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Trimethyltrioxane (Paraldehyde) and Its Halomethanes Complexes: Crystallization, Structures, and Analysis of Packing Motifs† Published as part of the Crystal Growth & Design Mikhail Antipin Memorial virtual special issue D. S. Yufit,*,# O. V. Shishkin,‡,§ R. I. Zubatyuk,‡ and J. A. K. Howard# #

Durham University, Durham DH1 3LE, U.K. SSI “Institute for Single Crystals” of National Academy of Science of Ukraine, Kharkiv 61001, Ukraine § V. N. Karazin Kharkiv National University, Kharkiv 61202, Ukraine ‡

S Supporting Information *

ABSTRACT: Crystals of molecular complexes of trimethyltrioxane (TMT) with chloroform (CF), bromoform (BF), dichloromethane (DCM), and dibromomethane (DBM) as well as those of pure TMT were grown in situ and characterized by single crystal X-ray crystallography. The CF and BF complexes, as well as those of DCM and DBM, are isostructural. The packing motifs were examined using the vector analysis of pairwise energies of intermolecular interactions. The method shows some deficiencies of the traditional approach based on the analysis of geometrical parameters of short intermolecular contacts.

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INTRODUCTION It is difficult to underestimate the role of noncovalent interactions in supramolecular chemistry and crystal engineering. The most prominent among these interactions are, of course, hydrogen bonds.1 However, in the absence of classical O(N)− H···O strong hydrogen bonds, the interactions of other types, such as stacking interactions, C−H···X interactions, and various halogen bonds, have taken the leading role in formation of a crystal and govern packing motifs. In recent years, the focus of attention of crystal engineering studies shifted toward the halogen bonds D···Hal-C (D = Hal, N, O, S) which are now widely used in the constructing of supramolecular entities.2 However, the energy of halogen bonds typically is comparable with that of other above-mentioned weak interactions, and it makes the accurate description of molecular packing a challenging task. It is not just a question of terminologythe correct description of packing motifs is important for analysis of various properties of the crystal, such as, for example, the behavior of the crystal during the compression or melting. In our previous papers,3 we described the recently developed method of analysis of topology of pairwise intermolecular interactions.4,5 While the energies of intermolecular contacts and formation of supramolecular associates based on van der Waals interactions has been investigated before,6,7 the addition of the graphical vector representation provides a crystallographer with a powerful tool for analysis of packing motifs and gives a new insight into the nature of intermolecular interactions. In continuation of these

studies, we report in present paper the application of this method for the structures of new low-melting molecular complexes (LmMC) of trimethyltrioxane with haloformes. The LmMC are very attractive models for probing intermolecular interactions as they usually consist of relatively small molecules, and the number of intermolecular interactions in these complexes is limited.8 Previously we reported the analysis of packing motifs in the structures of corresponding dioxane complexes. It was interesting to see how the replacement of cyclic diether for triether affects intermolecular interactions and therefore the packing of molecules in crystal. In order to obtain a reference point, the structure determination of pure TMT has also been performed. It has to be noted that all compounds mentioned in this paper are liquid under ambient conditions, and a method of in situ cryocrystallization was applied to obtain single crystals. This method is the most commonly used for crystallization of compounds that are liquid9 or even gaseous10 under ambient conditions and has been originally described by Boese et al.11

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All chemicals were obtained from commercial sources and were used without any further purification. Thoroughly mixed together equimolar amounts of reagents were transferred into a borosilicate glass capillary (OD 0.3 mm, Capillary Tube Supplies Ltd.) and sealed at both ends. The sealed capillary was glued to a metal pin and mounted on a Bruker SMART CCD 6000 diffractometer (λMo Kα, graphite monochromaReceived: March 12, 2014 Revised: June 26, 2014

†

Part 6 of “Low-Melting Molecular Complexes”. For part 5, see ref 3. © XXXX American Chemical Society

EXPERIMENTAL SECTION

A

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Table 1. Crystal Data and Structure Refinement for TMT compound

TMT

CF−TMT

BF−TMT

DCM−TMT

DBM−TMT

empirical formula formula weight melting point, K data collection temperature/K crystal system space group a/Å b/Å c/Å α/° β/° γ/° volume/Å3 Z ρcalc mg/mm3 μ/mm−1 F(000) reflections collected independent reflections/Rint data/restraints/parameters goodness-of-fit on F2 final R1/wR2 indexes [I ≥ 2σ(I)] final R1/wR indexes [all data] largest diff peak/hole/e Å−3

