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Crystal structure of nicarbazin, (C13H10N4O5)(C6H8N2O)

Published online by Cambridge University Press:  18 March 2024

James A. Kaduk Open the ORCID record for James A. Kaduk [Opens in a new window] ,
A. Dosen Open the ORCID record for A. Dosen [Opens in a new window]  and
Thomas N. Blanton Open the ORCID record for Thomas N. Blanton [Opens in a new window]
James A. Kaduk*
Affiliation:
Illinois Institute of Technology, 3101 S. Dearborn St., Chicago, IL 60616, USA North Central College, 131 S. Loomis St., Naperville, IL 60540, USA
A. 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: [email protected]
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Abstract

The crystal structure of nicarbazin has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Nicarbazin is a co-crystal of 4,4′-dinitrocarbanilide (DNC) and 2-hydroxy-4,6-dimethylpyrimidine (HDP) molecules. Nicarbazin crystallizes in space group P-1 (#2) with a = 6.90659(8), b = 12.0794(4), c = 13.5040(7) Å, α = 115.5709(11), β = 102.3658(6), γ = 91.9270(4)°, V = 982.466(5) Å3, and Z = 2. The DNC and HDP molecules are linked by two strong N–H⋯O and N–H⋯N hydrogen bonds, and the HDP molecules are linked into centrosymmetric dimers by another N–H⋯O hydrogen bond. These strong hydrogen bonds link the molecules into layers parallel to the ab-plane and parallel stacking of both DNC and HDP molecules is prominent in the structure. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

Keywords

nicarbazinCarbigran®crystal structureRietveld refinementdensity functional theory
Type
New Diffraction Data
Information
Powder Diffraction , Volume 39 , Issue 2 , June 2024 , pp. 105 - 110
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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
Copyright © The Author(s), 2024. Published by Cambridge University Press on behalf of International Centre for Diffraction Data

I. INTRODUCTION

Nicarbazin (sold under the brand names Carbigran®, Nicarb®, and many others) is an equimolar complex of 4,4′-dinitrocarbanilide and 2-hydroxy-4,6-dimethylpyrimidine. It is used as a coccidiostat for poultry by inhibiting the reproduction of coccidia parasites, particularly in chickens selected for human consumption. Nicarbazin also finds application as a contraceptive for Canada geese and pigeons. The systematic name (CAS Registry Number 330-95-0) is 1,3-bis(4-nitrophenyl)urea 4,6-dimethyl-1H-pyrimidin-2-one. A two-dimensional molecular diagram is shown in Figure 1.

Figure 1. The 2D molecular structure of nicarbazin. The 4,4′-dinitrocarbanilide molecule is on the left, and 2-hydroxy-4,6-dimethylpyrimidine is on the right.

Nicarbazin can be obtained by the reaction of 4,4′-dinitrocarbanilide (DNC) and 2-hydroxy-4,6-dimethylpyrimidine (HDP) in methanol (Rogers et al., Reference Rogers, Brown, Brown, Kazazis, Leanza, Nichols, Ostlind and Rodino1983). Such complexes are prepared to enhance the solubility of DNC in water, but re-crystallization (to single crystals) proved impossible. We are unaware of any published X-ray powder diffraction data for nicarbazin.

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 (Gates-Rector and Blanton, Reference Gates-Rector and Blanton2019).

II. EXPERIMENTAL

Nicarbazin was a commercial reagent, purchased from TargetMol (Batch #114902), 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 (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 0.458208(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 indexed using peaks of >1% relative intensity with JADE Pro 8.6 (MDI, 2022) on a high-quality primitive triclinic unit cell with a = 6.90659, b = 12.0794, c = 13.5040 Å, α = 115.5709, β = 102.3658, γ = 91.9270°, V = 982.466 Å3, and Z = 2. The suggested space group was P-1, which was confirmed by the successful solution and refinement of the structure. A reduced cell search in the Cambridge Structural Database (Groom et al., Reference Groom, Bruno, Lightfoot and Ward2016) yielded one hit, but no related structures.

