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Crystal structure of decoquinate, C24H35NO5

Published online by Cambridge University Press:  16 October 2024

Tawnee M. Ens ,
James A. Kaduk Open the ORCID record for James A. Kaduk [Opens in a new window] ,
Megan M. Rost ,
Anja Dosen Open the ORCID record for Anja Dosen [Opens in a new window]  and
Thomas N. Blanton Open the ORCID record for Thomas N. Blanton [Opens in a new window]
Tawnee M. Ens
Affiliation:
North Central College, 131 S. Loomis St., Naperville, IL 60540, USA
James A. Kaduk*
Affiliation:
North Central College, 131 S. Loomis St., Naperville, IL 60540, USA Illinois Institute of Technology, 3101 S. Dearborn St., Chicago, IL 60616, USA
Megan M. Rost
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square, PA, 19073-3273, USA
Anja Dosen
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square, PA, 19073-3273, USA
Thomas N. Blanton
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square, PA, 19073-3273, USA
*
a)Author to whom correspondence should be addressed. Electronic mail: kaduk@polycrystallography.com

Abstract

The crystal structure of decoquinate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Decoquinate crystallizes in space group P21/n (#14) with a = 46.8261(5), b = 12.94937(12), c = 7.65745(10) Å, β = 91.972(1), V = 4640.48(7) Å3, and Z = 8 at 295 K. The crystal structure consists of alternating layers of hydrocarbon chains and ring systems along the a-axis. Hydrogen bonds link the ring systems along the b-axis. The rings stack along the c-axis. The two independent decoquinate molecules have very different conformations, one of which is typical and the other has an unusual orientation of the decyl chain with respect to the hydroxyquinoline ring system, facilitating chain packing. The powder pattern has been submitted to the ICDD for inclusion in the Powder Diffraction File™ (PDF®).

Keywords

decoquinateDeccox®crystal structureRietveld refinementdensity functional theory

Information

Type
New Diffraction Data
Information
Powder Diffraction , Volume 40 , Issue 1 , March 2025 , pp. 57 - 64
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Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited.
Copyright
© The Author(s), 2024. Published by Cambridge University Press on behalf of International Centre for Diffraction Data

I. INTRODUCTION

Decoquinate (marketed under the trade names Deccox and Decoxy) was approved by the FDA in 2004 for animal feed use and shows antimicrobial and antiparasitic properties as a veterinary medication (https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?fr=558.195; Souza et al., Reference Souza, Moreira and Marcelino2022). Decoquinate is used primarily to treat coccidiosis caused by parasites including Eimeria and Toxoplasmosis caused by Toxoplasma in some domestic animals. Though most often connected with animals, coccidiosis can occur in humans, particularly through contact with domestic dogs and cats. When infected with these parasitic infections, the primary symptom is diarrhea. However, in some cases, the infection can lead to miscarriage and abortion of embryos. To combat diarrhea in young animals, decoquinate can be administered in the early stages to be effective against infection (Taylor and Bartram, Reference Taylor and Bartram2012). The systematic name (CAS Registry Number 18507-89-6) is ethyl 6-(decyloxy)-7-ethoxy-4-hydroxyquinoline-3-carboxylate. A two-dimensional molecular diagram of decoquinate is shown in Figure 1.

Figure 1.

The two-dimensional structure of decoquinate.

International Patent Application WO 2020/140197 A1 (Wang et al., Reference Wang, Liang, Fan, Huang, Zhao, Qin and Chen2020) claims decoquinate compositions prepared by hot-melt extrusion for use against malaria parasites. The application also contains X-ray powder data for pure decoquinate active pharmaceutical ingredient; however, no crystal structure is reported.

This work was carried out as part of a project (Kaduk et al., Reference Kaduk, Crowder, Zhong, Fawcett and Suchomel2014) to determine the crystal structures of large-volume commercial pharmaceuticals and include high-quality powder diffraction data for them in the Powder Diffraction File (Kabekkodu et al., Reference Kabekkodu, Dosen and Blanton2024).

