LAPW methodology were carried out for the hexafluorobenzene–pyrene, hexafluorobenzene–triphenylene, hexachlorobenzene–pyrene and hexachlorobenzene–triphenylene complexes using as starting points the X-ray crystal geometries measured in our laboratory. The structures of hexachlorobenzene–pyrene and hexachlorobenzene–triphenylene are reported for the first time. Using the tools of the quantum theory of atoms in molecules, the following six types of intermolecular interactions were identified: π⋯π, π⋯X, π⋯H, X⋯H, H⋯H and X⋯X where X = F or Cl. The electron density and related properties at the bond critical points and the NCI index allow to classify them as closed-shell weak interactions. The alternating regions of positive and negative electrostatic potential of chlorine and a larger deformation density than the one observed in fluorine, allow to understand the stronger pairwise interactions involving Cl. The cohesion energies were also computed, being more negative those for the molecular crystals involving hexachlorobenzene. This observation was rationalized in terms of the properties of the electron density at the intermolecular contacts. It was also found that dispersion is the most stabilizing long-range contribution to the dimerization energies of several related model systems. These results suggest that the properties of the electron density and the energetic stabilizing contributions provide complementary viewpoints for the understanding of the intermolecular interactions in these crystals.
In particular, much effort has been made to analyze the hexafluorobenzene–arene interactions either theoretically from molecular calculations16–18 or experimentally (in thermodynamic, spectroscopic and X-ray diffraction studies).19–22 These systems frequently crystallize in a parallel stacking motif, as in the case of the hexafluorobenzene–benzene adduct, and are considered as supramolecular synthons.1,23 The C6F6–C6H6 dimer has been used as a benchmark for evaluating the energetic components of this type of interactions. From a variety of post Hartree–Fock and dispersion-corrected density functional theory calculations, it is now clear that electrostatics alone can not explain the parallel-displaced intermolecular arrangement of the hexafluorobenzene–benzene complex and other perhaloarene–arene interactions.9,16,18,24–26 For example, according to symmetry adapted perturbation theory investigations, the dispersion contribution is the largest stabilizing component in the hexafluorobenzene–pyrene complex and in the (C6X6)2 and C6X6–C6H6 dimers, being X a halogen atom.9,26,27
The molecular interactions in organic crystals of arenes, haloarenes or their mixtures have been analyzed with theoretical methods, mostly using empirical atom–atom potentials.28–31 There are also quantum mechanical studies, for example, for the calculation of lattice parameters of the co-crystals of hexafluorobenzene with several polycyclic aromatic hydrocarbons (PAHs) and for the assessment of the stabilizing components in solid C6Cl6 and other halogenated compounds.21,32,33 From the interactions taking place in this type of crystals, it has been suggested that halogen–halogen bonds may be as strong as hydrogen bonds.34 However, the F⋯F contacts are often classified as closed-shell weak interactions.35,36 In this context, the descriptors and partitioning scheme of three-dimensional space based on the properties of the electron density, ρ(), within the quantum theory of atoms in molecules (QTAIM), has proved to be a suitable framework for the analysis of non-covalent interactions in molecular solids, solving some of the ambiguities of the interpretations based solely on geometric criteria.37–39 As examples, the nature of the interactions in pure hexachlorobenzene, other chlorinated compounds and a fluorinated benzene derivative have been analyzed with theoretical or experimental electron densities.32,33,40
The previous discussion shows the existing interest in characterizing the interactions involving halogenated aromatic compounds in the solid state. The study of hexahalobenzene–arene crystals provides a great opportunity for exploring a diversity of intermolecular interactions; the analysis of this type of systems has not been carried out before in terms of the electron density. It is also important to point out that crystal structures of hexachlorobenzene–arene complexes have not been published so far. Because of the similar properties of the hexachloro- and hexafluoro-benzene dimers, it is proposed here that the C6Cl6–arene crystals will have the same motif as the C6F6–arene ones, in which the Cl⋯H and Cl⋯Cl interactions should provide further stabilization that can be quantified with the properties of ρ(). In this work, the adducts hexafluorobenzene–pyrene (1), hexafluorobenzene–triphenylene (2), hexachlorobenzene–pyrene (3) and hexachlorobenzene–triphenylene (4) are studied through solid-state DFT calculations. The corresponding crystal structures were optimized using as starting point the atomic positions obtained from X-ray diffraction experiments carried out in our laboratory. From these, the crystal structures of 3 and 4 are reported for the first time. The topological analysis of ρ(
) was carried out using the theoretical structure factors in order to evaluate the interactions stabilizing these molecular crystals. In addition, molecular calculations of selected clusters based on the crystal structures were performed to complement the solid state results. Additionally, an energetic analysis of the four adducts was performed. The cohesion energies of the crystals and interaction energies of selected model dimers were computed; the corresponding trends are discussed and compared with the properties of ρ(
).