Structures of the constituent molecules were downloaded from PubChem (Kim et al., Reference Kim, Chen, Cheng, Gindulyte, He, He, Li, Shoemaker, Thiessen, Yu, Zaslavsky, Zhang and Bolton2019) as Conformer3D_CID_1511764.sdf and Conformer3D_CID_9509.sdf. Conformer3D_CID_1511764.sdf was trimmed to remove substituents. They were converted to *.mol2 files using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020), and to Fenske–Hall Z-matrices using Open Babel (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) using sinθ/λ max = 0.32 Å−1. Analysis of potential hydrogen bonding patterns indicated that N35 was protonated (N3⋯O33~2.4 Å), so H49 was added to N35 using Materials Studio (Dassault Systèmes, 2021).

Rietveld refinement was carried out using GSAS-II (Toby and Von Dreele, Reference Toby and Von Dreele2013). Only the 2.0–25.0° portion of the pattern was included in the refinement (d min = 1.058 Å). Initial refinements indicated the presence of extra (unindexed) peaks. NaCl was identified as being present and was added to the refinement as a second phase. Its concentration refined to 0.6 wt.%. A few very weak additional peaks indicated the presence of at least one additional impurity phase. 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 restraints contributed 1.4% to the final χ 2. The hydrogen atoms were included in calculated positions, which were recalculated during the refinement using Materials Studio (Dassault Systèmes, 2021). The Uiso was grouped by chemical similarity. The Uiso for the H atoms was fixed at 1.3× the Uiso of the heavy atoms to which they are attached. A second-order spherical harmonic model was included in the refinement. The refined texture index was 1.001(0). The peak profiles were described using the generalized microstrain model. The background was modeled using a six-term shifted Chebyshev polynomial, plus a peak at 5.86° 2θ to model the scattering from the Kapton capillary and any amorphous component.

The final refinement of 136 variables using 23,037 observations and 75 restraints yielded the residuals Rwp = 0.0991 and goodness of fit (GOF) = 1.90. The largest peak (0.32 Å from N7) and hole (1.62 Å from C20) in the difference Fourier map were 0.31(6) and −0.23(6) eÅ−3, respectively. The largest errors in the difference plot (Figure 2) are attributed to impurity peaks.

Figure 2. The Rietveld plot for the refinement of nicarbazin. The blue crosses represent the observed data points, and the green line is the calculated pattern. The red line is the background curve. The cyan curve is the normalized error plot. The vertical scale has been multiplied by a factor of 20× for 2θ > 9.0°.

The crystal structure of nicarbazin was optimized (fixed experimental cell) and population analysis was carried out using density functional theory techniques as implemented in CRYSTAL17 (Dovesi et al., Reference Dovesi, Erba, Orlando, Zicovich-Wilson, Civalleri, Maschio, Rerat, Casassa, Baima, Salustro and Kirtman2018). 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 ~79 h.

III. RESULTS AND DISCUSSION

The root-mean-square Cartesian displacements between the Rietveld-refined and DFT-optimized structures of nicarbazin are 0.069 Å for DNC and 0.026 Å for HDP (Figures 3 and 4). The excellent agreement provides strong evidence that the structure is correct (van de Streek and Neumann, Reference van de Streek and Neumann2014). The following discussion concentrates on the DFT-optimized structure. The asymmetric unit (with atom numbering) is illustrated in Figure 5. The best view of the crystal structure is down the b-axis (Figure 6). Prominent is the parallel stacking of both DNC and HDP molecules. The mean plane of the DNC molecule is 18,1,−5, and that of the HDP molecule is 6,−3,16. The Mercury Aromatic Analyser indicates two strong interactions between the DNC molecules, with distances of 4.19 Å. Strong hydrogen bonds link the molecules into layers parallel to the ab-plane

Figure 3. Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of the 4,4′-dinitrocarbanilide (DNC) molecule in nicarbazin. The rms Cartesian displacement is 0.069 Å. Image generated using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020).

Figure 4. Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of the 2-hydroxy-4,6-dimethylpyrimidine (HDP) molecule in nicarbazin. The rms Cartesian displacement is 0.026 Å. Image generated using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020).

Figure 5. The asymmetric unit of nicarbazin, 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).

Figure 6. The crystal structure of nicarbazin, viewed down the b-axis. Image generated using Diamond (Crystal Impact, 2022).

All of the bond distances, bond angles, and 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). Quantum chemical geometry optimization of isolated DNC and HDP molecules (DFT/B3LYP/6-31G*/water) using Spartan ‘18 (Wavefunction, 2020) indicated that both molecules are in essentially their minimum-energy conformations. Solid-state interactions, though important to the crystal energy, do not result in molecular changes.

