Alexander G.
Shtukenberg
*a,
Qiang
Zhu
*bc,
Damien J.
Carter
d,
Leslie
Vogt
e,
Johannes
Hoja
fg,
Elia
Schneider
e,
Hongxing
Song
e,
Boaz
Pokroy
h,
Iryna
Polishchuk
h,
Alexandre
Tkatchenko
fg,
Artem R.
Oganov
ic,
Andrew L.
Rohl
d,
Mark E.
Tuckerman
ejk and
Bart
Kahr
al
aDepartment of Chemistry, Molecular Design Institute, New York University, New York City, NY 10003, USA. E-mail: shtukenberg@mail.ru
bDepartment of Physics and Astronomy, High Pressure Science and Engineering Center, University of Nevada Las Vegas, Nevada 89154, USA. E-mail: qiang.zhu@unlv.edu
cDepartment of Geosciences, Stony Brook University, Stony Brook, NY 11794, USA
dCurtin Institute for Computation and Department of Chemistry, Curtin University, P.O. Box U1987, Perth, 6845, Western Australia, Australia
eDepartment of Chemistry, New York University, New York City, NY 10003, USA
fFritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4–6, Berlin, 14195, Germany
gPhysics and Materials Science Research Unit, University of Luxembourg, 1511 Luxembourg, Luxembourg
hDepartment of Materials Science and Engineering, Russell Berrie Nanotechnology Institute, Technion Israel Institute of Technology, Haifa 32000, Israel
iSkolkovo Institute of Science and Technology, Skolkovo Innovation Center, 3 Nobel St., Moscow 143026, Russia
jCourant Institute of Mathematical Sciences, New York University, New York City, NY 10003, USA
kNew York University-East China Normal University Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
lDepartment of Advanced Science and Engineering (TWIns), Waseda University, Wakamatsucho, 3-2, Shinjuku, 162-0056 Tokyo, Japan
First published on 15th May 2017
Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and the need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.
The rich polymorphism of coumarin (Scheme 1), a simple organic compound used in perfumes, medicine, agriculture, and as a precursor for drug synthesis, was broached by Bernauer, who identified two forms in 1929 that crystallized from the melt in the presence of some naturally occurring resins.3 Both forms were spherulitic polycrystalline aggregates. Moreover, both forms gave banded spherulites with optical signatures characteristic of ensembles of helically twisted fibrils.3 Coumarin initially attracted our attention for this reason.4,5 Kofler and Geyr recognized two coumarin forms in 1934 which were identified as monoclinic and orthorhombic on the basis of optical measurements.6 Lindpainter recognized three forms with distinct melting points (68.5°, 64.5°, and 55°) in 1939.7 However, only one crystal structure is available in the Cambridge Structural Database (CSD).8–10
Another form, which turned out to be one of Bernauer's forms, was once again discovered by crystallizing coumarin from the melt in porous poly(cyclohexylethylene) and porous glass bead (diameter of pores 7.5–55 nm) media.11 However, its crystal structure was not solved. We repeated Bernauer's crystallization procedures and obtained not one, but four new polymorphs of coumarin. We endeavoured to solve all four new crystal structures and address the following challenges.
(1) Crystal structure determination from a suitable single crystal is nowadays a routine task for X-ray diffraction analysis. However, for many materials only powder X-ray diffraction (PXRD) data are available. Solving crystal structures from PXRD is still a challenge.12 Moreover, metastable forms often undergo rapid polymorph conversions and tend to grow concomitantly with other forms, significantly complicating the collection of high quality data required for many crystal structure solution approaches. Alternatively, there has been tremendous progress in the field of crystal structure prediction (CSP) to obtain models of low energy structures.13,14 Non-uniqueness of structure solutions solely from PXRD leads to erroneous structures in the literature (e.g., a high pressure phase of Mg(BH4)2 was initially solved from PXRD,15 but later was corrected by CSP16). Matching the predicted structures with available, but not necessarily high-resolution, PXRD data provides an alternative way to arrive at the structure. A unit cell delivered by PXRD can delimit CSP, whereas CSP can serve as a check on any structural model developed; iteratively, and in tandem, they work best. Here we use CSP to help solve four new crystal structures of coumarin from PXRD data. Together with the form previously reported in the CSD, the five different forms make coumarin a member of a very small family of multimorphic rigid molecules under ambient conditions.17
(2) It is challenging to rank the lattice energies of polymorphs based on theory. The energy differences for organic polymorphs, dominated by intermolecular interactions, are usually within a few kJ mol−1. Accuracies within 5 kJ mol−1 can now be achieved with van der Waals (vdW) inclusive density functional theory (DFT).18,19 Even higher accuracies, within 1 kJ mol−1, can be achieved by using computationally demanding wave-function based electronic structure methods but the applicability of these methods to practically relevant molecular crystals is currently limited.20 In the absence of strong hydrogen bonds, crystalline coumarin is an ideal system to study vdW interactions. Using data on the newly obtained coumarin polymorphs, we evaluated a variety of vdW-inclusive methods based on DFT and address the importance of many-body interactions. Furthermore, we investigated the finite temperature effect with, and beyond, the harmonic approximation.