II. EXPERIMENTAL

Decoquinate was a commercial reagent, purchased from TargetMol (Batch #113288), 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 beamline 11-BM (Antao et al., Reference Antao, Hassan, Wang, Lee and Toby2008; 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 0.45808(2) Å from 0.5 to 50° 2θ with a step size of 0.001° and a counting time of 0.1 s/step. The high-resolution powder diffraction data were collected using 12 silicon crystal analyzers that allow for high angular resolution, high precision, and accurate peak positions. A mixture of silicon (NIST SRM 640c) and alumina (NIST SRM 676a) standards (ratio Al2O3:Si = 2:1 by weight) was used to calibrate the instrument and refine the monochromatic wavelength used in the experiment.

The pattern was difficult to index. The long 46 Å axis means that most of the low-angle peaks are of the form h00 and hk0, and it was difficult to define the short axis. After several attempts (with smaller c-axes), the pattern was indexed using JADE Pro (MDI, 2024) on a primitive monoclinic unit cell with a = 46.77298, b = 12.95209, c = 7.65585 Å, β = 91.97°, V = 4635.24 Å3, and Z = 8. The suggested space group was P2 1/n, 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 19 hits but no decoquinate derivatives.

The decoquinate molecule was downloaded from PubChem (Kim et al., Reference Kim, Chen, Cheng, Gindulyte, He, He, Li, Shoemaker, Thiessen, Yu, Zaslavsky, Zhang and Bolton2023) as Conformer3D_CID_29112.sdf. The downloaded conformation turns out to be similar to that of molecule 2. It was converted to a *.mol2 file using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020). The crystal structure was solved using Monte Carlo simulated annealing techniques as implemented in EXPO2014 (Altomare et al., Reference Altomare, Cuocci, Giacovazzo, Moliterni, Rizzi, Corriero and Falcicchio2013) using two decoquinate molecules as fragments. The torsion angles of the decyl side chains were fixed at approximately 180°. One of the ten solutions had a figure of merit much better than the others.

Rietveld refinement was carried out with GSAS-II (Toby and Von Dreele, Reference Toby and Von Dreele2013). Only the 1.0–20.0° portion of the pattern was included in the refinements (d min = 1.319 Å). The region 1.51–1.96° 2θ, which contains a peak from the Kapton capillary, was excluded from the refinement. 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). The Mogul average and standard deviation for each quantity were used as the restraint parameters. The hydroxyquinoline rings were restrained to be planar. The hydrogen atoms were included in calculated positions, which were recalculated during the refinement using Materials Studio (Dassault Systèmes, 2023). The Uiso of the heavy atoms were grouped by chemical similarity. The Uiso for the H atoms were fixed at 1.3× the Uiso of the heavy atoms to which they are attached. The peak profiles were described using the generalized microstrain model (Stephens, Reference Stephens1999). The background was modeled using a 6-term shifted Chebyshev polynomial, with a peak at 6.18° to model the scattering from the Kapton capillary and an amorphous component.

The final refinement of 216 variables using 18,586 observations and 142 restraints yielded the residuals R wp = 0.1060 and goodness of fit = 2.02. The largest peak (1.18 Å from C92) and hole (1.57 Å from O69) in the difference Fourier map were 0.17(4) and −0.17(4) eÅ−3, respectively. The final Rietveld plot is shown in Figure 2. The largest features in the normalized error plot are in the shape of the lowest-angle 200 peak.

Figure 2.

The Rietveld plot for the refinement of decoquinate. 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 vertical scale has been multiplied by a factor of 20× for 2θ > 1.5° 50× for 2θ > 9.0°.

The crystal structure of decoquinate was optimized (fixed experimental unit cell) with density functional techniques using VASP (Kresse and Furthmüller, Reference Kresse and Furthmüller1996) through the MedeA graphical interface (Materials Design, 2024). 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 2 × 1 × 1 mesh and took ~126 h. Single-point density functional calculations (fixed experimental cell) and population analysis were carried out using CRYSTAL23 (Erba et al., Reference Erba, Desmarais, Casassa, Civalleri, Donà, Bush, Searle, Maschio, Daga, Cossard, Ribaldone, Ascrizzi, Marana, Flament and Kirtman2023). The basis sets for the H, C, N, and O atoms in the calculation were those of Gatti et al. (Reference Gatti, Saunders and Roetti1994). The calculations were run on a 3.5 GHz PC using 8 k-points and the B3LYP functional and took ~11 h.

