Tracing a Crystallization Pathway of an RT Liquid, 4-Fluorobenzoyl

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Tracing a Crystallization Pathway of a RT Liquid, 4-Fluorobenzoyl Chloride: Metastable Polytypic Form as an Intermediate Phase Amol G. Dikundwar, and Tayur Narasingarao Guru Row Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/cg500460n • Publication Date (Web): 20 Aug 2014 Downloaded from http://pubs.acs.org on August 21, 2014

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Crystal Growth & Design

Tracing a Crystallization Pathway of a RT Liquid, 4Fluorobenzoyl Chloride: Metastable Polytypic Form as an Intermediate Phase Amol G. Dikundwar and Tayur N. Guru Row* Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India Fax: (+91) 80-23601310; Tel: (+91) 80-23932796; E-mail: [email protected] RECEIVED DATE (to be automatically inserted after your manuscript is accepted if required according to the journal that you are submitting your paper to)

When quenched with liquid N2, a room temperature liquid, 4-fluorobenzoyl chloride generates a new crystalline form that appears to be polytypic to the earlier reported form. The structural and energetic correlations between these forms trace a crystallization pathway of the compound.

KEYWORDS 4-Fluorobenzoyl chloride, Crystallization pathways, Polytypism, Halogen Bonding, Cryocrystallography, Crystal Engineering.

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Understanding mechanistic steps involved in the formation of molecular aggregates is one of the key issues in the design and synthesis of supramolecular structures of interest.1 Unlike many chemical reactions, which represent equilibrium processes, crystallization of organic molecules under the conditions of supersaturation is a non-equilibrium process and hence obscures the mechanistic information about nucleation and subsequent crystal growth.2 Nevertheless, there have been a few attempts, mainly based on spectroscopic studies, to identify the molecular aggregation units in solutions that are representatives of the supramolecular synthons in crystals.3 Some clues about the process of crystallization have also been obtained from the structural analysis of highly solvated and hydrated metastable molecular crystals.4 As crystallization from solution involves entropically directed expulsion of solvent into the bulk followed by aggregation and nucleation,5 presence of solvent molecules makes the overall scenario more complicated. Indeed, this allows a discussion on tracing “a crystallization pathway” than “the crystallization pathway”! Compounds that are liquids at ambient conditions offer a great opportunity in this regard. Many of these compounds can be crystallized in-situ in order to access their supramolecular organization in the solid state. In fact, the feebleness of apparent intermolecular interactions (C–H···π, π···π etc.) and a complete control over experimental parameters such as temperature and pressure of crystallization offer an increased possibility for accessing various potential crystalline forms (polymorphs) of a liquid. This has been well demonstrated for biphenyl ether,6 phenylacetylene,7 fluorophenylacetylenes8 and many other compounds that are liquids at room temperature.9 Computer assisted simulations of crystallization trajectories of liquids also support the existence of several metastable crystalline forms while forming a stable polymorph.10 In this paper, we intend to provide experimental insights on liquid-solid transformations of 4-fluorobenzoyl chloride (4FBZ, Figure 1a) probed with in-situ cryocrystallization experiments carried out under non-ambient conditions. Interestingly, the two crystalline forms obtained under different cooling protocols, appearing to be polytypic with a close structural relationship, allow tracing a plausible crystallization pathway of 4FBZ.


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Figure 1 (a) Chemical structure of 4-fluorobenzoyl chloride, 4FBZ; (b) Gas phase geometry optimized structure of 4FBZ with the torsion angle φ(Cortho-Cipso-Ccarbonyl-Cl)= 0.02°; (c) Non-planar molecular conformation of 4FBZ in Form I with φ= 11.65°; (d) Near planar molecular conformation of 4FBZ in Form II with φ= 0.42°.