Coumarin II spontaneously crystallizes at 4–50 °C. At higher temperatures, nucleation does not occur, whereas 4 °C is the lowest temperature at which experimental data was obtained. II forms spherulites consisting of irregular, curved, and highly birefringent crystallites, whose size increases with temperature (Fig. 1a and b). Below 31 and 35 °C, II is accompanied by spontaneously nucleated IV and V, respectively.
Although IV does not nucleate above 31 °C, it can crystallize at higher temperatures by seeding. In the whole temperature range, it forms banded spherulites (Fig. 1a, c and d) with the twist period or pitch (π rotation of the fiber around the growth direction) increasing with temperature (Fig. 2). Such behaviour is typical for the banded spherulites and should be related to thinner crystallites and higher driving forces for crystallization at lower temperatures.4 Spherulites alternate between optically positive (slow direction radial) and negative (slow direction tangential) along the radii, indicating that the intermediate refractive index NY is radial and that the minimum (NX) and maximum (NZ) refractive indices are exchanged as the radii twist, thereby forming concentric bands of optical contrast between crossed polarizers (Fig. 1a, c and d). At temperatures below 25 °C, two twist periods can coexist within one spherulite (Fig. 1c and 2), a rare and puzzling behaviour that was reported before for banded spherulites of ε resorcinol.14
Fig. 2 Twist period (pitch, P) of coumarin IV crystallized in the presence of 21 wt% Canada balsam as a function of growth temperature, T. Note two very different coexisting pitches below 25 °C. |
Coumarin V is a minor form, whose largest fraction (up to 10%) was obtained at ∼30 °C; at higher temperatures the nucleation rate is too low whereas at lower temperatures V is easily replaced by IVvia cross-nucleation events (Fig. 1e). Coumarin V forms relatively large crystallites that sometimes organize themselves into spherulites. The spherulites can also be banded with twist periods greater than 0.3 mm (Fig. 1f) and maximum refractive index NZ oriented radially.
Among all five forms, twisted crystals have been observed for coumarin IV and V only. Form I does not crystallize as fine needles are typically required for twisted morphologies. The reasons for the presence of twisted morphologies in IV and V and its absence in II and III are not clear. As demonstrated by the aggregate of experimental data, twisting does not seem to be directly related to the crystal structure, so that different polymorphs of the same material can show twisted and non-twisted morphologies.4 However, if IV or V are twisted, the other crystals of the pair are likely twisted too.
Form IV held at T > 50 °C for a few minutes transforms into III; prismatic crystals (Fig. 1g) form that are elongated parallel to the elongation of fibers in the original spherulite (Fig. 3). Comparison of interference colors also suggests some correspondence between crystallite orientations of these phases in the perpendicular plane (Fig. 1h).
Fig. 3 Phase transformation of coumarin IV to III at 57 °C observed with a polarized light optical microscope. Concentration of Canada balsam 21 wt%. |
Coumarin II transforms to I by nucleation and growth. Transformation of other forms usually occurs via motion of the growth front of I nucleated elsewhere, often in the course of coumarin sublimation and recrystallization. Form II can directly nucleate and grow inside V. Coumarin III can also grow inside V if they are in close contact. Likewise, II can grow into III and IV. These phase relationships were observed at and above room temperature (Fig. 4). The free energy ranking obtained from these relationships (I < II < III < IV < V) is corroborated with the ranking obtained from melting temperatures (Table 1).
Polymorph | Melting point, Tm, °C | ΔGb, kJ mol−1 | ||
---|---|---|---|---|
No additive | No additive, ref. 11 | Canada balsam, 21 wt% | ||
a n/d – not determined. b Difference in free energy at Tm(I) ΔG = (Tm(I) − Tm)ΔH/Tm(I), where the heat of fusion ΔH = 18.4 kJ mol−1. c An accurate value of Tm is hard to establish because of coumarin dissolution in Canada balsam. d T m = 54 °C was estimated by comparing differences Tm(I) − Tm measured with and without Canada balsam. Based on the melting points, polymorphs II, IV, and V were presumably discovered by Lindpainter.7 | ||||
Coumarin I | 69.7(2) | 71 | 63.9(10)c | 0 |
Coumarin II | 66.2(2) | n/d | 59.4(5) | 0.19 |
Coumarin III | 66.0(2) | n/d | 61.3(2) | 0.20 |
Coumarin IV | 64.9(7) | 65 | 59.4(10)c | 0.26 |
Coumarin V | n/d | n/d | 50.9(20)c | ∼0.84d |
Measurement of melting points, Tm, using differential scanning calorimetry (DSC) was impossible for any form except I due to fast polymorph transformation. Consequently, the melting points were measured with a hot stage (Table 1), and the data obtained from DSC (Tm = 69.7 °C; heat of fusion, ΔH = 18.4 kJ mol−1, (lit. 17.2(4) kJ mol−1 (ref. 11))) were used for calibration of the Tm obtained with a hot stage. Although the values of Tm for coumarin crystallized in the presence of Canada balsam are shifted with respect to coumarin without additives, the differences between melting points of different polymorphs are comparable and can serve as a measure of the free energy difference between polymorphs. The micro-Raman spectra of coumarin polymorphs are similar (Fig. 5a) and close to the spectra reported for coumarin solutions.21 Nevertheless, all polymorphs can be distinguished by the distinct signatures in the Raman spectra (Fig. 5b).
