II. EXPERIMENTAL

Quizartinib was a commercial reagent, purchased from TargetMol (Batch #T2066), and was used as-received. The white powder was packed into a 0.5-mm-diameter Kapton capillary and rotated during the measurement at ~2 Hz. The powder pattern was measured at 298(1) K at the Wiggler Low Energy Beamline (Leontowich et al. Reference Leontowich, Gomez, Diaz Moreno, Muir, Spasyuk, King, Reid, Kim and Kycia2021) of the Brockhouse X-ray Diffraction and Scattering Sector of the Canadian Light Source using a wavelength of 0.819563(2) Å (15.1 keV) from 1.6 to 75.0° 2θ with a step size of 0.0025° and a collection time of 3 minutes. The high-resolution powder diffraction data were collected using eight Dectris Mythen2 X series 1K linear strip detectors. NIST SRM 660b LaB₆ was used to calibrate the instrument and refine the monochromatic wavelength used in the experiment.

The pattern was indexed using DICVOL14 (Louër and Boultif Reference Louër and Boultif2014) on a primitive triclinic unit cell with a = 13.936(11), b = 17.939(24), c = 19.899(8) Å, α = 115.24(5), β = 93.65(5), γ = 100.96(5), V = 4,358.57 Å³, and Z = 6. The space group was assumed to be P-1, which was confirmed by the successful solution and refinement of the structure. A reduced cell search of the Cambridge Structural Database (Groom et al. Reference Groom, Bruno, Lightfoot and Ward2016) yielded no hits.

A quizartinib molecule was downloaded from PubChem (Kim et al. Reference Kim, Chen, Cheng, Gindulyte, He, He and Li2023) as Conformer3D_COMPOUND_CID_24889293.sdf. It was converted to a *.mol2 file using Mercury (Macrae et al. Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock and Platings2020). The structure was solved by Monte Carlo-simulated annealing techniques, as implemented in EXPO2014 (Altomare et al. Reference Altomare, Cuocci, Giacovazzo, Moliterni, Rizzi, Corriero and Falcicchio2013), using three molecules as fragments and incorporating a bump penalty. The structure solution contained a void, identified using Mercury with a probe radius of 1.2 Å. An O atom was placed in this void (probably a water molecule). In a preliminary refinement, its position remained constant, and its occupancy refined close to unity. Thus, the compound we studied appears to be a 1/3 hydrate. The hydrogen atoms were added to the water molecule using Materials Studio (Dassault Systèmes 2023), and the structure was optimized using VASP (Kresse and Furthmüller Reference Kresse and Furthmüller1996) through the MedeA graphical interface (Materials Design, Inc., 2024a).

Rietveld refinement, starting from the VASP-optimized structure, was carried out with GSAS-II (Toby and Von Dreele Reference Toby and Von Dreele2013). Only the 2.0–30.0° portion of the pattern was included in the refinements (d _min = 1.583 Å). All non-H-bond distances and angles were subjected to restraints, based on a Mercury/Mogul Geometry Check (Bruno et al. Reference Bruno, Cole, Kessler, Luo, Motherwell, Purkis and Smith2004; Sykes et al. Reference Sykes, McCabe, Allen, Battle, Bruno and Wood2011). The Mogul average and standard deviation for each quantity were used as the restraint parameters. The imidazobenzthiazol and benzene ring systems were restrained to be planar. The restraints contributed 7.5% to the overall χ ². There was another void region identified, but placing an O atom there led to a small refined occupancy and movement too close to other atoms, so the atom was removed from the model. The hydrogen atoms were included in calculated positions, which were recalculated during the refinement using Materials Studio (Dassault Systèmes 2023). We did not attempt to refine the displacement coefficients in such a complex structure with limited data. The peak profiles were described by a uniaxial microstrain model, with [100] as the unique axis. A second-order spherical harmonic model was included for the preferred orientation. The background was modeled using a six-term shifted Chebyshev polynomial, with a peak at 11.15° to model the scattering from the Kapton capillary and any amorphous component.

The final refinement of 384 variables using 11,201 observations and 339 restraints yielded the residual R _wp = 0.06965. The largest peak (2.01 Å from C178) and hole (1.57 Å from C88) in the difference Fourier map were 0.22(6) and − 0.21(6) eÅ⁻³, respectively. The final Rietveld plot is shown in Figure 3. The largest features in the normalized error plot are in the shapes of some of the strong low-angle peaks.

Figure 3.

