I. INTRODUCTION
Raltegravir potassium (marketed as Isentress®) was approved by the U.S. Food and Drug Administration on 12 October 2007 for the treatment of human immunodeficiency virus (HIV) infection. It belongs to the integrase inhibitors class of drugs, working by inhibiting an HIV enzyme integrase that is responsible for the insertion of viral complimentary DNA into the host genome during the pathogenesis of HIV (Croxtall and Keam, Reference Croxtall and Keam2009). Patent publications WO2010/140156 (Parthasaradhi et al., Reference Parthasaradhi, Rathnakar, Raji, Muralidhara and Subash2010) and WO2011/024192 (Jetti et al., Reference Jetti, Jonnalagadda, Raval and Datta2011) described the production of different polymorphs of raltegravir potassium, including amorphous and crystalline forms I, II, III, and H1, but their crystal structures have not been reported. The systematic name (CAS registry number 871038-72-1) is potassium 4-[(4-fluorophenyl)methylcarbamoyl]-1-methyl-2-[2-[(5-methyl-1,3,4-oxadiazole-2-carbonyl)amino]propan-2-yl]-6-oxopyrimidin-5-olate. A two-dimensional molecular structure diagram of the anion is shown in Figure 1.
The molecular structure of the raltegravir anion.
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. This structure is a result of a collaboration among ICDD, Illinois Institute of Technology, Poly Crystallography Inc., and Argonne National Laboratory to measure high-quality synchrotron powder patterns of commercial pharmaceutical ingredients, include these reference patterns in the PDF, and 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
Raltegravir potassium, a commercial reagent purchased from Jalor-Chem Co. Ltd., was used as-received. The white powder was packed into a 1.5 mm diameter Kapton capillary, and rotated during the measurement 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 0.413 906 Å from 0.5° to 50° 2θ with a step size of 0.001° and a counting time of 0.1 s/step. The pattern was indexed on a primitive monoclinic unit cell having a = 15.6156, b = 8.1485, c = 16.1334 Å, β = 94.165°, V = 2047.44 Å3, and Z = 4 using DICVOL06 (Louër and Boultif, Reference Louër and Boultif2007). The space group was indicated to be P21/c by EXPO2009 (Altomare et al., Reference Altomare, Camalli, Cuocci, Giacovazzo, Moliterni and Rizzi2009). A search of this cell in the Cambridge Structural Database (Allen, Reference Allen2002) yielded 85 hits, but no crystal structure for raltegravir potassium.
A raltegravir anion 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, Vandermeersch and Hutchison2011). Initial attempts to solve the structure by simulated annealing techniques using this molecule and a potassium atom failed. Since the potassium cation would almost certainly be coordinated to the ionized hydroxyl oxygen, a potassium was added to O23 at a distance of 2.64 Å, and the geometry of the complex was optimized in Spartan ‘14 using molecular mechanics techniques. The hydrogen atoms were removed, and the molecule was saved as a .mol2 file. This file was converted into a MOPAC-format file using OpenBabel. This converted file was used to solve the structure using the simulated annealing module of EXPO2013 (Altomare et al., Reference Altomare, Cuocci, Giacovazzo, Moliterni, Rizzi, Corriero and Falcicchio2013).
Rietveld refinement was carried out using General Structure Analysis System (GSAS) (Larson and Von Dreele, Reference Larson and Von Dreele2004). Only the 1°–25° portion of the pattern was included in the refinement. The C1–H10 phenyl group was refined as a rigid body. All other 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 restraints contributed 5.21% 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 (Materials Studio; Accelrys, 2013). 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 (Thompson et al., Reference Thompson, Cox and Hastings1987; Finger et al., Reference Finger, Cox and Jephcoat1994), which includes the Stephens (Reference Stephens1999) anisotropic strain broadening model. The background was modeled using a three-term shifted Chebyshev polynomial and a five-term diffuse scattering (Debye) function, to model the scattering from the Kapton capillary and any amorphous component of the sample. The final refinement of 121 variables using 24 070 observations (23 999 data points and 71 restraints) yielded the residuals R wp = 0.074, R p = 0.061, and χ 2 = 1.690. The largest peak (0.45 Å from N17) and hole (1.95 Å from C18) in the difference Fourier map were 0.64 and −0.73 e Å−3, respectively. The Rietveld plot is included as Figure 2. The largest errors are in the shapes and intensities of a few low-angle peaks.