Fig. 5 Raman spectra of coumarin polymorphs. (b) Enlarged segment of (a) emphasizing spectral differences. |
With only the structural data for the polycrystalline samples from PXRD, polymorphism of coumarin was explored using two independent CSP methods. To solve the unknown crystal structures, we performed a systematic crystal structure search with evolutionary algorithms for structure generation and DFT energy ranking (called CSPA in this work). This search was complemented by a second CSP method employing a classical force field (called CSPB).
To solve the unknown crystal structures within the CSPA protocol, we performed a systematic crystal structure search based on the evolutionary algorithms implemented in the USPEX code.22–25 The most significant feature of this approach is that molecular geometry is the only structural input. The number of asymmetric units (Z′) and choices of space groups, specified by the user, define the extent of the crystal structure search. Optionally, one can set the unit cell, if the lattice constants are known. The DMACRYS code26 was use to perform the structure relaxations within USPEX. In DMACRYS, the distributed multipole analysis model was constructed by using the calculated Møller–Plesset MP2/6-31G(d,p) charge density from Gaussian09 (ref. 27) and the FIT28 empirical repulsion-dispersion potentials.
We initially conducted a blind search for coumarin crystal structures with Z′ = 1 and 2 for the 30 most common space groups, similar to blind test conditions.13 Among the 100 low-energy structures, we immediately found two models that matched the experimental PXRD of II (Fig. 6a) and V (Fig. 7). PXRD calculated for predicted structures were visually compared with experimental PXRD data, and the lattice constants and peak profiles were refined using a Rietveld method for the promising candidates to figure out if a match occurred.
However, no matches for III and IV were obtained. Therefore, we determined the lattice constants using the indexing software McMaille v3.04.29 The calculated unit cell for IV was found to be orthorhombic with a = 14.220(5), b = 6.025(2), c = 24.792(6) Å. For III, single crystals with typical sizes 2 mm × 0.15 mm × 5 μm (Fig. 1g) were obtained by recrystallizing IV between two glass slides at 54–58 °C for an hour. With the help of a microdiffractometer equipped with a 2D detector, we collected about 40 reflections, determined their corresponding diffraction vectors,30 and found an orthorhombic unit cell with a = 13.79(10), b = 6.02(7), c = 16.98(12) Å. Using these parameters, we performed two independent structure searches with these cells, namely Z′ = 2 for III and Z′ = 3 for IV, for the common space groups P21/c, P21212, P212121, Pca21, and Pna21. The lowest-energy structures from the fixed cell searches matched the experimental PXRD patterns (see Fig. 6b and ESI Fig. S1 for III and Fig. 6c and ESI, Fig. S2† for IV, respectively). We then repeated the prediction for the same space groups without specifying cell parameters for both Z′ = 2 and Z′ = 3. Forms III and IV were identified in each search, confirming that the results obtained from fixed-cell optimizations are indeed low-energy structures. Interestingly, we also found that the comparison of diffraction patterns confirms that the metastable form reported in ref. 11 corresponds to IV.
After finding the candidate structure models, the lattice constants were refined using the Rietveld method implemented in the FullProf suite31 (Table 2 and ESI, Table S1†). For II (room temperature), III (T = 90 K and room temperature), IV (T = 90 K and room temperature), and V (room temperature) the atomic coordinates were also refined by fixing coumarin molecules as rigid bodies using the FullProf suite and Bruker TOPAS 5 (ref. 32) software; final cif files are listed in ESI† and agreement factors are shown in Table 3. In order to check whether the refinement leads to significant structural change, the models before and after refinement were expanded to clusters consisting of 20 molecules and then compared using the COMPACK algorithm.33 The calculated root mean-squared deviation (RMSD) values are generally very small, <0.3 Å (Table 3), confirming the excellent agreement between experiment and theory.
