II. EXPERIMENTAL

Prednicarbate was a commercial reagent, purchased from United States Pharmacopeia (Lot #F01F172), and was used as-received. The white powder was packed into a 1.5 mm diameter Kapton capillary, and rotated during the measurement at ~50 Hz. The powder pattern was measured at 295 K at beam line 11-BM (Lee et al., Reference Lee, Shu, Ramanathan, Preissner, Wang, Beno, Von Dreele, Ribaud, Kurtz, Antao, Jiao and Toby2008; Wang et al., Reference Wang, Toby, Lee, Ribaud, Antao, Kurtz, Ramanathan, Von Dreele and Beno2008) of the Advanced Photon Source at Argonne National Laboratory using a wavelength of 0.412826 Å from 0.5 to 50° 2θ with a step size of 0.001° and a counting time of 0.1 s step⁻¹.

The pattern was indexed on an orthorhombic unit cell with a = 7.703, b = 10.760, c = 31.368, V = 2599.9 Å³, and Z = 4 using N-TREOR (Altomare et al., Reference Altomare, Cuocci, Giacovazzo, Moliterni, Rizzi, Corriero and Falcicchio2013). The suggested space group was P2₁2₁2₁. A reduced cell search in the Cambridge Structural Database (Groom et al., Reference Groom, Bruno, Lightfoot and Ward2016) combined with the chemistry C, H, and O yielded 21 hits, but no structures of prednicarbate. A prednicarbate was built in Spartan ’18 (Wavefunction, 2018), saved as a .mol2 file and converted into a Fenske-Hall Z-matrix using OpenBabel (O'Boyle et al., Reference O'Boyle, Banck, James, Morley, Vandermeersch and Hutchison2011). The structure was solved using FOX (Favre-Nicolin and Černý, Reference Favre-Nicolin and Černý2002) with prednicarbate as the fragment. One of the 45 cycles had a cost factor lower than the rest.

Rietveld refinement was carried out using GSAS II (Toby and Von Dreele, Reference Toby and Von Dreele2013). Only the 1.0–23.0° portion of the pattern was included in the refinement (d _min = 1.035 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, Smith, Taylor, Cooper, Harris and Orpen2004; Sykes et al., Reference Sykes, McCabe, Allen, Battle, Bruno and Wood2011) of the molecule. The Mogul average and standard deviation for each quantity were used as the restraint parameters. The hydrogen atoms were included in calculated positions, which were recalculated during the refinement using Materials Studio (Dassault, 2018). The position of the active hydrogen, H33, was derived by analysis of potential hydrogen bonding patterns. The U _iso were grouped by chemical similarity. The background was modeled using a 6-term shifted Chebyshev polynomial, with a one additional peak.

The final refinement of 129 variables using 22 097 observations (22 000 data points and 97 restraints) yielded the residuals R _wp = 0.0903 and GOF = 1.47. The largest peak (0.18 Å from C10) and hole in the difference Fourier map were 0.56 and −0.49(11) eÅ⁻³, respectively. The largest errors in the fit (Figure 2) are in the shapes of some of the strong low angle peaks.

Figure 2.

(Colour online) The Rietveld plot for the refinement of prednicarbate. The blue crosses represent the observed data points, and the green line is the calculated pattern. The cyan curve is the normalized error plot. The vertical scale has been multiplied by a factor of 10× for 2θ > 7.5°, and by a factor of 40× for 2θ > 40.0°.

A density functional geometry optimization was carried out using CRYSTAL14 (Dovesi et al., Reference Dovesi, Orlando, Erba, Zicovich-Wilson, Civalleri, Casassa, Maschio, Ferrabone, De La Pierre, D-Arco, Noël, Causà and Kirtman2014). The basis sets for the H, C, and O atoms were those of Gatti et al. (Reference Gatti, Saunders and Roetti1994). The calculation was run on eight 2.1 Ghz Xeon cores (each with 6 Gb RAM) of a 304-core Dell Linux cluster at IIT, using 8 k-points and the B3LYP functional, and took ~122 h.

III. RESULTS AND DISCUSSION

The powder pattern for the prednicarbate sample studied here is similar enough to that reported by (Neto et al., Reference Neto, de Araujo, dos Santos, Cosentino, Carvalho and Matos2015) to conclude that they both represent the same material (Figure 3). Our material is not Form A (crystalized from the melt) as reported by Sohn and Kim (Reference Sohn and Kim2002), but seems to correspond to commercial material Form B. From our study, the refined atom coordinates of prednicarbate and the coordinates from the DFT optimization are reported in the CIFs attached as Supplementary Material.

Figure 3.

(Colour online) Comparison of the synchrotron pattern (red) of prednicarbate with the laboratory diffraction pattern from Neto et al. (Reference Neto, de Araujo, dos Santos, Cosentino, Carvalho and Matos2015). The literature pattern (measured using CuKα radiation) was digitized using UN-SCAN-IT (Silk Scientific, 2013) and scaled to the synchrotron wavelength of 0.412826 Å Using Jade 9.8 (MDI, 2018).