Analysis of the contributions to the total crystal energy of the structure using the Forcite module of Materials Studio (Dassault Systèmes, 2021) suggests that the intramolecular deformation energy contributions are small and equally distributed among bond, angles, and torsion terms. The intermolecular energy is dominated by electrostatic attractions, which in this force field analysis also include hydrogen bonds. The hydrogen bonds are better analyzed using the results of the DFT calculation.

Hydrogen bonds are prominent in the structure (Table I). The DNC and HDP molecules are linked by two strong N–H⋯O and N–H⋯N hydrogen bonds, and the HDP molecules are linked into centrosymmetric dimers by another N–H⋯O hydrogen bond (Figure 7). Both the HDP⋯HDP and DNC⋯HDP links have graph sets R2,2(8) (Etter, Reference Etter1990; Bernstein et al., Reference Bernstein, Davis, Shimoni and Chang1995; Shields et al., Reference Shields, Raithby, Allen and Motherwell2000). These strong hydrogen bonds link the molecules into layers parallel to the ab-plane. The energies of the N–H⋯O hydrogen bonds were calculated using the correlation of Wheatley and Kaduk (Reference Wheatley and Kaduk2019). Both methyl and ring hydrogen atoms in the HDP act as donors in intermolecular C–H⋯O hydrogen bonds. Most of the ring hydrogen atoms in the DNC participate in intramolecular C–H⋯O hydrogen bonds to the nitro groups and the urea carbonyl oxygen atom O1.

TABLE I. Hydrogen bonds (CRYSTAL17) in nicarbazin

a Intramolecular.

Figure 7. The principal hydrogen bonds in the crystal structure of nicarbazin. Image generated using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020).

The volume enclosed by the Hirshfeld surface of nicarbazin (Figure 8, Hirshfeld, Reference Hirshfeld1977; Turner et al., Reference Turner, McKinnon, Wolff, Grimwood, Spackman, Jayatilaka and Spackman2017) is 483.11 Å3, 98.35% of 1/2 the unit cell volume. The packing density is thus fairly typical. The only significant close contacts (red in Figure 8) involve the hydrogen bonds. The volume/non-hydrogen atom is smaller than usual, at 15.8 Å3.

Figure 8. The Hirshfeld surface of nicarbazin. 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 CrystalExplorer17 (Turner et al., Reference Turner, McKinnon, Wolff, Grimwood, Spackman, Jayatilaka and Spackman2017).

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 nicarbazin, with {001} as the major faces, or elongated morphology with [100] as the long axis. A second-order spherical harmonic model was included in the refinement. The texture index was 1.001(0), indicating that the preferred orientation was slight in this rotated capillary specimen.

IV. DEPOSITED DATA

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 .

ACKNOWLEDGEMENTS

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 and Saul Lapidus for their 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 2D molecular structure of nicarbazin. The 4,4′-dinitrocarbanilide molecule is on the left, and 2-hydroxy-4,6-dimethylpyrimidine is on the right.

Figure 1

Figure 2. The Rietveld plot for the refinement of nicarbazin. The blue crosses represent the observed data points, and the green line is the calculated pattern. The red line is the background curve. The cyan curve is the normalized error plot. The vertical scale has been multiplied by a factor of 20× for 2θ > 9.0°.

Figure 2

Figure 3. Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of the 4,4′-dinitrocarbanilide (DNC) molecule in nicarbazin. The rms Cartesian displacement is 0.069 Å. Image generated using Mercury (Macrae et al., 2020).

Figure 3

Figure 4. Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of the 2-hydroxy-4,6-dimethylpyrimidine (HDP) molecule in nicarbazin. The rms Cartesian displacement is 0.026 Å. Image generated using Mercury (Macrae et al., 2020).

Figure 4

Figure 5. The asymmetric unit of nicarbazin, with the atom numbering. The atoms are represented by 50% probability spheroids. Image generated using Mercury (Macrae et al., 2020).

Figure 5

Figure 6. The crystal structure of nicarbazin, viewed down the b-axis. Image generated using Diamond (Crystal Impact, 2022).

Figure 6

TABLE I. Hydrogen bonds (CRYSTAL17) in nicarbazin

Figure 7

Figure 7. The principal hydrogen bonds in the crystal structure of nicarbazin. Image generated using Mercury (Macrae et al., 2020).

Figure 8

Figure 8. The Hirshfeld surface of nicarbazin. 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 CrystalExplorer17 (Turner et al., 2017).