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Crystal structure of 3-[(3,4-dinitro-1H-pyrazol-1-yl)-NNO-azoxy]-4-nitro-1,2,5-oxadiazole

Published online by Cambridge University Press:  06 April 2021

A. O. Dmitrienko Open the ORCID record for A. O. Dmitrienko [Opens in a new window] ,
A. A. Konnov  and
M. S. Klenov
A. O. Dmitrienko*
Affiliation:
Department of Chemistry, M. V. Lomonosov Moscow State University, 1 Leninskie Gory, Moscow119991, Russian Federation
A. A. Konnov
Affiliation:
N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prosp., Moscow119991, Russian Federation
M. S. Klenov
Affiliation:
N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prosp., Moscow119991, Russian Federation
*
a)Author to whom correspondence should be addressed. Electronic mail: dmitrienka@gmail.com
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Abstract

The crystal structure of a novel high-energy density material 3-[(3,4-dinitro-1H-pyrazol-1-yl)-NNO-azoxy]-4-nitro-1,2,5-oxadiazole C5HN9O8 was determined and refined using laboratory powder diffraction data. The diffraction data and database analysis were insufficient to distinguish two candidate structures from the solution step. Density functional theory with periodic boundary conditions optimizations were used to choose the correct one. 3-[(3,4-Dinitro1H-pyrazol-1-yl)-NNO-azoxy]-4-nitro-1,2,5-oxadiazole crystallizes in space group Pbca with a = 8.3104(2) Å, b = 14.2198(5) Å, c = 19.4264(7) Å, V = 2295.66(14) Å3. The molecular conformation contains a weak intramolecular hydrogen bond C–H⋯O–N, and the structure is dominated by weak O⋯π and O⋯O contacts.

Keywords

Rietveld refinementDFT calculationshigh-energy density materials
Type
New Diffraction Data
Information
Powder Diffraction , Volume 36 , Issue 3 , September 2021 , pp. 176 - 180
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Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press on behalf of International Centre for Diffraction Data

I. INTRODUCTION

X-ray powder diffraction techniques are routinely used in the analysis of high-energy density materials (HEDMs). Their main objectives are phase analysis and calculation of crystal density at room temperature. When single-crystal experiments are unavailable, they are also used to determine the crystal structure (and thus confirm the molecular structure) (Klenov et al., Reference Klenov, Anikin, Guskov, Churakov, Strelenko, Ananyev, Bushmarinov, Dmitrienko, Lyssenko and Tartakovsky2016).

High-energy density materials containing the azoxy group are a subject of intensive research (Fischer et al., Reference Fischer, Klapötke, Reymann and Stierstorfer2014; Yu et al., Reference Yu, Wang, Yang, Wu, Lin, Ju, Lu and Cheng2015; Liu et al., Reference Liu, Zhang, Wang, Li, Zhang and Shreeve2016). However, only few (and not high-energy) compounds with an azoxy group bonded to a nitrogen atom of the heterocycle were reported (Moriarty et al., Reference Moriarty, Hopkins, Prakash, Vaid and Vaid1990; Semenov et al., Reference Semenov, Churakov, Chertanova, Strelenko, Ioffe and Tartakovskii1992). Additional N–N bond can increase the enthalpy of formation and thus energy density. A molecular diagram for 3-[(3,4-dinitro-1H-pyrazol-1-yl)-NNO-azoxy]-4-nitro-1,2,5-oxadiazole C5HN9O8 is shown in Figure 1.

Figure 1. The molecular structure of 3-[(3,4-dinitro-1H-pyrazol-1-yl)-NNO-azoxy]-4-nitro-1,2,5-oxadiazole.

II. EXPERIMENTAL

A. Safety precautions

Although we have encountered no difficulties during the preparation and handling of compound described in this paper, it is a potentially explosive energetic material that is sensitive to impact and friction. Mechanical actions of this energetic material, involving scratching or scraping, must be avoided. Any manipulations must be carried out by using appropriate standard safety precautions (face shield, ear protection, body armor, Kevlar® gloves, and grounded equipment).