Polymorph | Coumarin I9 | Coumarin IIa | Coumarin IIIa | Coumarin IVa | Coumarin Vb |
---|---|---|---|---|---|
a Data collected at ESRF. b Data collected with a microdiffractometer. Reported errors from least squares fitting of lattice parameters (1–2 × 10−4 Å) are too small to be physically meaningful. | |||||
Space group | Pca21 | P21 | P212121 | P212121 | P212121 |
a (Å) | 15.5023(11) | 3.980 | 17.066 | 24.722 | 4.868 |
b (Å) | 5.6630(4) | 15.291 | 6.038 | 5.994 | 6.882 |
c (Å) | 7.9102(6) | 5.858 | 13.888 | 14.310 | 20.851 |
β (°) | 90 | 85.76 | 90 | 90 | 90 |
V (Å3) | 694.4 | 355.5 | 1431.0 | 2120.5 | 698.4 |
Z, Z′ | 4, 1 | 2, 1 | 8, 2 | 12, 3 | 4, 1 |
Polymorph | T, K | Experimenta | CCDC code/dep. number | N | R p, % | R wp, % | R exp, % | χ 2 | RMSD, Åc |
---|---|---|---|---|---|---|---|---|---|
a ESRF – high-resolution PXRD data obtained at the synchrotron; GADDS – low-resolution PXRD data collected with a laboratory diffractometer. b N – number of reflections. c RMSD – root mean-squared deviation of CSP structure and the structure refined on experimental data. n.r. – not reported. | |||||||||
Coumarin I | 90 | Ref. 9 | COUMAR11 | n.r. | 2.43 | 2.43 | n.r. | n.r. | 0.123 |
295 | Ref. 10 | COUMAR12 | n.r. | 3.62 | 3.62 | n.r. | n.r. | 0.173 | |
Coumarin II | 298 | ESRF | 1542946 | 130 | 6.97 | 9.67 | 6.49 | 2.22 | 0.198 |
Coumarin III | 90 | ESRF | 1542947 | 849 | 9.82 | 12.79 | 9.44 | 1.83 | 0.234 |
298 | GADDS | 1542948 | 49 | 4.74 | 6.49 | 2.87 | 5.11 | 0.264 | |
Coumarin IV | 90 | ESRF | 1542949 | 1013 | 10.41 | 12.63 | 9.09 | 1.93 | 0.198 |
298 | ESRF | 1542950 | 1008 | 13.35 | 15.68 | 7.64 | 4.22 | 0.244 | |
Coumarin V | 298 | GADDS | 1542951 | 79 | 8.09 | 10.82 | 6.07 | 3.18 | 0.295 |
The crystal structures of all five polymorphs are shown in Fig. 8 and summarized in Table 2 and ESI, Table S1.† Four of the five polymorphs are orthorhombic, while II is monoclinic. The most stable I (space group Pca21) adopts a herringbone motif in the bc-plane. In the four other structures, coumarin molecules form stacks with molecular planes separated by 3.3–3.6 Å. In II and V, there are infinite stacks running parallel to the c and a directions, respectively. The major difference between these two structures is how the stacks alternate along the b and c axes. In II, there are two types of stacks with different orientations of molecules with respect to a common coordinate system. In V there are four such types forming two pairs with similar molecular orientations.
Fig. 8 Crystal structures of coumarin polymorphs I (a), II (b), III (c), IV (d), and V (e) and the percentage contributions to Hirshfeld area for the close intermolecular contacts (f). |
Coumarin III and IV belong to the orthorhombic space group P212121 but differ in the number of asymmetric units, Z′ = 2 and 3, respectively. They are characterized by similar parquet-like arrangement of stacks in the ac-plane, each containing four and six molecules, respectively. Similarity of molecular packing and closeness in lattice constants b and c can explain orientational relationships between III nucleating over IV with coinciding b axes and some correspondence in the ac-plane (Fig. 1h and 3).
In parallel to the CSPA scheme described above, a second CSP approach (CSPB) was employed to compare structure generation techniques, test the reliability of an OPLS-based classical force field, and check the thermal stability of predicted structures. In this approach, random structures were generated via the UPACK program suite34 using a rigid molecule with geometry from a PBE0/6-311G*35,36 DFT optimization in Gaussian09.27 A modified OPLS force field37 in which ESP charges were determined based on the computed electron density was used for energy evaluations. In the initial stage of CSPB, 1000 structures were generated for Z′ = 1 and 2 in each of the 13 space groups most common for organic molecules (P21/c, P, P212121, P21, Pbca, C2/c, Pna21, Cc, Pca21, C2, P1, Pbcn, Pc), with an external pressure of 1 bar. This search generated 58 unique structures within 5 kJ mol−1 of the lowest energy, which corresponds to coumarin I. The initial set of predicted structures also included II, III, and V within 7 kJ mol−1 of form I. A subsequent search with 5000 structures for each of the 13 space groups and using Z′ = 1, 2, and 3 resulted in a total of 104 unique structures found within 5 kJ mol−1 of I. Using a dedicated search with Z′ = 3 in the P212121 space group, coumarin IV was generated only once in 60000 random structures. However, many structures, including the observed forms with Z′ = 1 or 2, were predicted by both CSP methods (see ESI†) and are discussed further below.