III. RESULTS AND DISCUSSION

The powder pattern of this study is similar enough to that reported by Wang et al. (Reference Wang, Liang, Fan, Huang, Zhao, Qin and Chen2020) to suggest that they probably represent the same material (Figure 3). Wang's pattern is limited and of low quality, so the conclusion is tentative.

Figure 3.

Comparison of the synchrotron pattern from this study of decoquinate (black) to that reported by Wang et al. (Reference Wang, Liang, Fan, Huang, Zhao, Qin and Chen2020; green). The Wang et al. pattern (measured using Cu Kα radiation) was digitized using UN-SCAN-IT (Silk Scientific, 2013) and converted to the synchrotron wavelength of 0.458208(2) Å using JADE Pro (MDI, 2024). Image generated using JADE Pro (MDI, 2024).

The root-mean-square Cartesian displacement of the non-H atoms in the Rietveld-refined and VASP-optimized molecules is 0.153 Å for molecule 1 (Figure 4) and 0.214 Å for molecule 2 (Figure 5). The agreement is within the normal range for correct structures (van de Streek and Neumann, Reference van de Streek and Neumann2014). The asymmetric unit with the atom numbering is presented in Figure 6. The displacement parameters for the decyl chain in molecule 2 are larger than those of the other atoms. The remainder of this discussion will emphasize the VASP-optimized structure.

Figure 4.

Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of decoquinate molecule 1. The root-mean-square Cartesian displacement is 0.153 Å. Image generated using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020).

Figure 5.

Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of decoquinate molecule 2. The root-mean-square Cartesian displacement is 0.214 Å. Image generated using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020).

Figure 6.

The asymmetric unit of decoquinate, with the atom numbering. The atoms are represented by 50% probability spheroids. Image generated using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020).

The two independent decoquinate molecules have very different conformations (Figure 7). While the cores of the molecules are very similar, they differ in the orientation of the decyl group. All of the bond distances, bond angles, and most of the torsion angles fall within the normal ranges indicated by a Mercury Mogul Geometry check (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020). Only the C74–C76–C78–C80 (−96°) and O66–C80–C78–C76 (38°) torsion angles are flagged as unusual. Both of these lie on the tails of minor gauche populations of mainly trans torsion angles. These torsion angles reflect the orientation of the decyl chain with respect to the hydroxyquinoline ring system. Visually this looks unusual, compared to the more-normal orientation of molecule 1. Molecule 2 is unusual, presumably to yield better packing of the chains in the solid state.

Figure 7.

Comparison of decoquinate molecule 1 (green) and molecule 2 (orange). Image generated using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020).

Quantum chemical geometry optimization of the isolated molecules (DFT/B3LYP/6-31G*/water) using Spartan ‘20 (Wavefunction, 2020) indicated that molecule 2 is higher in energy than molecule 1 by 1.2 kcal/mol. The energies are thus very close, despite the different conformations. The global minimum-energy conformation (molecular mechanics force field) folds on itself to make the chain and ring system parallel. Solid-state interactions are thus important in determining the observed conformations.

The crystal structure consists of alternating layers of hydrocarbon chains and ring systems along the a-axis (Figure 8). Hydrogen bonds (discussed below) link the ring systems along the b-axis. The rings stack along the c-axis. The mean planes of both hydroxyquinoline ring systems are approximately −3,0,1. The distances between the centroids of the ring systems are 4.786 and 5.566 Å.

Figure 8.

The crystal structure of decoquinate is viewed down the b-axis. 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 bond distance, bond angle, and torsion angle distortion terms contribute significantly to the intramolecular energy. The intermolecular energy is dominated by van der Waals and electrostatic attractions, which, in this force field analysis, also include hydrogen bonds. The hydrogen bonds are better analyzed using the results of the DFT calculations.