3-[(3,4-Dinitro-1H-pyrazol-1-yl)-NNO-azoxy]-4-nitro-1,2,5-oxadiazole was synthesized in three steps from known 1-amino-3,4-dinitropyrazole (Yin et al., Reference Yin, Zhang, He, Parrish and Shreeve2014) as part of Russian Science Foundation project 19-13-00276.

The compound is an impact and friction-sensitive explosive, so caution is needed during sample preparation. The sample was ground in an agate mortar in small (~5 mg) portions and placed between two Kapton films with a PTFE spatula.

The powder pattern was measured on a Bruker AXS D8 Advance Vario powder diffractometer equipped with primary monochromator (CuKα 1, λ = 1.54056 Å) and 1D LynxEye PSD. Data were collected at room temperature in the range 2–60° in 2θ with a 0.01° 2θ step size and 1 s step−1 in transmission mode (Figure 2).

Figure 2. Final observed (black), calculated (red), and difference profiles for the Rietveld refinement.

The diffraction pattern was indexed on a primitive orthorhombic cell with a = 8.3104(2) Å, b = 14.2198(5) Å, c = 19.4264(7) Å using the SVD (singular value decomposition) index algorithm (Coelho, Reference Coelho2003) as implemented in Bruker TOPAS 5.0 (Coelho, Reference Coelho2018), and space group determination was carried out using statistical systematic absences analysis as implemented in ExtSym (Markvardsen et al., Reference Markvardsen, Shankland, David, Johnston, Ibberson, Tucker, Nowell and Griffin2008). The resulting most probable space group Pbca was later confirmed by structure solution and refinement.

Parallel tempering, as implemented in FOX (Favre-Nicolin and Černý, Reference Favre-Nicolin and Černý2002) was used to solve the crystal structure in direct space. The Rietveld refinement (with Bruker TOPAS 5.0) was carried out using bond and angle restraints derived from PW-DFT-D calculations and a “riding” model for the hydrogen atom. The restraint weight was automatically decreased during the refinement, and the refinement result of a more restrained model served as a starting structure for the next less restrained one. For a detailed explanation of the methodology, see Dmitrienko and Bushmarinov (Reference Dmitrienko and Bushmarinov2015).

PW-DFT-D calculations were performed in VASP5.4.4 (Kresse and Hafner, Reference Kresse and Hafner1993, Reference Kresse and Hafner1994; Kresse and Furthmüller, Reference Kresse and Furthmüller1996a, Reference Kresse and Furthmüller1996b) using the PBE functional (Perdew et al., Reference Perdew, Burke and Ernzerhof1996) corrected by the Grimme D3 van der Waals correction (Grimme et al., Reference Grimme, Antony, Ehrlich and Krieg2010) with Becke–Jonson damping (Grimme et al., Reference Grimme, Ehrlich and Goerigk2011). A plane-wave basis set with “normal” projector augmented wave (PAW) pseudopotentials (Blöchl, Reference Blöchl1994; Kresse and Joubert, Reference Kresse and Joubert1999) as supplied with VASP was employed. All optimizations were performed using an energy cutoff of 600 eV. Default 0.5 Å−1 k-point mesh and 2 k-points were used in all calculations.

Root-mean-square (rms) Cartesian displacement between the Rietveld-refined structure and the PW-DFT-D-optimized ones were calculated as suggested by Neumann (van de Streek and Neumann, Reference van de Streek and Neumann2014).

III. RESULTS AND DISCUSSION

Parallel tempering runs in FOX lead to two global minimization solutions with almost identical χ 2; their views in crystals are shown in Figures 3 and 4. The only difference between the structures is the mutual arrangement of C–H and N-lone pair fragments of the pyrazole ring.

Figure 3. General view of 1 in a crystal.

Figure 4. General view of 2 in a crystal.