(Colour online) The Rietveld plot for the refinement of raltegravir potassium. 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 4 for 2θ > 2.5° and by a factor of 20 for 2θ > 11.0°.
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, N, and O atoms were those of Gatti et al. (Reference Gatti, Saunders and Roetti1994), the basis set for F was that of Nada et al. (Reference Nada, Catlow, Pisani and Orlando1993), and the basis set for K was that of Dovesi et al. (Reference Dovesi, Roetti, Freyria Fava, Prencipe and Saunders1993). The calculation used eight k-points and the B3LYP functional.
III. RESULTS AND DISCUSSION
The refined atom coordinates of raltegravir potassium 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 0.06 Å, and the maximum deviation is 0.16 Å, at the methyl group C36 (Figure 3). The excellent agreement between the refined and optimized structures is strong evidence that the structure is correct (van de Streek and Neumann, Reference van de Streek and Neumann2014). 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.
(Colour online) Comparison of the refined and optimized structures of raltegravir potassium. The Rietveld-refined structure is colored red and the DFT-optimized structure is in blue.
(Colour online) The molecular structure of raltegravir potassium, with the atom numbering. The atoms are represented by 50% probability spheroids.
(Colour online) The crystal structure of raltegravir potassium, viewed down the b-axis.
Rietveld-refined crystal structure of raltegravir potassium.
DFT-optimized (CRYSTAL09) crystal structure of raltegravir potassium. The lattice parameters were fixed at the experimental values.
Most bond distances, angles, and torsion angles fall within the normal ranges indicated by a Mercury Mogul Geometry Check, but several geometrical features are flagged as unusual (Table III). Many of these occur in the C4N2 ring C16–C21 in the center of the molecule; this ring is also close to the K coordination. Several unusual torsion angles occur in the C25–C31 portion of the molecule, but there are only a few comparison angles. Apparently, the geometry of this molecule is somewhat unusual.
Unusual geometrical features in raltegravir potassium.
The most prominent feature of the crystal structure is the chains of edge-sharing 7-coordinate K parallel to the b-axis. The coordination is KO5N2, and the K–N bonds are the longest, as expected from the bond valence r 0 (2.13 and 2.26 Å for K–O and K–N, respectively) (Breese and O'Keefe, Reference Breese and O'Keefe1991). The raltegravir molecule chelates to the K through N17 and O15. The bond valence sum for the K is 1.01. The Mulliken overlap populations are small and positive (<0.008 e), suggesting that the K–O/N bonds have a small degree of covalent character, but are mainly ionic.
Conformational analysis of the raltegravir anion (Hartree–Fock/3-21G/water) suggests that the solid-state conformation is at least 22 kcal mole−1 higher in energy than the minimum-energy conformation, and that K coordination and the hydrogen bonds contribute significantly to the observed structure. An analysis of the contributions to the total crystal energy using the Forcite module of Materials Studio (Accelrys, 2013) suggests that significant contributions to the crystal energy come from bond, angle, and torsion distortion terms. The crystal 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 carbonyl oxygen O23 participates in two strong hydrogen bonds (Table IV). The N13–H39···O23 bond is intermolecular. The graph sets (Etter, Reference Etter1990; Bernstein et al., Reference Bernstein, Davis, Shimoni and Chang1995; Shields et al., Reference Shields, Raithby, Allen and Motherwell2000) are S1,1(6) and R1,1(7), hydrogen bonds, respectively; the seven-membered ring includes the K. Several weak C–H···O/F hydrogen bonds (both intra- and inter-molecular) apparently help determine the conformation of the raltegravir anion in the solid state. The crystal structure can be described as having K-containing layers in the bc-plane, with double layers of CH4F phenyl rings halfway between them.
Hydrogen bonds in raltegravir potassium.
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 raltegravir potassium, with {100} as the principal faces. A second-order spherical harmonic preferred orientation model was included in the refinement, but the texture index was only 1.002; preferred orientation was not significant for this rotated capillary specimen. The powder pattern of raltegravir potassium is included in the PDF as entry 00-064-1499.
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. The authors thank Lynn Ribaud for his assistance in data collection and Corrado Cuocci for his help in using the simulated annealing module of EXPO2013.