Complex | 1 | 2 | 3 | 4 |
Formula | C6F6·C16H10 | C6F6·C18H12 | C6Cl6·C16H10 | C6Cl6·C18H12 |
FW | 388.30 | 414.34 | 487.03 | 513.07 |
T/K | 100(2) | 130(2) | 240(2) | 100(2) |
Space group | P21/c | P21/c | P![]() |
P21/c |
a/Å | 6.8764(1) | 13.9028(10) | 7.367(3) | 17.2096(3) |
b/Å | 13.2307(2) | 7.1867(4) | 8.555(2) | 7.2895(1) |
c/Å | 9.1980(1) | 17.3403(14) | 15.803(5) | 18.0874(3) |
α/° | 90 | 90 | 94.02(2) | 90 |
β/° | 106.215(1) | 92.478(6) | 102.77(3) | 116.651(2) |
γ/° | 90 | 90 | 89.86(3) | 90 |
Z | 2 | 4 | 2 | 4 |
λ/Å | 0.71073 | 0.71073 | 0.71073 | 0.71073 |
θmax | 30.507 | 25.248 | 25.253 | 30.438 |
Nref. | 2454 | 3127 | 3494 | 6156 |
Rint | 0.0250 | 0.0366 | 0.0295 | 0.0516 |
R1 | 0.0363 | 0.0967 | 0.0663 | 0.0255 |
wR | 0.1205 | 0.3199 | 0.1847 | 0.0711 |
GooF | 1.557 | 1.114 | 1.125 | 1.150 |
Geometry optimizations of the crystal structures of the systems 1–4 were carried out with the Wien2K code41 using the PBEsol density functional employing the linearized augmented plane wave (LAPW) method. DFT-D3 gradients42 with three-body terms and the Becke–Johnson damping function were included in order to properly account for the long-range interactions in the optimization of the atomic positions.43 The cell parameters were fixed to the experimental values given in Table 1 and the atomic coordinates obtained from the refinements were used as input data at the outset. The convergence of the integrations in reciprocal space was tested for the smallest unit cell using up to 10 k-points; it was found that 1 k-point was appropriate for the sizable cells and insulator features of all the solids. The following muffin-thin radii (RMT) were used for the atoms in all the structures: RMT(H) = 0.56, RMT(C) = 1.12, RMT(F) = 1.30 and RMT(Cl) = 1.60. The criterion used for the number of plane waves was RKmax = 3.0, because of the small size of the H atoms. Graphical representations of the crystalline structures were created with mercury.44 Because of the difficulties inherent to an appropriate description of ρ() by the LAPW method, single point calculations at the optimized geometries (obtained from the Wien2K calculations) were carried out with the Crystal14 (ref. 45) code at the PBEsol/6-21G(d,p) level of theory. Static structure factors, corresponding to a 0.5 Å resolution, were generated with the XFAC keyword included in Crystal14. The theoretical ρ(
) was constructed by means of a multipole refinement fitted against the static structure factors with the XD2006 package,46 which is based on the Hansen–Coppens formalism.47 The deformation density maps, as well as the topological analysis of ρ(
) within the QTAIM framework, were carried out with the WinXPRO program.48 The electrostatic potentials were visualized with Moliso.49 A description of the results of the multipole refinement is provided in the ESI.†
The cohesive energy was calculated as Ecoh = EAB − EA − EB, where EAB stands for the energy of the adduct in solid-state, and EA and EB for the molecular energies of the A and B monomers, respectively. Each of the latter values was obtained after optimizing the molecular geometry with one molecule per unit cell so that the closest contacts are at least 8 Å apart. The RKmax parameter for the perhalogenated species was set to 6.0 to achieve energetic consistency with the calculations of the adducts. In addition, dimerization energies of selected A–B pairs were computed with the PIXEL method using the PIXEL-CLP program package.50–52
Single point calculations of molecular hexamers of 1–4 were carried out at the PBE/6-311++G(d,p) level of theory with Gaussian 09.53 Each hexamer consists of 3 perhaloarene and 3 arene molecules fixed at the optimized crystalline geometry, selected in such a way that each type of non-covalent interaction appears at least once (see discussion below for the non-covalent interactions classification). The topological analysis of ρ() of the molecular clusters was carried out with the AIMALL package.54 The NCI index55 was obtained with the program NCIPLOT55,56 and visualized with VMD.57
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Fig. 1 Crystal packing of 1–4. The a, b and c cell axes are shown in red, green and blue, respectively. |
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Fig. 2 Molecular graphs of (a) 1 and (b) 4 in the solid and in a molecular cluster using the same atomic coordinates. BCPs are depicted in red and bond paths in gray. |