To test the thermal stability of the generated structures, the observed polymorphs and 20 other low-energy structures were equilibrated using molecular dynamics (MD). For this subset of possible polymorphs, these simulations were performed at 300 K and 1 bar via flexible-cell isothermal–isobaric MD (see Methods for details). After an expected thermal expansion of the cell volumes (<5% for observed polymorphs), all structures tested were found to be stable under these conditions.
As reported in Table 1 and Fig. 4, experimental observations indicate that the order of stability for the five coumarin polymorphs is I > II > III > IV > V, which was not observed in the final energy ranking for either CSP method. It is well known that the energy ranking of predicted crystal structures remains challenging.13 To explore the performance of different ranking methods on a set of polymorphs, an extensive analysis based on DFT and free energy calculations is reported below.
In order to account for the missing long-range interactions in standard DFT, various methods have been proposed to explicitly incorporate vdW interactions. One common approach is to add, a posteriori, an energy term of the general form of −C6/R6, which describes a pairwise level the first term of vdW interactions between two dipoles in a multipole expansion. The C6 term represents the dipole–dipole dispersion coefficient between the two atoms involved and R is the interatomic distance. This scheme is used for example in Grimme's DFT-D43 and DFT-D2 (ref. 44) methods (using fixed empirical dispersion coefficients), and by the Tkatchenko–Scheffler (TS)45 method, in which the dispersion coefficients are explicitly dependent on the electron density. The DFT-D3 scheme46 includes in addition, dipole-quadrupole terms and optionally also three-body dipolar interactions, while the exchange-dipole moment (XDM) methods41 treat vdW interactions on a pairwise level up to quadrupole–quadrupole contributions. Another approach is to obtain dispersion interactions by designing functionals that explicitly include nonlocal correlations (though still based on pairwise addition), such as vdW-DF,47 vdW-DF2 (ref. 48), and their empirically optimized versions (optB88 and optPBE).19 Furthermore, Tkatchenko and coworkers proposed the many-body dispersion (MBD) method,49 which describes many-body dipolar interactions up to infinite order and also includes electrodynamic response effects. It was found that the MBD method substantially outperforms the original TS scheme, in particular for molecular crystals.50 In addition, it was found that the use of MBD together with a hybrid functional can be necessary for obtaining correct stability rankings for molecular crystals.51
The performance of various vdW-inclusive methods has been recently reviewed18,38 and benchmarked on a range of systems.52,53 A study of the C21 reference set by some authors of this work has shown that accurate geometries and lattice energies can be obtained with the vdW-DF2 functional.54 Therefore, we used the vdW-DF2 functional implemented in the Quantum ESPRESSO code55 to relax 50 low-energy structures after merging results from CSPA and CSPB. Not surprisingly, all observed metastable coumarin forms (namely, II, III, IV, and V) have very small energy differences relative to I (Fig. 9). However, it is well known that CSP methods generate more thermodynamically plausible structures than the number of known polymorphs.56 Indeed, several structures were generated by both CSP methods (see ESI† for a direct comparison), with a number of low energy structures within 5 kJ mol−1 of coumarin I sharing similar packing modes. For the 50 vdW-DF2 optimized structures (Fig. 9a), we also calculated energies using PBE+TS (Fig. 9b) and PBE+MBD (Fig. 9c) methods at the vdW-DF2 optimized structures with the all-electron code FHI-aims.62 With PBE+TS, a variety of structures have stabilities between the experimentally observed I and V. In contrast, in the PBE+MBD ranking, forms I–V are all observed within the 9 most stable structures, with 3 of 4 other experimentally non-observed structures being structurally very similar to I (see below). This remarkable energy separation between observed and non-observed structures already shows the importance of many-body interactions for the description of polymorph stabilities.