The Rietveld plot for quizartinib hydrate. The blue crosses represent the observed data points, and the green line is the calculated pattern. The cyan curve is the normalized error plot, and the red line is the background curve. The blue tick marks indicate the peak positions. The vertical scale has been multiplied by a factor of 10× for 2θ > 16.5̊.

The crystal structure of quizartinib hydrate was optimized (fixed experimental unit cell) with density functional theory techniques using VASP (Kresse and Furthmüller Reference Kresse and Furthmüller1996) through the MedeA graphical interface (Materials Design, Inc., 2024a). The calculation was carried out on 32 cores of a 144-core (768-GB memory) HPE Superdome Flex 280 Linux server at North Central College. The calculation used the GGA-PBE functional, a plane wave cutoff energy of 400.0 eV, and a k-point spacing of 0.5 Å⁻¹, leading to a 1 × 1 × 1 mesh, and took ~42 hours. Single-point density functional theory calculations (fixed experimental cell) and population analysis were carried out using CRYSTAL23 (Erba et al. Reference Erba, Desmarais, Casassa, Civalleri, Donà, Bush and Searle2023). The basis sets for the H, C, N, and O atoms in the calculation were those of Gatti, Saunders, and Roetti (Reference Gatti, Saunders and Roetti1994), and that for S was that of Peintinger, Vilela, and Bredow (Reference Peintinger, Vilela Oliveira and Bredow2013). The calculations were run on a 3.5-GHz PC using 10k-points (SHRINK 3 3) and the B3LYP functional, and took ∼18.2 hours.

III. RESULTS AND DISCUSSION

As noted in the Introduction, this material does not correspond to any of the reported forms of quizartinib. It was, however, purchased commercial material, so it may be encountered by others.

The root-mean-square difference of the non-H atoms in the Rietveld-refined and VASP-optimized structures, calculated using the Mercury CSD-Materials/Search/Crystal Packing Similarity tool, is 0.358 Å (Figure 4). The root-mean-square Cartesian displacement of the non-H atoms in the Rietveld-refined and VASP-optimized structures of molecules 1–3, calculated using the Mercury Calculate/Molecule Overlay tool, are 0.280, 0.421, and 0.282 Å, respectively (Figures 5– 7). The agreements are near the upper end of the normal range for correct structures (van de Streek and Neumann Reference van de Streek and Neumann2014). There is a close contact between O147 and H185 in the refined structure. The asymmetric unit is illustrated in Figure 8. The remaining discussion will emphasize the VASP-optimized structure.

Figure 4.

Comparison of the Rietveld-refined (colored by atom type) and VASP-optimized (green) structures of quizartinib hydrate, calculated using the Mercury CSD-Materials/Search/Crystal Packing Similarity tool. The root-mean-square Cartesian displacement is 0.358 Å. Image generated using Mercury (Macrae et al. Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock and Platings2020).

Figure 5.

Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of molecule 1 in quizartinib hydrate. The root-mean-square Cartesian displacement is 0.280 Å. Image generated using Mercury (Macrae et al. Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock and Platings2020).

Figure 6.

Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of molecule 2 in quizartinib hydrate. The root-mean-square Cartesian displacement is 0.421 Å. Image generated using Mercury (Macrae et al. Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock and Platings2020).

Figure 7.

Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of molecule 3 in quizartinib hydrate. The root-mean-square Cartesian displacement is 0.282 Å. Image generated using Mercury (Macrae et al. Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock and Platings2020).

Figure 8.

The asymmetric unit of quizartinib hydrate. This ball-and-stick image was generated using Mercury (Macrae et al. Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock and Platings2020).

The three independent molecules have different conformations. Molecules 1 and 2 are most similar (rms Cartesian displacement = 1.679 Å, decreasing to 1.385 Å by inverting one of the molecules). Molecules 1 and 3 have an rms displacement of 2.411 Å, and molecules 2 and 3 have an rms displacement of 2.650 Å. Molecules 1 and 2 are more linear in conformation, whereas molecule 3 is kinked.

Most of the bond distances and bond angles fall within the normal ranges indicated by a Mercury Mogul Geometry check (Macrae et al. Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock and Platings2020). The sulfur–carbon bond distances S1–C24, S73–C96, and S145–C168 are flagged as unusual. The optimized values are 1.800–1.801 Å, and the Mogul average is 1.739(20) Å, resulting in Z-scores of 3.0. Extended length bonds involving S have been previously reported (Vibha et al. Reference Vibha, Prachality, Reddy, Ravikantha and Thipperudrappa2023) in VASP-optimized structures, so the calculations may not be as accurate as we might hope. The three equivalent angles C34–C31–C29, C106–C103–C101, and C178–C175–C173 (124.4°; average = 129.6(15)°; Z-score = 3.5) are flagged as unusual. Molecules 1–3 have unusual torsion angles involving rotations about 7, 6, and 4 bonds. Most lie on the tails of distributions of similar torsion angles, but rotations about the N10–C40 and N82–C112 bonds in molecules 1 and 2 are truly unusual.