Polytypism, also known as 1-dimensional polymorphism, is “the ability of a solid material to exist in several different modifications, each of which may be regarded as built up by stacking layers of (nearly) identical structure and composition, and if the modifications differ only in the stacking sequence”.11 The phenomenon of polytypism has been well studied in inorganic solids,12 whereas it has been relatively less explored and has often been confused with polymorphism in molecular crystals.13 In fact, there are surprisingly few reports in literature that actually discuss the issue of polytypism in molecular crystals and refer to them as ‘organic polytypes’.14,15,16 In most of the reported cases, two or more structural variants coexist in the same crystal as intergrowths resulting in a composite crystal.14,17 However, well defined, individual, structurally pure, molecular polytypic structures are known for 1,1dicyano-4-(4-dimethylaminophenyl)-1,3-butadiene and 3-methoxydicyanovinylbenzene.15,16 A recent thorough investigation by Bond et al.18 on polymorphs of Aspirin opens up a new complex structural arena of molecular polytypes highlighting the importance and challenges associated with quantitative studies of these systems.19 In the context of crystallization studies, molecular polytypic structures could be of immense importance as they provide a clear picture of hierarchy of intermolecular interactions i. e. supramolecular synthons20 followed in the process of crystallization. Thus, similar robust intralayer and ACS Paragon Plus Environment

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considerably different yet energetically equivalent interlayer architectures in various polytypes of a molecule can serve as indicators for different possible intermolecular events that take place during nucleation and eventual crystal growth. In situ cryocrystallization of 4FBZ results in a crystal which belongs to the space group P21/c (Z=4) with the cell constants of a= 9.720(1) Å; b= 9.112(1) Å; c= 7.517(1) Å; β= 96.72(1)°; V= 661.3(1) Å3 which has been recently reported by us and we refer to this structure as Form I.21 Instead of a normal cooling on the diffractometer, when the same capillary filled with the compound was directly quenched in liquid N2 and immediately transferred to the cryostream at 90 K, the resulting crystalline solid could be indexed with cell constants a= 6.955(4) Å; b= 9.014(5) Å; c= 11.195(6) Å; α= 90°; β= 106.42(2)°; γ= 90°; V= 673.2(1) Å3, again belonging to the monoclinic system. After the acquisition of full data set, subsequent structure solution and refinements, the crystal structure revealed to be once again P21/c, Z=4 (Form II).22 To our knowledge, this is one among the rare examples, where a simple molecule such as 4FBZ can adopt two different crystal structures both belonging to the most favoured space group for molecular crystals, P21/c with one molecule in the asymmetric unit. The two crystal forms differ in terms of molecular conformation, specifically in the orientation of acid chloride group (–COCl) with respect to a plane of the phenyl ring. In Form I, the –COCl group orients itself slightly out-of-plane of the ring with the torsion angle φ(Cortho-Cipso-Ccarbonyl-Cl) being 11.65° (figure 1c) whereas, in Form II it lies almost coplanar with the ring (torsion angle, φ= 0.42°, figure 1d). Surprisingly, with such considerable difference in molecular conformations, the intermolecular packing of the two forms seem to be similar with the formation of two dimensional molecular sheets through well defined Cl···F hetero-halogen contacts (3.153 Å and 3.283 Å in forms I and II, respectively) and C–H···O and C–H···F hydrogen bonds as shown in figure 2(a) and 2(b).


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(a) Form I

(b) Form II 2D molecular layers (sheets)

(c) Form I

(d) Form II

Overlay of two adjacent molecular layers (sheets)

(e) Form I

(f) Form II Interlayer stacking patterns

Figure 2 Comparison of packing features of Form I and Form II structures. (a) and (b) 2D molecular sheets formed with Cl···F hetero-halogen bonds, C–H···O and C–H···F hydrogen bonds; (c) and (d) interlayer overlay of 2-D sheets in Form I and Form II; (e) and (f) interlayer packing patterns for Form I and Form II, respectively. ACS Paragon Plus Environment