In order to analyze the packing modes and intermolecular interactions, we use the fingerprint plots derived from Hirshfeld surfaces (Fig. 8 and 10 and ESI, Fig. S6†).57,58 We had previously used fingerprint plots in our study of pentamorphic 1,8-dihydroxyanthraquinone, another rare example of a multimorphic rigid molecule where we discovered three new polymorphs59 albeit single crystals from solution. The fingerprint plots of coumarin and 1,8-dihydroxyanthraquinone are surprisingly similar. In both cases (see ESI, Fig. S6† for coumarin), the lowest energy structure has “antennae” with internal (di) and external (de) distances of (1.4, 1.0 Å) and (1.0, 1.4 Å). This is indicative of C–H⋯O intermolecular distances which are shorter than the vdW distances (in this context, we consider them as weak hydrogen bonds). The “wings” of the fingerprint plots are due to C–H⋯π interactions. This combination is typical for herringbone structures such as these. The fingerprint plots of all the new polymorphs of coumarin are shown in ESI, Fig. S6,† and all of them contain a bright spot centered at di ∼ 1.9 Å, de ∼ 1.9 Å characteristic of π⋯π stacking, although the intensity does change. Again, this motif is found in three of the metastable polymorphs of 1,8-dihydroxyanthraquinone.
Fig. 10 Three polytypic forms of I observed in CSP (which can be found in ESI† in a separate crystallographic information file referred as structure_02, structure_03, and structure_05, respectively). |
The percentage contributions of the close intermolecular contacts shown in Fig. 8 provide greater insight into the packing in the different polymorphs. All structures are dominated by C⋯H, O⋯H and H⋯H interactions. Although there are large changes in C⋯H and H⋯H across the series, the changes in O⋯H are smaller. Coumarin I has a relatively small C⋯C contribution and a correspondingly large C⋯H contribution, consistent with a herringbone type structure. In contrast, II is the opposite; it has a large C⋯C contribution expected for a structure with significant π⋯π stacking and a smaller C⋯H contribution. Coumarin V, the only other structure with Z′ = 1 has a breakdown that is intermediate between I and II. It does exhibit π⋯π stacking but the oblique angle of the molecules relative to each other in the crystal structure reduces the C⋯C interaction and provides for greater C⋯H contributions than in I. Both symmetry independent molecules in III have intermediate C⋯C contributions but quite different C⋯H contributions. The two symmetry independent molecules π stack with each other, leading to the C⋯C contribution. This dimer motif is then packed in such a way that there are no π⋯π interactions between dimers. The difference in C⋯H contributions is due to one molecule of the dimer interacting with O atoms around its edges, whereas the other interacts with H atoms. Coumarin IV is a mix of medium and high C⋯C interactions, a consequence each molecule a being sandwiched between a molecule of b and c, hence π-stacking with its two neighbours.
According to the lattice energy versus density plot at the level of PBE+MBD on top of the vdW-DF2 optimized structures (Fig. 9c), there are four other structures in the energy window of experimentally observed structures. Among these four, the one with highest energy is likely to be ruled out when a more accurate setting is applied. The remaining three structures are found to exhibit nearly identical 2D fingerprint plot patterns relative to I (Fig. S6†). Small differences arise in the contributions of the close intermolecular contacts shown in Fig. 10. Molecule a in structure_02 has a breakdown extremely similar to I. However, the other two molecules are different with a higher C⋯C contribution almost exclusively at the expense of the C⋯H contribution. Furthermore, the two molecules in structure_03 have almost identical breakdowns. This is evident in the fingerprint plots, where there is increased π⋯π stacking in two molecules in structure_03 and two molecules in structure_02. The difference between these molecules and the third molecule in structure_02 and molecules in I is clear in Fig. 10. Columns of molecules running along c doubled up in structure_02 and structure_03 lead to some π⋯π interactions, whereas the alternate columns in I do not. Finally, the four molecules in structure_05 all have contributions that are similar to I.
This analysis shows that all of these structures can be regarded as built up by stacking layers of the same units, differing only in the stacking sequence along various axes, similar to the stacking faults predicted for benzene at high pressure.60 Thus, they belong to the same polytypic family. We note that 30% of the low-energy structures predicted by both CSP methods were observed polymorphs or polytypes, providing an encouraging result for structure validation. From the calculated lattice energies, the energy penalty for alternative polytypes is quite small, but these structures have not been directly observed experimentally. These polytypes in coumarin may be kinetically unstable due to fast transformations to the more favorable known forms during crystal growth, making them unable to form large domains. The cocrystallization of low-energy polytypes may also play a role in the formation of twisted fibers in spherulites by creating long-range elastic stress fields.