Both C–H and N-lone pair fragments contain seven electrons and it can be difficult to distinguish them even for a medium quality single-crystal experiment. For Rietveld refinement where both atomic thermal parameters and Fourier maps are noisy, there is no way to do it reliably. In most cases, such ambiguity can be resolved by examining intermolecular contacts. But high-energy density material structures often lack strong hydrogen or halogen intermolecular bonds and contain only weak O⋯O and O⋯π contacts (Fedyanin et al., Reference Fedyanin, Lyssenko, Fershtat, Muravyev and Makhova2019). Structures 1 and 2 share most contacts, the only differences are weak intramolecular C–H⋯O hydrogen bond with formation of 6-member cycle in 1 and weak intermolecular C–H⋯π interaction in 2. No unusual contacts were found in either structure; it is not immediately obvious which structure is correct.

Another way to choose the correct solution is to optimize both structures with an appropriate quantum chemistry method and examine resulting energies and geometries. If one of the structures has much higher energy or the atomic coordinates vary significantly from experimental ones, we should dismiss that solution (van de Streek and Neumann, Reference van de Streek and Neumann2010). If energies and atomic positions are close, we should consider a statically disordered structure.

For structure 1, PW-DFT-D-optimized energies are −1297.188/−1297.284 eV for fixed/relaxed cell calculations. For structure 2, optimized energies are −1294.912/−1295.495 eV. So, structure 1 is more than 5 kcal mol−1 more energetically favorable. The difference is large: considering Boltzmann distribution at room temperature coexisting of two forms is improbable. Thus, we should dismiss structure 2 and accept structure 1.

After the solution step, the difference between 1 and 2 was merely a swap of C–H and N fragments in the pyrazole ring or, equivalently, 180° change in the C2–N4–N5–N6 torsion angle. Now, it is possible to discuss more subtle geometric features of the calculated structures; all the values discussed are related to the free-cell calculations. The most considerable differences are in the bond angle C5–N6–N5 (134.1° for 1 and 118.1° for 2), the torsion angle C2–N4–N5–N6 (173.2° for 1 and 171.7° for 2), and the dihedral angle between planes containing pyrazole and furazan rings (68.7° for 1 and 62.8° for 2). The differences are associated with the intramolecular hydrogen bond in structure 1.

Rietveld refinement was performed with fixed-cell energy-optimized structure 1 as source of bond and angle restraints. Final refinement with 98 variables and 56 restraints over 5536 data points yielded R p/R p′/R wp/R wp′/R Bragg = 6.08/16.96/8.41/17.47/2.31%, GOF = 1.26. The resulting Rietveld plot is shown in Figure 2. The rms Cartesian displacement between free-cell energy-optimized structure 1 and final Rietveld-refined structure is 0.083, which is within the range expected for correct structures. Comparison of the final Rietveld-refined structure with fixed-cell energy-minimized structures 1 and 2 is shown in Figure 5.

Figure 5. Comparison of energy-optimized structures 1 (cyan), 2 (red), and Rietveld-refined 1 (magenta).

Figure 6 depicts the packing of 1. The shortest intermolecular contact in the structure is the O⋯π interaction between the nitro group and the furozan cycle with the O⋯C distance 2.851 Å. Other notable contacts are NO2⋯O2N (O⋯O distance is 2.938 Å), NO2⋯N(O)N (O⋯N distance is 2.930 Å), and another NO2⋯π (O⋯C distance is 2.937 Å). A lack of strong intermolecular interactions is typical for HEDMs.

Figure 6. Fragment of the crystal packing of 1 (view along the a-axis).

IV. DEPOSITED DATA

The Crystallographic Information File (ak170.cif) that contains the results of the Rietveld refinement and the raw powder diffraction pattern, and four files (VASP_1_refined_cell.cif, VASP_1_fixed_cell.cif, VASP_2_refined_cell.cif, VASP_2_fixed_cell.cif) related to the PW-DFT-D calculations using VASP were deposited with ICDD. The VASP files were used to obtain the bond length and angle restraints and for geometry discussion. These data files can be requested at info@icdd.com. The first file is also available from CCDC 2025381.