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On close inspection of the packing features, it is observed that the similar 2D sheets stack differently in each case. Figures 2(c) and 2(d) provide a clear picture for the stacking modes in Form I and Form II, respectively. In both the cases, blue and red coloured molecular sheets represent the adjacent layers of molecules (2D sheets). In Form I, the two –COCl groups, of the two overlapping molecules, one from the lower layer (blue) and another from the upper layer (red) appear to be at meta positions (1,3 positions) to each other. Whereas, in Form II, the adjacent layers overlap (with offset) such that the – COCl groups appear to be oriented at para positions (1,4 positions), that is, “anti” to each other. Comparison of interlayer patterns of the structures, viewed down the b-axis as shown in figures 2(e) and 2(f) brings forward a clear distinction between forms I and II. Because of the notable difference in molecular conformations (orientations of the –COCl groups) of 4FBZ in the two crystalline forms, it is important to examine its molecular geometry in the gas phase. Indeed, the gas phase geometry [calculated using Gaussian 0923 at b3lyp/6-31G++(d,p) level] turned out to be a completely planar one with the torsion angle of almost zero degree (φ= 0.2°, figure 1b). This indicates that the molecules in the liquid 4FBZ are likely to be planar and warrants the near planar geometry of the molecules in the kinetically captured phase, Form II, which could only be accessed by the abrupt arrest of the molecules of liquid when quenched sharply with liq N2. However, when allowed to crystallize under normal cooling protocols, 4FBZ assumes a slightly nonplanar conformation (φ= 11.65°; the conformational energy barrier between forms II and I is 0.75 kJmol-1) to facilitate the efficient intermolecular packing in the solid state.24 Comparison of cohesive energies [calculated by periodic ab-initio calculations using CRYSTAL09 package25; see SI for details] of the two forms clearly shows up the extra stability [∆E= −2.53 kcal/mol] of Form I over Form II. This extra stability of Form I can be attributed to the carbonyl-carbonyl (CO···CO) dipolar interactions (shown by black dotted lines in figure 2(c)) between the slightly tilted (favourably oriented!)24 –COCl groups of 4FBZ molecules of the adjacent layers in addition to the feeble π···π contacts of the phenyl rings.


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It is important to note that, although similar intralayer patterns of Cl···F, C–H···O and C–H···F interactions persist in form II, all the interaction distances are considerably longer (see SI; table S1) and the volume of the unit cell is also larger (by ~5%).22 Notably, short π···π contacts between the centrosymmetric dimers with anti –COCl groups is a distinct feature of Form II over Form I. Hirshfeld surface analyses (carried out using CrystalExplorer, Version 3.1)26 of the two forms unambiguously support this observation. Figure 3 shows the Hirshfeld surfaces of Form I and Form II structures mapped with the dnorm along with the corresponding fingerprint plots. The contacts shorter than van der Waals separations show up as red spots on a largely blue surface. The short Cl/F and H/O interactions in Form I are characterized by small red spots while relatively longer similar contacts (Cl/F and H/O) in Form II show up no red spots on the surface. Hence, the dnorm surface proves to be extremely useful in identifying the subtle differences in intermolecular contacts in forms I and II.

(a) Hirshfeld surfaces [mapped with dnorm]


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(b) Fingerprint plots Form I

Form II

Figure 3 Comparison between the (a) Hirshfeld surfaces mapped with dnorm over the range -0.4 to 1.4. Neighbouring molecules associated with close Cl···F and C–H···O contacts are shown along with distances between the atoms involved; (b) Fingerprint plots of Form I and Form II of 4FBZ.

The fingerprint plots convincingly demonstrate important distinguishing features of the two forms because of their high sensitivity to the immediate environment of the molecule and are unique for a given molecule in a particular polymorph.27 Dominant interactions in both the forms are C–H···O, C– H···F and C–H···Cl hydrogen bonds which show up as the pairs of spikes at the bottom left of the plots as shown in figure 3b (i.e. the short di and de pair for C–H···O/C–H···F (overlapped) and the longer di and de pair for C–H···Cl). Participation in a planar stacking arrangement of molecules (π-π stacking) shows up as a red region near the centre of the plot in Form II, in the vicinity of (di, de) ~ 1.8-2.0 Å, a range typical of the interplanar spacing of the planar aromatic fragments.27 This feature which is very prominent in Form II and, absent in Form I indicates higher contribution of π···π contacts in Form II over Form I. Breakdown of the fingerprint plots provide contribution from individual interactions towards overall stability of the structures as shown in figure 4.

Figure 4 Percentage contributions to the Hirshfeld surface area for the various close intermolecular contacts for molecules in forms I and II of 4FBZ. ACS Paragon Plus Environment

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In addition, comparison of the maps of curvedness28 (a function of the root-mean-square curvature) of the Hirshfeld surfaces which typically show large regions of green (relatively flat) separated by dark blue edges (large positive curvature) offers meaningful insights in the analysis of forms I and II. These maps are used to identify characteristic packing modes; in particular planar stacking arrangements and find significant relevance in this case as the structures mainly differ in the ways in which adjacent molecular layers contact one another. Figure 5 shows the curvedness plots of the two structures. In form II, the curvedness surfaces show broad, relatively flat regions characteristic of a better planar stacking of molecules compared to that seen for Form I again confirming the stronger π···π contacts in Form II over Form I in accordance with the results obtained from breakdown of the fingerprint plots (figure 4).