The electron density at the BCP, ρb, is used as a measure of non-covalent interaction strength and is the property emphasized in this study. In addition, other topological descriptors60,61 evaluated at the intermolecular BCPs are also taken into consideration. Table S1 of the ESI† contains the average values the following scalar fields at the BCPs in the crystals: the Laplacian, ∇2ρb; the electronic energy density, Hb; the potential energy density, Vb; and its ratio with the positive definite kinetic energy density, |Vb/Gb|. All these properties are small and, except for Vb, positive for the four complexes allowing to classify the 6 groups of contacts as weak closed-shell interactions. The NCI index of W. Yang et al.55 is also used as a complement for analysis of intermolecular interactions from a non-local perspective. The NCI isosurfaces shown in Fig. S2 of the ESI,† show similar trends and corroborate the weak nature of the interactions. These surfaces appear in the internuclear regions of all six types of contacts with those for π⋯π and π⋯X appearing jointly as a flat surface. Fig. S2† also shows the steric clashes in the middle of the rings, whose pattern is associated in this approach with ring stress.55 In addition, the deformation density, Δρ(), a useful tool for the visualization of the anisotropic distribution of ρ(
),62 is shown in Fig. 3 for a fluorine atom in 1 and a chlorine atom in 3, respectively; the electrostatic potential projected on ρ(
) = 0.1 e Å−3 envelopes is also displayed for dimers in these two systems. It is clear that the Cl atoms have the largest deformation of ρ(
). Moreover, in contrast to fluorine, they have a region of positive electrostatic potential values which certainly affects their interactions, as has been reported for other systems.62
The ρb values for the crystalline structures are plotted in Fig. 4 versus those in the molecular clusters, . The slope and intercept are close to the ideal 1 and 0 values, respectively, although some dispersion of the data is also observed. This result is a consequence of the molecular nature of these solids. The largest deviation is found for the X⋯H interactions, for which
is in general larger than ρb, although this might just be consequence of constraining all the κ parameters of the H atoms to the same value.
Fig. 5 depicts the values of ρb as a function of the distance in each pair of atoms for the six groups of intermolecular contacts. In average, the strength of all the pairwise interactions decreases when increasing the internuclear distance, as expected. As can be seen in Fig. 5(a), the π⋯π contacts are stronger for the adducts formed by the fluorinated compounds because of their shorter intermolecular distances. The BCP associated with the largest distance in Fig. 5(a) corresponds to a non-parallel interaction. Conversely, according to Fig. 5(b), the chlorinated complexes have more and stronger π⋯X interactions than the fluorinated ones even for same distance values.
π⋯H contacts are only observed in 2 and 4, perhaps because their crystal structures involve rotated adjacent layers (Fig. 2). According to the values of ρb displayed in Fig. 5(c), the topological properties at the intermolecular BCPs shown in Table S1† and because of the large deviation of the C–H⋯C fragments from linearity, it is not possible to classify these interactions as weak hydrogen bonds. It is also worth mentioning that most of these interactions are close to conflict structural catastrophes that could yield non-parallel π⋯π interactions upon small geometric perturbations.
X⋯H is the most copious interaction in the four complexes for which Fig. 5(d) shows the broad distribution of ρb values with respect to X–H distances. The larger values for the perchlorinated complexes suggest that substitution of fluorine by chlorine results in stronger X⋯H interactions. This observation is in agreement with findings in a molecular beams study of CH2FCl⋯H2CO clusters where these two interactions are present and compete with each other; accordingly, the Cl⋯H interaction is favored over the one involving fluorine.63 The presence of C–H⋯Cl contacts is common in crystals64 and they have been classified as a non-conventional hydrogen bonds.65 However, the NCI surfaces of the complexes in Fig. S1† are characteristic of very weak hydrogen bonds66 and the properties ρ() do not allow for their unambiguous identification as hydrogen bonds. In addition, as Table S1† shows, both C–H⋯F and C–H⋯Cl interactions are close to the van der Waals limit.
