I. INTRODUCTION
Rilpivirine (TMC278, trade name Edurant) was developed by Tibotec for the treatment of acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) infection. Rilpivirine works as a second-generation non-nucleoside reverse transcriptase inhibitor (NNRTI) (Goebel et al., Reference Goebel, Yakovlev, Pozniak, Vinogradova, Boogaerts, Hoetelmans, de Béthune, Peeters and Woodfall2006), and was approved by the U.S. Food and Drug Administration (USFDA) in May 2011. It has the systematic name 4-{[4-({4-[(E)-2-cyanovinyl]2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile. A two-dimensional molecular structural diagram is shown in Figure 1.
Figure 1. The molecular structure of rilpivirine.
The presence of high-quality reference powder patterns in the Powder Diffraction File (PDF; ICDD, Reference Kabekkodu2014) is important for phase identification, particularly by pharmaceutical, forensic, and law enforcement scientists. The crystal structures of a significant fraction of the largest dollar volume pharmaceuticals have not been published, and thus calculated powder patterns are not present in the PDF-4 databases. Sometimes experimental patterns are reported, but they are generally of low quality. Accordingly, a collaboration among ICDD, Illinois Institute of Technology (IIT), Poly Crystallography Inc., and Argonne National Laboratory has been established to measure high-quality synchrotron powder patterns of commercial pharmaceutical ingredients, to include these reference patterns in the PDF, and to determine the crystal structures of these Active Pharmaceutical Ingredients (APIs).
Even when the crystal structure of an API is reported, the single-crystal structure was often determined at low temperature. Most powder measurements are performed at ambient conditions. Thermal expansion (often anisotropic) means that the peak positions calculated from a low-temperature single-crystal structure often differ significantly from those measured at ambient conditions. These peak shifts can result in failure of default search/match algorithms to identify a phase, even when it is present in the sample. High-quality reference patterns measured at ambient conditions are thus critical for easy identification of APIs using standard powder diffraction practices.
II. EXPERIMENTAL
Rilpivirine was commercial reagent, purchased from Carbosynth Company (Lot #FR158451201F), and was used as-received. The white powder was packed into a 1.5 mm diameter Kapton capillary, and rotated during the experiment at ~50 cycles s−1. 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 0.413691 Å from 0.5° to 50° 2θ with a step size of 0.001° and a counting time of 0.1 s per step; the total exposure to the beam was ~1.3 h. The pattern was indexed on a primitive monoclinic unit cell having a = 8.390, b = 13.895, c = 16.039 Å, β = 90.9°, and V = 1869.6 Å3 using Jade 9.5 (MDI, 2013). A search of this cell in the Cambridge Structural Database (CSD; Allen, Reference Allen2002) yielded 104 hits, but no crystal structure for rilpivirine. The systematic absences determined the space group to be P21/c (a common space group for organic compounds), which was confirmed by successful solution and refinement of the structure.
A rilpivirine molecule was built and its conformation optimized using Spartan ‘14 (Wavefunction, 2013), and saved as a mol2 file. This file was converted into a Fenske–Hall Z-matrix file using OpenBabel (O'Boyle et al., Reference O'Boyle, Banck, James, Morley and Hutchison2011). This molecule was used to solve the structure with FOX (Favre-Nicolin and Černý, Reference Favre-Nicolin and Černý2002). The maximum sin θ/λ used in the solution was 0.3 Å−1.
Rietveld refinement was carried out using GSAS (Larson and Von Dreele, Reference Larson and Von Dreele2004). Only the 2°–25° 2θ portion of the pattern was included in the refinement. The two phenyl groups were refined as rigid bodies. 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 N1–C6 aromatic ring was subjected to a planar restraint with a standard deviation of 0.01 Å. The restraints contributed 2.78% to the final χ 2. Isotropic displacement coefficients were refined, grouped by chemical similarity. The hydrogen atoms were included in calculated positions, which were recalculated during the refinement. The U iso of each hydrogen atom was constrained to be 1.3× that of the heavy atom to which it is attached. The peak profiles were described using profile function #4, which includes the Stephens (Reference Stephens1999) anisotropic strain-broadening model. The background was modeled using a three-term shifted Chebyshev polynomial and a ten-term diffuse scattering function to describe the scattering from the Kapton capillary and any amorphous content of the sample. The final refinement of 90 variables using 23 002 observations yielded the residuals wRp = 0.0699, Rp = 0.0568, DWd = 0.828, and χ 2 = 1.307. The largest peak (1.26 Å from C18) and hole (0.63 Å from C15) in the difference Fourier map were 0.21 and −0.21 eÅ−3, respectively. The Rietveld plot is included as Figure 2. The largest errors are in the shapes of the lowest-angle peaks, and may reflect subtle changes in the specimen during the measurement.
Figure 2. (Color online) The Rietveld plot for the refinement of rilpivirine. The red crosses represent the observed data points, and the green line is the calculated pattern. The magenta curve is the difference pattern, plotted at the same vertical scales as the other patterns. The vertical scale has been multiplied by a factor of 5 for 2θ > 7.5°, and by a factor of 20 for 2θ > 13.5°.