(a)

(b)

Figure 4. Hirshfeld surfaces for a cluster of four molecules in (a) Form I and (b) form II, mapped with curvedness (ref. 28). Notice the increased flatness of Form II surfaces over Form I surfaces. Although repeated several times, the quality of Form II crystals obtained by quenching 4FBZ in liq N2 was just ‘satisfactory’ for single crystal XRD analysis and each of the attempts to improve on the crystal quality by manual annealing29 (slow melting and re-growing) of the domain always resulted in its transformation to Form I crystal. From our experiments, it was clear that, even though stable enough to be isolated, Form II is a transient metastable crystalline state of 4FBZ and represents “on the way”7c,8,30 structure to Form I. It needs to be mentioned that the crystals of Form II were also found merohedrally


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twinned. Moreover, there exists a probability of presence of some amount of Form I domains in Form II ‘crystals’ or even several possible combinations of Form I and Form II! Comparative analysis of the two structures indeed provides meaningful insights into the crystallization pathway of 4FBZ. Given a chance, the molecular layers in Form II slides over each other so as to strengthen the intralayer Cl···F, C–H···O and C–H···F interactions and facilitate interlayer CO···CO contacts. The out-of-plane orientation of –COCl group (φ= 11.65°) in the crystalline state appears to be crucial for the antiparallel CO···CO31 and Cl···F mediated intermolecular close packing in the solid state. Once transformed in this manner, the symmetry relations among the molecules of adjacent layers change leading to the assignment of a new unit cell and hence a new crystallographic structure i. e. a new form. It is important to note that, in forms I and II, the lengths of the cell edges a and c have been interchanged (with slight deviations) with the edge length b being almost the same. This suggests that during transformation, the molecules reorient themselves such that the 2-fold unique axis (axis b) remains virtually the same in the two structures whereas; the glide plane symmetry interchanges between the axes a and c keeping the two dimensional isostructurality32 and the standard space group setting P21/c intact. In simple words, Form II structure can be envisaged in a nonstandard space group P21/a (using metric transformation: [0 0 -1 0 1 0 1 0 0]) with the same order of cell edges of Form I (a’ = c, b, c’ = a) and a new oblique angle β’ (180-β). Keeping the consistency in the cell parameters, this setting (P21/a) would be more helpful in following the transformation of Form II structure to Form I structure.


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Figure 6 Schematic illustration of derivation of Form I structure (P21/c) from Form II structure (P21/a) of 4FBZ. Notice the centrosymmetric arrangement of π-stacked dimers in Form II and the noncentrosymmetric arrangement of π-stacked layers in Form I. The 2D molecular sheets shown in ‘wireframe model’ and ‘ball and stick’ model represent the upper and lower layers, respectively (viewed down the c-axis).


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Figure 6 shows a schematic illustration of the conversion pathway from Form II to Form I. The 2D molecular sheets shown in ‘wireframe model’ and ‘ball and stick’ model represent the upper and lower layers, respectively (viewed down the c-axis of Form II, P21/a). When the upper layer (wireframe) is displaced diagonally i.e. “half” translation along a-axis and “half” translation along baxis, the resulting interlayer arrangement turns out to be that of Form I structure (–COCl groups at 1,3 positions). According to the conventional definition, this is a clear cut case of polytypism [“layers in different polytypic structures may exhibit slight structural differences and may not be isomorphic in the strict crystallographic sense”11] however, the concomitant changes in molecular conformation and intermolecular packing (especially CO···CO contacts) also qualify it to be referred to as polymorphism! In summary, a simple molecule 4FBZ presents a special case of polymorphism with the two (2D-) isostructural crystal forms in the same space group [P21/c, Z=4] that can be referred to as ‘Organic polytypes’. The powerful and “customizable” technique of in situ cryocrystallization of liquids under drastic conditions allows one to access its otherwise inaccessible, energetically less favoured crystalline forms (polytypes/polymorphs) that are intermediates in the process of crystallization thereby providing the chronology of intermolecular recognition events along the crystallization pathway.

ACKNOWLEDGMENTS AGD thanks the CSIR for a SRF. TNG thanks the DST for the award of a J. C. Bose fellowship.

Supporting Information Available. Experimental details of in situ cryocrystallization, DSC plot and ORTEP diagrams of forms I and II of 4FBZ with intermolecular hydrogen bonds and crystal data (CIFs). Details of cohesive energy calculations of Form I and Form II. This material is available free of charge via the Internet at http://pubs.acs.org.