C6H12O3 132.16 255−257 200 orthorhombic Pbca 12.8475(12) 8.1256(5) 14.3082(13) 90 90 90 1493.7(2) 8 1.175 0.093 576.0 11806 1735/0.021 1735/0/131 1.068 0.0328/0.0868 0.0468/0.0985 0.12/−0.12

C6H12O3 x CHCl3 251.52 218−219 190 monoclinic P21/c 11.579(9) 13.627(10) 7.941(4) 90 107.00(2) 90 1198.2(14) 4 1.394 0.741 520.0 9914 2775/0.0306 2775/0/170 1.087 0.0386/0.0941 0.0630/0.1077 037/−0.34

C6H12O3 x CHBr3 384.90 238−239 120 monoclinic P21/c 11.632(3) 14.062(3) 8.2400(10) 90 107.01(1) 90 1288.8(5) 4 1.984 9.368 736.0 8920 2430/0.1341 2430/0/121 0.974 0.0554/0.1238 0.1224/0.1465 0.50/−0.76

C6H12O3 x CH2Cl2 217.08 225−227 210 orthorhombic Pmn21 11.703(3) 10.490(2) 4.4154(7) 90 90 90 542.07(18) 2 1.330 0.569 228.0 4264 1146/0.0389 1146/1/85 1.022 0.0356/0.0892 0.0530/0.1010 0.14/−0/20

C6H12O3 x CH2Br2 306.00 245−246 230 orthorhombic Pmn21 12.016(2) 10.6738(14) 4.4634(5) 90 90 90 572.45(14) 2 1.775 7.053 300.0 4664 1234/0.0489 1234/1/68 0.984 0.0444/0.1134 0.0586/0.1223 0.33/−0.42

This diagram or “hedgehog” represents an image of the molecule in terms of intermolecular interactions in the crystal, and it may be multiplied by all symmetry operations of the crystal structure, thus providing a general picture of the topology of intermolecular interactions in the crystal.

tor) using a special attachment.12 The temperature of the sample was controlled by a Cryostream (Oxford Cryosystems) open-flow nitrogen cryostat. The detailed experimental procedure of in situ crystal growing was described in our previous communication.3a All data sets were collected in two 180° ω-scans and corrected for absorption effects. All structures were solved by direct methods and refined by full-matrix leastsquares against all data using SHELX13 and OLEX214 program packages. The refinement parameters and crystallographic information are given in Table 1. Crystallographic data for the structure have been deposited with the Cambridge Crystallographic Data Centre as supplementary publication CCDC 990926−990930. Methods of Calculations. The analysis of supramolecular architecture of the crystals under consideration was performed using an energetic approach suggested earlier.4,5 The first coordination sphere of each molecule in the asymmetric part of unit cell was determined separately, as it was suggested before, using “Molecular Shell calculation” option of Mercury program (version 3.1).15 The energies of intermolecular interactions were calculated within density functional theory16,17 using B3LYP functional18−20 augmented by the D3 empirical correction for dispersion interactions21 with def2TZVP basis set.22 Values of interaction energies were corrected for basis set superposition errors using counterpoise procedure.23 All calculations were performed using ORCA program.24 The analysis of the topology of intermolecular interactions in the crystal is based on vector properties of intermolecular interactions as it was described earlier.4 According to this approach, an intermolecular interaction between two molecules in the crystal may be described by a vector originated in geometrical center of one molecule and directed toward the geometrical center of the second molecule. The length of this vector is calculated using the following equation:

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RESULTS AND DISCUSSION Crystal Structure of Trimethyltrioxane (TMT). The TMT molecule in the crystal occupies a general position and adopts a chair conformation with equatorial orientation of all methyl groups (Figure 1a). This conformation remains unchanged in all molecular complexes of TMT discussed below. Such a conformation of the TMT molecule leads to a nonequal distribution of the molecular electrostatic potential with more negative area on the “oxygen” side of the molecule (Figure 1b). One could expect the formation of triple C−H···O weak interactions between the most acidic tertiary hydrogen atoms of the cyclic carbon atoms and the oxygen atoms of a neighboring molecule. A number of such contacts are present in the structure of dioxane26 where they bind molecules in columns (HT polymorph) or 3D network (LT polymorph). It is interesting to notice that the authors have finished the paper with the phrase “...no intermolecular contacts of interest are present”. The TMT structure is quite different from the dioxane ones, and only one such independent contact (C2−H2···O2(3/2 − x, −1/2 + y, z), C···O 3.510 Å, H···O 2.59 Å, C−H−O 153.9°) exists in it. These contacts link the molecules in the zigzag chains along crystallographic b-axis. The energy of interaction between two neighboring molecules within this chain (−5.4 kcal/mol) is higher than that for any other pair formed by basic molecule (BM). The results of calculations show that molecules in the chain are bonded mainly by general electrostatic and dispersion interactions, while the electrostatic contribution of corresponding C−H···O interaction is small (Table 2). The nonlinearity of chains leads to significant asymmetry of the energy of interactions of the basic molecule (BM) with the

L i = (R iE i)/2Estr where Ri is a distance between geometrical centers of interacting molecules, Ei is the energy of interaction between these two molecules and Estr is the energy of the strongest pairwise interaction in the crystal. Application of this approach makes it possible to construct the energy-vector diagram or “hedgehog” of intermolecular interactions reflecting spatial distribution of intermolecular interactions of the basic molecule with the molecules belonging to its first coordination sphere. B

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Figure 1. (a) Molecule TMT (thermal ellipsoids here and on all other figures are shown at 50% probability level) in crystal and labeling scheme; (b and c) the molecular electrostatic potential on the Hirshfeld surface on two sides of the TMT molecule (CrystalExplorer25).

molecules belonging to adjacent chains (Figure 2). The energy of interaction of BM to the molecules of adjacent (along the a-axis) chain (−8.5 kcal/mol) is almost comparable with energy of interaction of this BM to neighboring molecules within the chain (−10.8 kcal/mol). The energy of interactions of the same BM with molecules of another chain is significantly smaller (−1.5 kcal/mol) because BM forms three close contacts with the molecules of first neighboring chain and only one contact with the molecule of the second chain (Figure 2B). It is more convenient to use a double step (two neighboring molecules) of zigzag chain for the description of distribution of energy of intermolecular interactions between neighboring chains. The

Figure 2. Zig-zag-chain in the structure of TMT (A) and energy vector representation of the TMT packing (view along (0 0 1)) (B).

Table 2. Energy of Strongest Pairwise Intermolecular Interactions and Parameters of Corresponding Intermolecular Contacts in Studied LmMC Mol. 1

Mol. 2

Eint, kcal mol−1

symm operation

contact

distance, Å

TMT TMT TMT TMT

TMT TMT TMT

CF TMT CF

TMT TMT TMT

BF TMT BF

TMT TMT TMT

TMT DC(B)M TMT

TMT TMT TMT

1.5−x, −0.5 + y, z 1 − x, −0.5 + y, 1.5 − z −0.5 + x, y, 1.5 − z CF−TMT x, y, z x, 1.5 − y, 0.5 + z; x, 1.5 − y, −0.5 + z 2 − x, 1 − y, 1 − z BF−TMT x, y, z x, 1.5 − y, 0.5 + z; x, 1.5 − y, −0.5 + z 2 − x, 1 − y, 1 − z DCM−TMT (DBM−TMT) x, y, 1 + z; x, y, −1 + z x, y, z 1.5 − x, 1 − y, −0.5 + z; 1.5 − x, 1 − y, 0.5 + z C

−5.4 −3.0 −2.5

C2−H···O2 C1−H···O3 C5−H···O2

2.59 2.87 2.65

−6.3 −4.5 −2.4

C7−H···O2 C1−H···O3 Cl2···O1

2.25 2.53 3.159

−6.8 −4.1 −3.5

C1s−H···O1 C2−H···O3 Br2···O2

2.23 2.49 3.092

−4.6 (−4.16) −4.2 (−4.71) −3.1 (−2.89)

C1−H···O2 C1s−H···O1 C4−H···O2

3.18 (3.33) 2.39 (2.31) 2.71 (2.79)

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energy of interaction between molecules within the same chains in this case still remains the highest (−16.2 kcal/mol). This value is by 1.5−5.1 times higher that energy of interaction of BM to neighboring chains, and the energy distribution becomes more uniform (Figure 3). Thus, it confirms that zigzag chains represent the primary basic structural motif of the TMT crystal.