Only two classical hydrogen bonds are present in the crystal structure (Table I). Both N6–H54⋯O5 and N71–H119⋯O70 hydrogen bonds link the ring systems along the b-axis. The graph set (Etter, Reference Etter1990; Bernstein et al., Reference Bernstein, Davis, Shimoni and Chang1995; Motherwell et al., Reference Motherwell, Shields and Allen2000) of each is C1,1(6). The energies of the N–H–O hydrogen bonds were calculated using the correlation of Wheatley and Kaduk (Reference Wheatley and Kaduk2019). Several C–H⋯O hydrogen bonds link the ring systems, and one methyl group of an ethoxyl group participates in a C–H⋯O hydrogen bond.

TABLE I.

Hydrogen bonds (CRYSTAL23) in decoquinate.

a Intramolecular.

The volume enclosed by the Hirshfeld surface of decoquinate (Figure 9, Hirshfeld, Reference Hirshfeld1977; Spackman et al., Reference Spackman, Turner, McKinnon, Wolff, Grimwood, Jayatilaka and Spackman2021) is 1146.54 Å3, which constitutes 98.83% of the unit cell volume. The packing density is thus fairly typical. The only significant close contacts (red in Figure 9) involve the hydrogen bonds. The volume/non-hydrogen atom is larger than normal, measuring 19.3 Å3.

Figure 9.

The Hirshfeld surface of decoquinate. 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. Image generated using CrystalExplorer (Spackman et al., Reference Spackman, Turner, McKinnon, Wolff, Grimwood, Jayatilaka and Spackman2021).

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 decoquinate, with {200} as the major faces. A second-order spherical harmonic model was included in the refinement. The texture index was 1.006, indicating that the preferred orientation was not significant in this rotated capillary specimen.

IV. DEPOSITED DATA

The powder pattern of decoquinate from this synchrotron data set has been submitted to the ICDD for inclusion in the Powder Diffraction File. The Crystallographic Information Framework (CIF) files containing the results of the Rietveld refinement (including the raw data) and the DFT geometry optimization were deposited with the ICDD. The data can be requested at pdj@icdd.com.

Acknowledgements

The 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 Saul Lapidus for his assistance in the data collection.

Conflicts of interest

The authors have no conflicts of interest to declare.

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Figure 0

Figure 1. The two-dimensional structure of decoquinate.

Figure 1

Figure 2. The Rietveld plot for the refinement of decoquinate. 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 vertical scale has been multiplied by a factor of 20× for 2θ > 1.5° 50× for 2θ > 9.0°.

Figure 2

Figure 3. Comparison of the synchrotron pattern from this study of decoquinate (black) to that reported by Wang et al. (2020; green). The Wang et al. pattern (measured using Cu Kα radiation) was digitized using UN-SCAN-IT (Silk Scientific, 2013) and converted to the synchrotron wavelength of 0.458208(2) Å using JADE Pro (MDI, 2024). Image generated using JADE Pro (MDI, 2024).

Figure 3

Figure 4. Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of decoquinate molecule 1. The root-mean-square Cartesian displacement is 0.153 Å. Image generated using Mercury (Macrae et al., 2020).

Figure 4

Figure 5. Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of decoquinate molecule 2. The root-mean-square Cartesian displacement is 0.214 Å. Image generated using Mercury (Macrae et al., 2020).

Figure 5

Figure 6. The asymmetric unit of decoquinate, with the atom numbering. The atoms are represented by 50% probability spheroids. Image generated using Mercury (Macrae et al., 2020).

Figure 6

Figure 7. Comparison of decoquinate molecule 1 (green) and molecule 2 (orange). Image generated using Mercury (Macrae et al., 2020).

Figure 7

Figure 8. The crystal structure of decoquinate is viewed down the b-axis. Image generated using Diamond (Crystal Impact, 2023).

Figure 8

TABLE I. Hydrogen bonds (CRYSTAL23) in decoquinate.

Figure 9

Figure 9. The Hirshfeld surface of decoquinate. 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. Image generated using CrystalExplorer (Spackman et al., 2021).