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Crystal data: Form I CCDC 860574; MF: C7H4Cl1F1O1; monoclinic; a = 9.7208(14) Å; b = 9.1128(13) Å; c = 7.5178(11) Å; β = 96.727(2) °, V = 661.37(2) Å3; T = 90(1) K; space group, P21/c, Z = 4; ρcalcd = 1.59 g/cc; reflns measured, 5925; unique reflns, 1161; no. of parameters = 107; Robs = 0.035; wR2obs = 0.090; ∆ρmin,max = –0.363, 0.448 eÅ-3; goof = 1.07. Form II CCDC 992439; MF: C7H4Cl1F1O1; monoclinic; a = 6.9554(37) Å; b = 9.0141(47) Å; c = 11.1954(59) Å; β = 106.423(9) °, V = 673.28(20) Å3; T = 90(1) K; space group, P21/c, Z = 4; ρcalcd = 1.56 g/cc; reflns measured, 2880; unique reflns, 1156; no. of parameters = 92; Robs = 0.088; wR2obs = 0.269; ∆ρmin,max = –0.482, 0.719 eÅ-3; goof = 1.16.

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Gaussian 09, Revision A.1, Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, Jr., J. A.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, Ö.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. Gaussian, Inc., Wallingford CT, 2009.

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Upon crystallization, a small rearrangement of the functional groups have been observed in several examples: (a) Bernstein, J.; Hagler, A. T.; J. Am. Chem. Soc. 1978, 100, 673−681; Nangia, A. Acc. Chem. Res., 2008, 41, 595–604; (b) Bond, A. D. Curr. Op. Solid State Mater, ACS Paragon Plus Environment

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2009, 13, 91–97; (c) Back, K. R.; Davey, R. J.; Grecu, T.; Hunter, C. A.; Taylor, L. S. Cryst. Growth Des., 2012, 12, 6110–6117. 25

(a) Dovesi, R.; Orlando, R.; Civalleri, B.; Roetti, R.; Saunders, V. R.; Zicovich-Wilson, C. M.; Z. Kristallogr., 2005, 220, 571–573; (b) Dovesi, R.; Saunders, V. R.; Roetti, R.; Orlando, R.; Zicovich-Wilson, C. M.; Pascale, F.; Civalleri, B.; Doll, K.; Harrison, N. M.; Bush, I. J.; D’Arco, P.; Llunell, M. CRYSTAL09 User's Manual, University of Torino, Torino, 2009.

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(a) CrystalExplorer (Version 3.1), Wolff, S. K.; Grimwood, D. J.; McKinnon, J. J.; Turner, M. J.; Jayatilaka, D.; Spackman, M. A. University of Western Australia, 2012; (b) Spackman, M. A.; Jayatilaka, D. CrystEngComm, 2009, 11, 19–32.

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(a) Spackman M. A.; McKinnon, J. J. CrystEngComm, 2002, 4, 378–392; (b) McKinnon, J. J.; Jayatilaka, D.; Spackman, M. A. Chem Commun., 2007, 3814–3816.

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McKinnon, J. J.; Spackman, M. A.; Mitchell, A. S. Acta Cryst., 2004, B60,627–668.

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By manual annealing, we refer to the process of slow (random) movement of N2 cryojet in vertical and/or horizontal directions in order to achieve the zone melting and recrystallization of the solidified compound in the capillary.

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Saha, D.; Madras, G.; Guru Row, T. N. Cryst. Growth Des., 2011, 11, 3213–3221.

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Allen, F. H.; Baalham, C. A.; Lommerse J. P. M.; Raithby P. R., Acta Cryst., 1998, B54, 320– 329.

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Fabian, L.; Kalman, A. Acta Cryst., 2004, B60, 547–558.


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Page 16 of 16

Graphical Abstract:

Tracing a Crystallization Pathway of a RT Liquid, 4-Fluorobenzoyl Chloride: Metastable Polytypic Form as an Intermediate Phase Amol G. Dikundwar and Tayur N. Guru Row* A link between the two polytypic crystalline forms of a room temperature liquid 4-fluorobenzoyl chloride obtained under different experimental conditions traces a crystallization pathway of the compound.


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Tracing a Crystallization Pathway of an RT Liquid, 4-Fluorobenzoyl

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