ACKNOWLEDGEMENTS

The study was funded by RFBR according to the research project № 1933-60075. M. S. Klenov and A. A. Konnov acknowledge financial support from the Russian Science Foundation (project 19-13-00276) for the synthesis of the title compound. The in crystal calculations were carried out using the equipment of the shared research facilities of HPC computing resources at Lomonosov Moscow State University (Sadovnichy et al., Reference Sadovnichy, Tikhonravov, Voevodin, Opanasenko and Vetter2013).

References

Blöchl, P. E. (1994). “Projector augmented-wave method,” Phys. Rev. B 50(24), 17953–17979.CrossRefGoogle ScholarPubMed
Coelho, A. A. (2003). “Indexing of powder diffraction patterns by iterative use of singular value decomposition,” J. Appl. Crystallogr. 36(1), 86–95.CrossRefGoogle Scholar
Coelho, A. A. (2018). “TOPAS and TOPAS-academic: an optimization program integrating computer algebra and crystallographic objects written in C++,” J. Appl. Crystallogr. 51(1), 210–218.CrossRefGoogle Scholar
Dmitrienko, A. O. and Bushmarinov, I. S. (2015). “Reliable structural data from Rietveld refinements via restraint consistency,” J. Appl. Crystallogr. 48(6), 1777–1784.CrossRefGoogle Scholar
Favre-Nicolin, V. and Černý, R. (2002). “FOX, “free objects for crystallography”: a modular approach to ab initio structure determination from powder diffraction,” J. Appl. Crystallogr. 35(6), 734–743.CrossRefGoogle Scholar
Fedyanin, I. V., Lyssenko, K. A., Fershtat, L. L., Muravyev, N. V., and Makhova, N. N. (2019). “Crystal solvates of energetic 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane molecule with [bmim]-based ionic liquids,” Cryst. Growth Des. 19(7), 3660–3669.CrossRefGoogle Scholar
Fischer, D., Klapötke, T. M., Reymann, M., and Stierstorfer, J. (2014). “Dense energetic nitraminofurazanes,” Chemistry 20(21), 6401–6411.CrossRefGoogle ScholarPubMed
Grimme, S., Antony, J., Ehrlich, S., and Krieg, H. (2010). “A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-d) for the 94 elements H-Pu,” J. Chem. Phys. 132(15), 154104.CrossRefGoogle ScholarPubMed
Grimme, S., Ehrlich, S., and Goerigk, L. (2011). “Effect of the damping function in dispersion corrected density functional theory,” J. Comput. Chem. 32(7), 1456–1465.CrossRefGoogle ScholarPubMed
Klenov, M. S., Anikin, O. V., Guskov, A. A., Churakov, A. M., Strelenko, Y. A., Ananyev, I. V., Bushmarinov, I. S., Dmitrienko, A. O., Lyssenko, K. A., and Tartakovsky, V. A. (2016). “Serendipitous synthesis of (tert-butyl-NNO-azoxy)acetonitrile: reduction of an oxime moiety to a methylene unit,” Eur. J. Org. Chem. 2016(22), 3845–3855.CrossRefGoogle Scholar
Kresse, G. and Furthmüller, J. (1996a). “Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set,” Comput. Mater. Sci. 6(1), 15–50.CrossRefGoogle Scholar
Kresse, G. and Furthmüller, J. (1996b). “Efficient iterative schemes for ab initio total energy calculations using a plane-wave basis set,” Phys. Rev. B 54(16), 11169–11186.CrossRefGoogle Scholar
Kresse, G., and Hafner, J. (1993). “Ab initio molecular dynamics for liquid metals,” Phys. Rev. B 47(1), 558–561.CrossRefGoogle ScholarPubMed
Kresse, G., and Hafner, J. (1994). “Ab initio molecular-dynamics simulation of the liquid-metal–amorphous-semiconductor transition in germanium,” Phys. Rev. B 49(20), 14251–14269.CrossRefGoogle ScholarPubMed