Fig. 5(e) shows the ρb values for the H⋯H interactions, the so-called hydrogen–hydrogen bonds.67 Whereas 1–3 have intermolecular contacts of this type, these appear in the intramolecular regions of 2 and 4, as can be seen in Fig. 2 for both the crystals and the molecular clusters. It has been argued that the hydrogen–hydrogen bond might be an artifact of the closeness between hydrogen atoms without any stabilizing effect.68,69 Nevertheless, there is increasing evidence derived from theoretical and experimental works, in both molecular and solid-state complexes, concluding that this type of interactions has an actual stabilizing effect.61,70 For instance, Hathwar et al.71 estimated a stabilization of up to 6.6 kJ mol−1 by H⋯H bonds in the crystal structure of orthorhombic rubrene, which shares some features with the arenes studied in this work. The topological properties at BCPs for these weak interactions are about the same order of magnitude as for the other contacts. The largest ρb values observed in Fig. 5(e) involve distances shorter than 2.40 Å, the sum of van der Waals radii. In addition, some disc-shaped NCI isosurfaces are similar to those found for the X⋯H interactions. All these results support the stabilizing effects of the intermolecular H⋯H bonds in the complexes.
The most contrasting difference between perfluorinated and perchlorinated complexes is found in the X⋯X interactions, Fig. 5(f). In comparison to the other groups, the ρb values at the Cl⋯Cl BCPs follows a monotonous attenuation. Interestingly, this behavior has also been found for Cl⋯Cl interactions in other chlorinated crystals.33 Whereas the F⋯F contacts appear only at separations smaller than 3.6 Å, the Cl⋯Cl interactions occur at distances as big as 4.4 Å, which are greater than for any other group. Compared to fluorine, the larger size of the intermolecular NCI surfaces, the alternating regions of positive and negative values of electrostatic potential and the larger deformation density of chlorine (both shown in Fig. 3) contribute to the ability of this atom to form stronger halogen–halogen bonds at larger distances.
In summary, Fig. 5 shows that in 3 and 4 the stabilizing effects are achieved at larger distances than in 1 and 2. At a fixed distance, ρb can be up to 5 times larger in chlorinated species in comparison with the fluorinated ones, which involves stronger interactions. Although it is incorrect to attribute the crystal packing of these compounds to the halogen–halogen interactions only, it is undeniable that they directly affect the structure of the chlorinated versus the fluorinated solids.
From the structural point of view, halogen–halogen interactions are commonly classified as type I (θ1 ≈ θ2) or type II (θ1 ≈ 90°, θ2 ≈ 180°), where θ1 and θ2 are the C–X1⋯X2 and X1⋯X2–C angles (X = halogen), respectively.72 The former are believed to be a consequence of close packing and the latter to the action of electrostatic forces. Table 2 contains the average values of ρb, interatomic distances and angles θ1 and θ2 for the X⋯X contacts in all four complexes. From this table, it seems troublesome to classify the geometrical arrangements of the complexes as type I or II. It has been suggested that these characteristics of the Cl⋯Cl interactions entail an interplay between a decrease in the repulsion and an increase of the attractive electrostatic atom–atom interactions, although dispersion and other contributions among entire molecules should be taken into account.27,62,73,74
Complex | ρ(![]() |
Distance | θ1 | θ2 |
---|---|---|---|---|
1 | 0.009 | 3.436 | 132.28 | 140.97 |
2 | 0.009 | 3.471 | 108.93 | 121.24 |
3 | 0.046 | 3.650 | 132.37 | 149.62 |
4 | 0.021 | 4.038 | 115.46 | 133.462 |
The cohesion energies calculated at the present level of theory for the crystal adducts are presented in Table 3. They show that the interactions involving C6Cl6 are stronger than those with C6F6, in agreement with the general trends of ρb in Fig. 5. Further information on how much of the cohesive energies is recovered by the atomic contact pairs can be obtained from potential energy density at the intermolecular BCPs using the Espinosa–Molins–Lecomte (EML) equation,78 in this case applied as E = 0.5∑biVbi, where the sum runs over all the intermolecular atom–atom contacts of one molecule of C6X6 and one of PAH in the unit cell. Further details are provided in the ESI.† As a result of using the Vb values from Table S1,† this procedure recovers on average 50% of the DFT cohesive energy. The empirical nature of the EML equation has been addressed in the literature emphasizing that coefficients other than 0.5, which was obtained for hydrogen bonded crystals, have been used elsewhere.79,80 It should also be emphasized that most of the times this equation underestimates Ecoh. Interestingly, the use of E′coh = ∑biVbi instead, essentially recovers the DFT cohesive energy, as shown in Table 3. In other words, the trends obtained with this approximation to the cohesive energies in terms of the atom–atom contacts are correct because the larger values of E′coh correspond to the C6Cl6–PAH crystals, advocating for a relevant role of the pairwise interactions as a whole in the stabilization of the complexes 1–4.