Figure 3. Sums of pairwise energies of interactions of basic molecules TMT located in a central zigzag chain to the molecules belonging to adjacent chains (view along the (010) direction). Values in parentheses correspond to the energy of interaction of two neighboring molecules (double step) of the basic chain.

Analysis of directionality of intermolecular interactions between columns clearly indicates that interaction of basic chain (containing BM) with two neighboring chains is considerably stronger as compared to others (Figure 3). These three chains form layer which is parallel to the (0 0 1) crystallographic plane. Energy of interactions between chains within this layer (−22.0 kcal/mol) is by 1.9 and 4.6 times higher than energy of interactions between the chains belonging to neighboring two layers. Thus, a layer of strongly bonded chains should be considered as a secondary basic structural motif27 of the TMT crystal. Crystal Structure of Molecular Complexes of Trimethyltrioxane with Chloroform (CF−TMT) and Bromoform (BF−TMT). The molecular structures of CF−TMT and BF− TMT are shown in Figure 4. In spite of the differences in chemical behavior of chlorine and bromine, the compounds are isostructural. The component of these cocrystals are linked together by Hal3C−H···O interaction in heterodimers. Interactions of this type were found in all previously studied LMMC of CF with cyclic ethers.3b Similarly to the structure of pure TMT (see above), only one (TMT)C−H···O interaction is present in the structures of CF/BF−TMT. The C···O distances in these cases (3.355 and 3.412 Å) are slightly shorter than that in TMT. There are also two more types of short intermolecular contacts: Hal···Hal 3.327 and 3.435 Å, corresponding to type II halogen bonds and type I halogen−halogen contacts28 and Hal···O (3.159 and 3.092 Å in the structures CF−TMT and BF−TMT respectively), which may be regarded as another type of halogen bond. It is impossible to estimate the particular role of each of

Figure 4. Molecular structures of CF−TMT (A) and BF−TMT (B) and heterotetramer in the structure CF−TMT (C).

these contacts in the crystal structures on the basis of geometrical parameters only, so the energy calculations were performed. Comparison of the crystal structure of the cocrystals of TMT with chloroform (CF) and bromoform (BF) demonstrated that they are isostructural not only from geometrical viewpoint but also according to topology of intermolecular interactions in the crystals. Not surprisingly the Hal3C−H···O interactions between the components of the cocrystals turned out to be the strongest ones (Table 2). The energy of interaction between molecules in these pairs (−6.3 and −6.8 kcal/mol for CF-TMT and BF-TMT, respectively) is by 1.4 and 1.7 times higher than energy of interaction between molecules in the next most strongly bonded pairs. Therefore, 1:1 molecular complexes TMT and CF or BF should be considered as main building units of these cocrystals.22 Adjacent pairs of the components (heterodimers) are linked in heterotetramers by the Cl(Br)···O halogen bonds, and these D

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heterotetramers, in turn, are bonded into zigzag chains along the (1 0 0) crystallographic direction by slightly stronger C−H···O interactions between TMT molecules (Figures 4 and 5).

Figure 6. Molecular structures of DCM−TMT (a) and DBM−TMT (b).

structures of CF/BF cocrystals and TMT itself, in the structure DCM/DBM−TMT the TMT molecules form perfect columns along the [0 0 1] crystallographic axis. Direction-specific C−H··· O interactions between TMT molecules are not present in such arrangementeach tertiary hydrogen atom forms two long H··· O contacts (3.18−2.26 Å and 3.26−3.34 Å in complexes of DCM and DBM respectively), which one may regard as very weak bifurcated hydrogen bonds. Adjacent columns are linked by weak C(Me)−H···O and Cl contacts. This information about the geometry of intermolecular interactions does not allow ranking them reliably, and therefore we cannot draw any conclusions about the packing motifs in these LmMC. So, the pairwise energy calculations were performed for DCM/DBM−TMT complexes. The results of calculations show that the strongest intermolecular interaction in the DCM−TMT complex exists between TMT molecules (E = −4.6 kcal/mol). Each TMT molecule has two such interactions with two neighboring TMT molecules in the column. It should be noted that bonding between the TMT molecules is provided only by general dispersion and electrostatic interactions. A slightly smaller energy of interaction (−4.2 kcal/mol) was obtained for a pair formed by TMT and DCM molecules. These TMT−DCM pairs are packed in columns in a head-to-tail manner. Such pairs cannot be considered as molecular complexes because the interaction between TMT and DCM is weaker than the interaction between two TMT molecules. They could be described as the strongly bonded molecular pairs (SBMP).