The root-mean-square Cartesian displacement of the non-hydrogen atoms of the Rietveld refined and the DFT optimized structures of prednicarbate is 0.113 Å (Figure 4). The maximum displacement is 0.318 Å, at C68. The excellent agreement between the refined and optimized structures is evidence that the experimental structure is correct (van de Streek and Neumann, Reference van de Streek and Neumann2014). The rest of this discussion concentrates on the CRYSTAL-optimized structure. The asymmetric unit (with atom numbering) is illustrated in Figure 5, and the crystal structure is presented in Figure 6.

Figure 4.

(Colour online) Comparison of the Rietveld refined (red) and CRYSTAL14-optimized (blue) structures of prednicarbate.

Figure 5.

(Colour online) The asymmetric unit of prednicarbate, with the atom numbering. The atoms are represented by 50% probability spheres.

Figure 6.

(Colour online) The crystal structure of prednicarbate viewed down the a-axis.

In the crystal structure (Figure 6) the long axis of the steroid ring system lies roughly parallel to the c-axis. The oxygenated side chains are orientated roughly perpendicular to the steroid ring system and are adjacent to each other, parallel to the ab-plane.

All of the bond angles and torsion angles and almost all of the bond distances fall within the normal ranges indicated by a Mercury Mogul Geometry check (Macrae et al., Reference Macrae, Bruno, Chisholm, Edington, McCabe, Pidcock, Rodriguez-Monge, Taylor, van de Streek and Wood2008). The C38–C1 distance of 1.593 Å (average = 1.561(9), Z-score = 3.3) is flagged as unusual. C38 has two bulky substituents, perhaps lengthening this bond, but the standard uncertainty on the average is exceptionally small.

Quantum chemical geometry optimizations (DFT/B3LYP/6-31G*/water) using Spartan ’18 (Wavefunction, 2018) indicated that the observed conformations of the molecule is 1.9 kcal mol⁻¹ higher in energy than the local minimum conformation. The global minimum energy conformation (found by molecular mechanics conformational search) is 1.4 kcal mol⁻¹ lower in energy than the observed conformation (Figure 7). The RMS Cartesian displacement is 0.829 Å. The main difference is in the conformation of the side chain that contains O62 and O64, which is rotated about 180° between the two structures. Since this side chain acts as an acceptor in four C–H···O hydrogen bonds while the other side chain is in acceptor in only two, it is fair to include that the hydrogen bonds play an important role in determining the solid state conformation, and thus that intermolecular interactions are important in determining the solid state conformation.

Figure 7.

(Colour online) Comparison between the observed conformation of prednicarbate (green) and the minimum energy conformation (orange).

Analysis of the contributions to the total crystal energy using the Forcite module of Materials Studio (Dassault, 2018) suggests that angle distortion terms are significant in the intramolecular deformation energy, as might be expected from a fused ring system. The intermolecular energy is dominated by electrostatic attraction, which in this force-field-based analysis includes hydrogen bonds. The hydrogen bonds are better analyzed using the results of the DFT calculation.

The only traditional hydrogen bond donor in the prednicarbate molecule is the hydroxyl group O32–H33, but this does not participate in an O–H···O hydrogen bond. The population analysis shows that (other than the covalent bond to O32) the only other significant interaction of H33 is an intramolecular one to the methyl hydrogen H35 (Table I). The hydroxyl group acts as an acceptor in two C–H···O hydrogen bonds. There are several other C–H···O hydrogen bonds, both intra and intermolecular. Although individually weak, in sum these contribute significantly to the crystalline energy. The nearest oxygen atoms to O32 are symmetry-related O32 at 4.495 Å, precluding the expected O–H···O hydrogen bond.

TABLE I.

Hydrogen bonds (CRYSTAL14) in prednicarbate.

a Intramolecular.

The volume enclosed by the Hirshfeld surface (Figure 8; Hirshfeld, Reference Hirshfeld1977; Turner, et al., Reference Turner, McKinnon, Wolff, Grimwood, Spackman, Jayatilaka and Spackman2017) is 640.60 Å³, 98.65% of 1/4 the unit cell volume. The molecules are thus not tightly packed. All of the significant close contacts (red in Figure 8) involve the hydrogen bonds.

Figure 8.

(Colour online) The Hirshfeld surface of prednicarbate. Intermolecular contacts longer than the sums of the van der Waals radii are colored blue, and contacts shorter than the sums of the radii are colored red. Contacts equal to the sums of radii are white.

The Bravais-Friedel-Donnay-Harker (Bravais, Reference Bravais1866; Friedel, Reference Friedel1907; Donnay and Harker, Reference Donnay and Harker1937) morphology suggests that we might expect platy morphology for prednicarbate, with {001} as the major faces. A 2nd-order spherical harmonic preferred orientation model was included in the refinement; the texture index was 1.000, indicating that preferred orientation was not present in this rotated capillary specimen. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File.