Kresse, G. and Joubert, D. (1999). “From ultrasoft pseudopotentials to the projector augmented-wave method,” Phys. Rev. B 59(3), 1758–1775.CrossRefGoogle Scholar
Liu, Y., Zhang, J., Wang, K., Li, J., Zhang, Q., and Shreeve, J. (2016). “Bis(4-nitraminofurazanyl-3-azoxy)azofurazan and derivatives: 1,2,5-oxadiazole structures and high-performance energetic materials,” Angew. Chem., Int. Ed. 55(38), 11548–11551.CrossRefGoogle ScholarPubMed
Markvardsen, A. J., Shankland, K., David, W. I. F., Johnston, J. C., Ibberson, R. M., Tucker, M., Nowell, H., and Griffin, T. (2008). “Extsym: a program to aid space-group determination from powder diffraction data,” J. Appl. Crystallogr. 41(6), 1177–1181.CrossRefGoogle Scholar
Moriarty, R. M., Hopkins, T. E., Prakash, I., Vaid, B. K., and Vaid, R. K. (1990). “Hypervalent iodine oxidation of amines in the presence of nitroso compounds: a method for the preparation of unsymmetrically substituted azoxy compounds,” Synth. Commun. 20(15), 2353–2357.CrossRefGoogle Scholar
Perdew, J. P., Burke, K., and Ernzerhof, M. (1996). “Generalized gradient approximation made simple,” Phys. Rev. Lett. 77(18), 3865–3868.CrossRefGoogle ScholarPubMed
Sadovnichy, V., Tikhonravov, A., Voevodin, V., and Opanasenko, V. (2013). “'Lomonosov': Supercomputing at Moscow State University,” in Contemporary High Performance Computing: From Petascale toward Exascale, edited by Vetter, Jeffrey S. (Chapman and Hall/CRC Computational Science, Boca Raton, USA), pp. 283–307.Google Scholar
Semenov, S. E., Churakov, A. M., Chertanova, L. F., Strelenko, Y. A., Ioffe, S. L., and Tartakovskii, V. A. (1992). “Synthesis of 1-(2,4,6-trichlorophenyl)2-(1,2,4-triazol-4-yl)-diazene-1-oxide,” Bull. Russ. Acad. Sci. Div. Chem. Sci. 41(2), 277–279.CrossRefGoogle Scholar
van de Streek, J. and Neumann, M. A. (2010). “Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations,” Acta Crystallogr. Sect. B Struct. Sci. 66(5), 544–558.CrossRefGoogle ScholarPubMed
van de Streek, J. and Neumann, M. A. (2014). “Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-d),” Acta Crystallogr. Sect. B Struct. Sci., Cryst. Eng. Mater. 70(6), 1020–1032.CrossRefGoogle Scholar
Yin, P., Zhang, J., He, C., Parrish, D. A., and Shreeve, J. M. (2014). “Polynitro-substituted pyrazoles and triazoles as potential energetic materials and oxidizers,” J. Mater. Chem. A 2, 3200–3208.CrossRefGoogle Scholar
Yu, Q., Wang, Z., Yang, H., Wu, B., Lin, Q., Ju, X., Lu, C., and Cheng, G. (2015). “N-trinitroethyl-substituted azoxyfurazan: high detonation performance energetic materials,” RSC Adv. 5(35), 27305–27312.CrossRefGoogle Scholar
Figure 0

Figure 1. The molecular structure of 3-[(3,4-dinitro-1H-pyrazol-1-yl)-NNO-azoxy]-4-nitro-1,2,5-oxadiazole.

Figure 1

Figure 2. Final observed (black), calculated (red), and difference profiles for the Rietveld refinement.

Figure 2

Figure 3. General view of 1 in a crystal.

Figure 3

Figure 4. General view of 2 in a crystal.

Figure 4

Figure 5. Comparison of energy-optimized structures 1 (cyan), 2 (red), and Rietveld-refined 1 (magenta).

Figure 5

Figure 6. Fragment of the crystal packing of 1 (view along the a-axis).