Fig. 11 Comparison of different vdW-inclusive methods in terms of optimized unit cell volumes ΔV/Vexpt in%, and energy rankings ΔU in kJ mol−1. Note that PBE+MBD and PBE(0)+MBD in FHI-aims used the relaxed geometry with light basis set at the level of PBE+MBD. For clarity, only eight vdW-inclusive methods are included in this figure. The overall comparison is shown in Fig. S7 in ESI.† |
The original vdW-DF scheme was found to notably overestimate the unit cell volumes and this has been remedied by its later derivatives (vdW-DF2, optPBE, optB88).19 Here, we observed the same trend. All methods except vdW-DF underestimate the unit cell volumes by 1.18 to 9.63% compared to the room temperature data (Fig. 11). The unit cell volumes obtained at 90 K are about 3.61% smaller than the room temperature data set, and most of the vdW-inclusive methods have optimized structures within ±2% of the 90 K data. The description of the theoretical cell volumes could in principle be further improved by using the so-called quasi-harmonic approximation, which captures thermal-expansion effects, or by optimizing the unit cells with an appropriate thermal pressure.41,63,64 All methods give rather consistent differences (<3%) for the five polymorphs indicating that the small volume disagreement could be treated as a systematic error. Furthermore, given that related vdW-inclusive methods using different functionals give the same energy ranking with different relative energies and optimized cell volumes (see vdW-DF methods in Fig. S7†), we choose to focus our analysis on the energy rankings calculated using the DFT methods.
Unlike comparing predicted atomic positions with X-ray crystal structure coordinates, the comparison of calculated lattice energies is more challenging. Unfortunately, we are unable to obtain the sublimation enthalpies from the experiment, since all metastable coumarins convert to stable form I. However, the relative stabilities at room temperature can be derived according to the observed phase transformations (Fig. 4), namely, I > II > III > IV > V. Although it is difficult to check whether the sequence would change at temperatures approaching 0 K, we will assume that this ranking is independent of temperature for the following reasons, a collection of circumstantial evidence: (1) I is very likely the most stable form, since I was the only known form for a long time and there is no low temperature phase transition yet reported; (2) III and IV should be energetically close due to their structural similarity; (3) V is the least stable phase since it only remains observable for a short time under ambient conditions.
Three methods (PBE-D2, XDM and PBE+TS) misrank II as the most stable form, while many methods identify III as the least stable form. Only three approaches using the MBD method (PBE+MBD in VASP and PBE/PBE(0)+MBD in FHI-aims), yield the results satisfying the above criteria, and coincidentally produce the same stability ranking as observed at room temperature (I > II > III > IV > V), despite the fact that magnitudes differ by 1 to 2 kJ mol−1 due to the choices of codes and functionals. This also agrees with our finding that the PBE+MBD model yields the best energy separation between observed and non-observed structures predicted by CSP. Although both PBE-D3 and XDM-B86B were found to have a similar level of accuracy as PBE(0)+MBD for X23 in a recent review,18 they clearly fail in the case of coumarin polymorphs. A possible explanation might be that these models fail to take into account the many-body interactions. Fig. 12 shows the lattice energy ranking notably changes by including the many-body contributions from pairwise up to 6th order within the MBD model, in which the term body refers to individual atoms. It can be seen that in this case, 3-body contributions are crucial for determining the relative stability ordering and higher-order contributions still modify the relative energies by up to 0.2 kJ mol−1. This analysis only shows the effect on the lattice energy but not for the geometry or vibrational free energies. The importance of many-body dispersion effects for energies and for response properties is discussed in a recent review.63 It has been found that MBD plays an essential role in the stability rankings on various systems such as aspirin65 and glycine.66 Our results suggest that coumarin crystals also exhibit strong many-body interactions, and this could serve as a supplementary data set to validate different vdW-inclusive models in addition to the widely used X23 set.
Fig. 12 Comparison of lattice energy differences for all observed coumarin polymorphs relative to form I with different cutoffs of many body interactions within the framework of PBE(0)+MBD at the fully relaxed PBE+MBD structures via MBD code (Jan Hermann, source code of program MBD, Zenodo 2016, http://doi.org/10.5281/zenodo.47528). |
PBE(0)+MBD | OPLS | ||||
---|---|---|---|---|---|
Polymorph | ΔE | ΔG (harmonic) | ΔE | ΔG (harmonic) | ΔG (anharmonic) |
a “n/d” – not determined. | |||||
Coumarin II | 0.27 | 0.70 | 1.58 | 2.02 | 4.5 ± 0.7 |
Coumarin III | 1.21 | 0.94 | 4.17 | 2.73 | n/d |
Coumarin IV | 1.78 | 0.90 | 3.72 | 1.47 | n/d |
Coumarin V | 2.18 | 0.17 | 5.47 | 4.22 | 16.0 ± 1.6 |
Therefore, we returned to the modified OPLS force field to further investigate thermal effects using classical MD. The classical force field energy ranking of optimized structures is I < II < IV < III < V. A comparison of relative energies over the full range of predicted structures shows that the DFT energies are typically only 60% of the OPLS-based energies (see ESI†), hence, an overestimate of the relative energies for observed polymorphs is expected (see Table 4). To calculate the relative free energies we first used the harmonic approximation as described above. Adding the vibrational free energy contribution to the fully optimized (0 K) structures, form IV becomes the second most stable polymorph above 250 K. The harmonic approximation of free energies shows the same trends as for PBE(0)+MBD, with the energy gap relative to form I decreasing at higher temperatures for all observed structures other than II. If the average cell vectors from the MD simulations at 300 K are used to account for thermal expansion, the energy differences relative to form I are reduced, with a free energy ranking of I < IV < III < II < V (see ESI, Fig. S9†). With the exception of form V, this ranking also agrees with the DFT results using experimental lattice vectors, suggesting that the classical force field can be used to obtain appropriate rankings with overestimated relative energies. However, both methods result in relative free energies at 300 K that are considerably larger than the estimates based on the heat of fusion for form I at the melting temperature (Table 1).