Figure 5. Packing of molecules (left) and vector representation of intermolecular interactions in the crystal of CF−TMT (right).

Stronger halogen bonds in BF−TMT crystal in comparison to the CF−TMT one result in a higher energy of interaction of a basic complex with two neighbors within the chain (−11.8 kcal/ mol for CF−TMT and −15.4 kcal/mol for BF−TMT). These values are by 1.7−3.0 (CF−TMT), 2.2−3.5 (BF−TMT) higher that energy of interaction between chains. Therefore, we suggest that these zigzag chains represent a basic structural motif of these crystals. Crystal Structure of Molecular Complexes of Trimethyltrioxane with Dichloro- (DCM−TMT) and Dibromomethane (DBM−TMT). The molecular complexes of TMT with DCM and DBM are also isostructural. In these cocrystals, both components occupy a special position on a mirror plane (Figure 6). The TMT and DCM/DBM molecules are linked together in pairs by Hal2CH−H···O interactions, usual for cocrystals of halomethanes. Second hydrogen atom of DCM/ DBM is directed toward adjacent dihalomethane molecule forming two symmetrical C−H···Hal contacts. In contrast to the E

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(−22.4 and −23.53 kcal/mol for DCM and DBM LmMC respectively) is 3.6−10.2 times higher than the energies of interactions of molecular pairs belonging to neighboring columns. More detailed analysis of interactions between columns reveals the existence of a layer along the (0 1 0) crystallographic plane containing the most strongly bonded columns. Energy of interaction between columns within layer (−12.4 and −11.56 kcal/mol for DCM and DBM LmMC respectively) is 2.0−2.6 times higher than the energy of interaction to columns belonging to neighboring layer. Thus, these layers represent secondary basic structural motif of the DCM−TMT cocrystal.

The results of calculations for the isostructural DBM−TNT crystal show the opposite energy distribution: the energy of TMT−DBM interaction (−4.71 kcal/mol) is slightly higher than that for the TMT−TMT pair (−4.16 kcal/mol). The difference in the energies of intermolecular interactions in these two pairs is small, but this DBM−TMT strongly bonded molecular pair probably should be regarded as a main building block of the DCM−TMT crystal. Columns of DCM/DBM−TMT molecular pairs represent a primary basic structural motif of the cocrystal. The energy of interaction between basic pair and two neighboring SBMPs

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CONCLUSIONS The reported analysis of the packing motifs in the LmMC of TMT is another illustration of the deficiency of the traditional approach to the description of the packing of molecular crystals based only on the geometry of intermolecular contacts. Indeed, using the geometrical parameters alone, it is hardly possible to find out that the strongest intermolecular interactions in the structure of DCM−TMT are those between TMT molecules in the columns rather than between components of the cocrystal. Hopefully, the pairwise energy calculations of intermolecular interactions, similar to those described in this report, gradually will become the main method of analysis of crystal packing motifs in molecular crystals.

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ASSOCIATED CONTENT

S Supporting Information *

Tables of geometrical parameters (bond lengths and angles) for studied compounds, the full tables of pairwise energies of intermolecular interactions and single-crystal X-ray crystallographic data in CIF format. This material is available free of charge via the Internet at http://pubs.acs.org/.

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AUTHOR INFORMATION

Corresponding Author

*E-mail: d.s.yufi[email protected]. Notes

The authors declare no competing financial interest.

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DEDICATION Dedicated to the memory of Prof. M. Yu. Antipin, the colleague and the friend. REFERENCES

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Figure 7. Packing of molecules (a) and vector representation of intermolecular interactions in the crystal of DCM−TMT (b). F

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