A density functional geometry optimization (fixed experimental unit cell) was carried out using CRYSTAL09 (Dovesi et al., Reference Dovesi, Orlando, Civalleri, Roetti, Saunders and Zicovich-Wilson2005). The basis sets for the H, C, and N atoms were those of Gatti et al. (Reference Gatti, Saunders and Roetti1994). The calculation used eight k-points and the B3LYP functional.
III. RESULTS AND DISCUSSION
The refined atom coordinates of rilpivirine are reported in Table I, and the coordinates from the density functional theory (DFT) optimization in Table II. The root-mean-square deviation of the non-hydrogen atoms is 0.09 Å, and the maximum deviation is 0.16 Å, at C14 (Figure 3). The discussion of the geometry uses the DFT-optimized structure. The asymmetric unit (with atom numbering) is illustrated in Figure 4, and the crystal structure is presented in Figure 5. A stereo view of the structure is included as Supplemental Figure S1.
Figure 3. (Color online) Comparison of the refined and optimized structures of rilpivirine. The Rietveld refined structure is colored red and the DFT-optimized structure is in blue.
Figure 4. (Color online) The molecular structure of rilpivirine, with the atom numbering. The atoms are represented by 50% probability spheroids.
Figure 5. (Color online) The crystal structure of rilpivirine, viewed down the a-axis. The hydrogen bonds are shown as dashed lines.
Table I. Rietveld refined fractional coordinates of rilpivirine. Space group P21/c, a = 8.39049(3) Å, b = 13.89687(4) Å, c = 16.03960(6) Å, β = 90.9344(3)°, V = 1869.995(11) Å3, and Z = 4.
Table II. DFT (CRYSTAL09) optimized fractional coordinates of rilpivirine. Space group P21/c, a = 8.39049(3) Å, b = 13.89687(4) Å, c = 16.03960(6) Å, β = 90.9344(3)°, V = 1869.995(11) Å3, and Z = 4.
All bond distances and angles fall within the normal ranges indicated by a Mercury Geometry Check (Macrae et al., Reference Macrae, Bruno, Chisholm, Edington, McCabe, Pidcock, Rodriguez-Monge, Taylor, van de Streek and Wood2008). Only the C16–C17–C18–N19 torsion angle of 6.9° (Z-score = 6.9) is flagged as unusual, but there are only three examples of this torsion angle in the CSD, so the score is not particularly meaningful. The Hirshfeld surface (Spackman and Jayatilaka, Reference Spackman and Jayatilaka2009) indicates that most of the intermolecular contacts are at or longer than the sums of the van der Waals radii (Figure 6). The only contacts shorter than the sums of the van der Waals radii are the hydrogen bonds. The volume enclosed by the Hirshfeld surface is 459.50 Å3, which is smaller than one-fourth of the cell volume (467.50 Å3). The molecules are relatively loosely packed. The small difference between the two volumes is consistent with the lack of voids in the crystal structure.
Figure 6. (Color online) The Hirshfeld surface of rilpivirine. Intermolecular contacts longer than the sums of 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.
An analysis of the contributions to the total crystal energy using the Forcite module of Materials Studio (Accelrys, 2013) suggests that the bond and angle distortion terms are small, and that torsion angle contributions are moderate. The energy appears to be dominated by electrostatic contributions, which in this force-field-based analysis include hydrogen bonds. The hydrogen bonds are better analyzed using the results of the DFT calculation.
The most prominent features of the crystal structure are the N7–H31···N28 and N20–H42···N3 hydrogen bonds (Table III). These form a R2,2(8) pattern (Etter, Reference Etter1990; Bernstein et al., Reference Bernstein, Davis, Shimoni and Chang1995; Shields, et al., Reference Shields, Raithby, Allen and Motherwell2000) which, along with C1,1(12) and longer chains, result in a three-dimensional hydrogen bond network. The C1,1(12) chains run approximately along the [201] direction. Intra- and intermolecular C–H···N hydrogen bonds also contribute to the crystal energy.
Table III. Hydrogen bonds in the DFT-optimized structure of rilpivirine.
The Bravais–Friedel–Donnay–Harker (Bravais, Reference Bravais1866; Friedel, Reference Friedel1907; Donnay and Harker, Reference Donnay and Harker1937) morphology suggests that we might expect blocky morphology for rilpivirine; no preferred orientation correction was necessary. The powder pattern of rilpivirine has been submitted to ICDD for inclusion in future releases of the PDF.
ACKNOWLEDGMENTS
Use of the Advanced Photon Source at Argonne National Laboratory was supported by the U. S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. This work was partially supported by the International Centre for Diffraction Data. We thank Lynn Ribaud for his assistance in data collection.
SUPPLEMENTARY MATERIALS AND METHODS
The supplementary material for this article can be found at http://www.journals.cambridge.org/PDJ