To further evaluate the free energy differences between structures at temperatures near the melting point, we extend the classical analysis to allow for anharmonic effects in the MD simulations. Although this could be done using λ-path integration from a harmonic or quasi-harmonic reference to a fully an harmonic description, as recently reviewed by Moustafa et al.,78 we chose instead, as in our previous studies69,70 to use thermodynamic integration to compute the free energy difference between polymorphs based on a given path between structures. Using steered MD simulations (see ESI† for details of the collective variables used for each supercell), the relative free energy of forms I, II, and V were calculated along paths that interconvert these structures. Even with classical MD, the computational cost of this approach limited the analysis to the polymorphs with 4 or fewer molecules in the unit cell.
The relative energy and free energy rankings for the coumarin polymorphs are summarized in Table 4. Importantly, these calculations show that including the vibrational free energy contribution changes the energy ranking of coumarin polymorphs for both DFT and classical force field methods, particularly when the thermally expanded lattice vectors are used (see ESI†). All structures other than form II have the same trend in relative free energy and become more likely at higher temperatures, consistent with the newly characterized polymorphs being crystallized from the melt. However, the fully anharmonic calculations show an even greater change in the relative free energies of polymorphs II and V. Even though the classical polymorph relative lattice energies are known to be overestimated, this result suggests that non-negligible contributions from anharmonic vibrations must be included to properly rank the stabilities of coumarin polymorphs at temperatures above 100 K, despite the considerable computational cost.
Another challenge of CSP techniques is that the ranking of predicted structures is based on calculated energies. Despite the fact that many vdW-inclusive methods have been proposed and more are under active development, our benchmark calculations on coumarin suggest that only a few models produce good agreement with experimental results. In particular, inclusion of many-body dispersion interactions is crucial for the stability ranking. Computation of harmonic free energies is used increasingly for polymorph ranking.13 However, the results for coumarin suggest that for some stability trends, harmonic free energies are not sufficient and anharmonic effects must be considered as well.
X-ray diffraction (XRD) patterns were collected using a Bruker AXS D8 DISCOVER GADDS microdiffractometer equipped with a VÅNTEC-2000 two-dimensional detector and a 0.5 mm MONOCAP collimator (Cu Kα radiation, step size 0.01°). The data collection was performed in reflection mode either from an as-grown crystalline film on a glass slide with the cover glass removed or from a powder detached from the glass slide and attached to a silicon wafer with a small amount of vacuum grease.
High-resolution synchrotron powder diffraction data were collected at the ID22 beamline of the ESRF at a wavelength of 0.41064(1) or 0.39992(1) Å, step size 0.002°. The powder of coumarin was detached from the glass slide and placed into 1 mm borosilicate glass capillary. The patterns were collected immediately afterwards at room temperature and at 90 K using a cryostream.
Raman spectra were collected with a Thermo Scientific DXR Raman microscope (laser wavelength 532 nm, laser power 4 mW) from an as-grown crystalline film on a glass slide covered with cover glass (coumarin V) or with the cover glass removed (coumarin I, II, III, and IV).
The melting point and the heat of fusion were measured using a Perkin-Elmer DSC 8000 differential scanning colorimeter (DSC) for ∼5 mg sample of coumarin sealed in a hermetic aluminium pan.
For the relative energy ranking of the experimentally observed forms, we optimized the structures using various vdW-inclusive methods available in Quantum ESPRESSO, VASP and FHI-aims. For Quantum ESPRESSO, the same parameter set as described in the previous section is used. In VASP, the plane-wave kinetic energy cutoff used is 1000 eV. For FHI-aims, light species default settings were used for lattice and geometry optimizations, while tight species default settings were used for the final energy calculations. For all geometry relaxation calculations, the Brillouin zone was sampled by uniform Г-centered meshes with the reciprocal space resolution at least 2π × 0.06 Å, with convergence criteria of 1 × 10−5 eV per atom for total energies, 5 × 10−3 eV Å−1 for forces.
Footnote |
† Electronic supplementary information (ESI) available: Crystallographic information files, powder diffraction patterns, lattice constants at 90 K, Hirshfeld surfaces, additional computational details and comparisons. see DOI: 10.1039/c7sc00168a |
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