Quantum chemical geometry optimization of isolated quizartinib molecules (DFT/B3LYP/6-31G*/water) using Spartan ‘24 (Wavefunction 2023) indicated that molecule 1 is lowest in energy, and that molecules 2 and 3 are 2.1 and 0.3 kcal/mol higher in energy. Molecules 1 and 2 are about equally similar to the minimum-energy conformation but differ in the orientations of the morpholine/benzothiazole and morpholone/oxazole rings, respectively. The minimum-energy conformation is extended, rather than compact (folded on itself). The quizartinib molecule is apparently very flexible, as large conformational changes result in small differences in energy. Presumably, intermolecular interactions are important in determining the observed solid-state conformations.

The complex crystal structure (Figure 9) is hard to describe succinctly. The molecules are positioned in quasi-parallel layers along the (110) plane. The actual layers are hard to see, and our best depiction is shown in Figure 9. The mean planes of the molecules are approximately (6, 8, −1), (2, 1, −1), and (6, 5, 5). The Mercury Aromatics Analyser indicates one moderate interaction between molecules 1 and 2, with a distance of 4.75 Å.

Figure 9.

The crystal structure of quizartinib hydrate, viewed down [011]. Image generated using Diamond (Crystal Impact 2023).

Analysis of the contributions to the total crystal energy of the structure using the Forcite module of Materials Studio (Dassault Systèmes 2023) indicates that the intramolecular energy is dominated by angle distortion terms, as might be expected for a molecule containing a fused ring system. The intermolecular energy is dominated by electrostatic attractions, which, in this force field-based analysis, also include hydrogen bonds. The hydrogen bonds are better discussed using the results of the DFT calculation.

There are perhaps not as many hydrogen bonds in the structure as anticipated (Table I). The water molecule makes a strong O217–H218···N8 hydrogen bond to the ring N atom N8. It makes a much weaker O217–H219···N155 to the amino group N155. The amino group N10 makes a strong N10–H69···O5 hydrogen bond to the carbonyl group O5 of an adjacent molecule 1. This links two molecule 1 units into dimers, with a graph set R2,2(8) (Bernstein et al. Reference Bernstein, Davis, Shimoni and Chang1995; Etter Reference Etter1990; Motherwell, Shields, and Allen Reference Motherwell, Shields and Allen2000). The comparable amino group N82 in molecule 2 forms only a weak N–H···N hydrogen bond to the ring atom N8 in molecule 1. The equivalent amino group N154 in molecule 3 forms a strong N–H···N hydrogen bond to the ring N153 in adjacent molecule 3, linking them into dimers with a graph set R2,2(8). Each molecule exhibits a unique pattern of C–H···O, C–H···N, or C–H···S hydrogen bonds.

TABLE I.

Hydrogen bonds (CRYSTAL23) in quizartinib hydrate

* Intramolecular.

The volume enclosed by the Hirshfeld surface of quizartinib hydrate (Figure 10; Hirshfeld Reference Hirshfeld1977; Spackman et al. Reference Spackman, Turner, McKinnon, Wolff, Grimwood, Jayatilaka and Spackman2021) is 2,145.94 Å³, 99.07% of 1/2 of the unit cell volume. The packing density is thus fairly dense. The only significant close contacts (red in Figure 10) involve the hydrogen bonds. Fingerprint plots indicate that H···H contacts make up 56.5% of the surface area. The volume/non-hydrogen atom is typical at 17.6 Å³.

Figure 10.

The Hirshfeld surface of quizartinib hydrate. Intermolecular contacts longer than the sum of the van der Waals radii are colored blue, and contacts shorter than the sum of the radii are colored red. Contacts equal to the sum of the radii are white. Image generated using CrystalExplorer (Spackman et al. Reference Spackman, Turner, McKinnon, Wolff, Grimwood, Jayatilaka and Spackman2021).

The Bravais–Friedel–Donnay–Harker (Bravais Reference Bravais1866; Donnay and Harker Reference Donnay and Harker1937; Friedel Reference Friedel1907) algorithm suggests that we should expect slightly elongated morphology for quizartinib hydrate, with [100] as the long axis. A second-order spherical harmonic model was included in the refinement. The texture index was 1.057(3), indicating that the preferred orientation was slight in this rotated capillary specimen.