Complex | Ecoh | E′coh | (C6X6)2 | (PAH)2 | C6X6–PAHa | C6X6–PAHb |
---|---|---|---|---|---|---|
a In astacked and bedge–edge intermolecular arrangements. | ||||||
1 | −45.7 | −46.8 | −0.3 | −3.7 | −7.8 | −1.6 |
2 | −42.0 | −40.6 | −0.7 | −5.4 | −7.4 | −1.8 |
3 | −60.2 | −61.6 | −1.9 | −3.5 | −12.4 | −2.9 |
4 | −58.9 | −61.8 | −2.0 | −5.2 | −13.9 | −4.0 |
Finally, the PIXEL method was used to estimate the long-range contributions to the dimerization energies (DE) of selected intermolecular pairs taken from the crystal structures. The resulting DE values are displayed in Table 3 and the corresponding long-range contributions are included in Table S2 of the ESI.† Four types of dimers were considered and the strongest one of each was analyzed. In all cases, the dispersion energy is the largest stabilizing component. The stacked C6X6–PAH dimers have the largest DE values and, from these, the chlorinated complexes are the most stable ones. The other dimers have smaller interaction energies in part because of their lateral arrangements dictated by the crystal packing. However, the remaining dimers of each type (for example, there are six C6Cl6 molecules around each C6Cl6 in 3) should also be taken into account to fully explain the cohesive energy. Concerning the atom–atom contacts defined in terms of the molecular graphs, not all six types are present simultaneously in these complexes: whereas the stacked C6X6–PAH dimers present π⋯π and π⋯X contacts, the edge–edge complexes have X⋯H interactions; in (PAH)2 only H⋯H and C⋯H contacts appear; and (C6X6)2 only have halogen–halogen bonds. If exclusively the ρb values were considered, the (C6Cl6)2 dimers should have the largest DE values. Despite that the energetics of complex formation cannot be fully accounted for by the Cl⋯Cl bonds, it is clear from these results that the charge distribution of the Cl atom (discussed before in terms of the electrostatic potential and the Δρ envelopes shown in Fig. 3) affects the crystal packing of 3 and 4 compared to the fluorinated solids.
The electron densities obtained from a multipole refinement of the theoretical structure factors were used to evaluate the nature of the intermolecular pairwise interactions taking place in the adducts by means of the quantum theory of atoms in molecules; the NCI index was also used to gain non-local complementary information. In addition, model molecular clusters were studied in order to make comparisons with the results for the solid state. The molecular graphs defined in terms of the gradient of the electron density and the topological descriptors evaluated at the bond critical points allowed to identify six types of closed-shell weak interactions in the crystals: π⋯π, π⋯X, π⋯H, X⋯H, H⋯H and X⋯X being X = F or Cl. Apart from minor discrepancies, they are also present in the corresponding molecular clusters, in agreement with the molecular nature of these solids. Another interesting finding is that, as in a wide variety of other types of crystals, the hydrogen–hydrogen bonds detected are of an stabilizing nature. In spite of weakening the π⋯π interactions, halogen substitution of fluorine by chlorine enhances the stabilizing contribution of the π⋯X, X⋯H and the halogen–halogen interactions. The cohesion energies of the crystals were also calculated. As an attempt to understand the observed trends of this property in terms of atom–atom contacts, a variant of the Espinosa–Molins–Lecomte equation was used. In agreement with the cohesive energies calculated using the DFT method, this procedure assigned the largest values to the crystals involving C6Cl6. In order to explore the relevance of non-local interactions between the charge distributions, the dimerization energies of several model systems were also computed. The dispersion contribution was found as the most influential stabilizing factor in all cases, being the stacked-displaced the most stable arrangement for all the dimers. Although the non-local features of the interaction between the charge distributions affect the stabilization of the crystals, the atom–atom contacts, accounted for by the properties of the electron density at the intermolecular bond critical points, play a key role in the crystal packing of the complexes.
Footnote |
† Electronic supplementary information (ESI) available. CCDC 1483082 and 1483083. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c6ra14957j |
This journal is © The Royal Society of Chemistry 2016 |