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Structure analysis of a phenylpyrazole carboxylic acid derivative crystallizing with three molecules in the asymmetric unit (Z′ = 3) using X-ray powder diffraction

Published online by Cambridge University Press:  11 April 2019

S. Ghosh
Affiliation:
Department of Physics, Chakdaha College, Chakdaha, Nadia, West Bengal, Pin-741222, India
S. Pramanik
Affiliation:
Department of Physics, Jadavpur University, Kolkata-700032, India Department of Physics, Dinabandhu Mahavidyalaya (Bongaon), Bangaon, West Bengal, Pin-743235, India
A. K. Mukherjee*
Affiliation:
Department of Physics, Jadavpur University, Kolkata-700032, India
*
a)Author to whom correspondence should be addressed. Electronic mail: akm_ju@rediffmail.com

Abstract

Crystal structure analysis of a pyrazole carboxylic acid derivative, 5-(trifluoromethyl)-1-phenyl-1H-pyrazole-4-carboxylic acid (1) has been carried out from laboratory powder X-ray diffraction data. The crystal packing in the pyrazole carboxylic acid derivative exhibits an interplay of strong O–H…O, C–H…N and C–H…F hydrogen bonds to generate a three-dimensional molecular packing via the formation of R22(8) and R22(9) rings. Molecular electrostatic potential calculations indicated that carbonyl oxygen, pyrazole nitrogen and fluorine atoms to be the strongest acceptors. The relative contribution of different interactions to the Hirshfeld surface of pyrazole carboxylic acid and a few related structures retrieved from CSD indicates that H…H, N…H and O…H interactions can account for almost 70% of the Hirsfeld surface area in these compounds.

Type
Technical Article
Copyright
Copyright © International Centre for Diffraction Data 2019 

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References

Aakeröy, C. B., Wijethunga, T. K., and Desper, J. (2015). “Molecular electrostatic potential dependent selectivity of hydrogen bonding,” New J. Chem. 39, 822828.Google Scholar
Allen, F. H., and Taylor, R. (2004). “Research applications of the Cambridge Structural Database (CSD),” Chem Soc Rev. 33, 463475.Google Scholar
Altomare, A., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Rizzi, R., and Werner, P.-E. (2000). “New techniques for indexing: n-TREOR in EXPO,” J. Appl. Crystallogr. 33, 11801186.Google Scholar
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A., Rizzi, R., Corriero, N., and Falcicchio, A. (2013). “EXPO2013: a kit of tools for phasing crystal structures from powder data,” J. Appl. Crystallogr. 46, 12311235.Google Scholar
Anderson, K. M., and Steed, J. W. (2007). “Comment on “On the presence of multiple molecules in the crystal asymmetric unit (Z′ > 1) by Gautam R. Desiraju,” CrystEngComm. 9, 328330.+1)+by+Gautam+R.+Desiraju,”+CrystEngComm.+9,+328–330.>Google Scholar
Anderson, K. M., Afarinkia, K., Yu, H.-W., Goeta, A. E., and Steed, J. W. (2006). “When Z′ = 2 is better than Z = 1 supramolecular centrosymmetric hydrogen-bonded dimers in chiral systems,” Cryst. Growth Des. 6, 21092113.Google Scholar
Anderson, K. M., Probert, M. R., Goeta, A. E., and Steed, J. W. (2011). “Size does matter—the contribution of molecular volume, shape and flexibility to the formation of co-crystals and structures with Z′ > 1,” CrystEngComm. 13, 8387.+1,”+CrystEngComm.+13,+83–87.>Google Scholar
Antila, J. C., Baskin, J. M., Barder, T. E., and Buchwald, S. L. (2004). “Copper−Diamine-Catalyzed N-arylation of pyrroles, pyrazoles, indazoles, imidazoles, and triazoles,” J. Org. Chem. 69, 55785587.Google Scholar
Arlin, J. B., Bhardwaj, R. M., Johnston, A., Miller, G. J., Bardin, J., MacDougall, F., Fernandes, P., Shankland, K., David, W. I. F., and Florence, A. J. (2014). “Structure and stability of two polymorphs of creatine and its monohydrate,” CrystEngComm. 16, 81978204.Google Scholar
Bader, R. F. W., Carroll, M. T., Cheeseman, J. R., and Chang, C. (1987). “Properties of atoms in molecules: atomic volumes,” J. Am. Chem. Soc. 109, 79687979.Google Scholar
Becke, A. D. (1988). “Density-functional exchange-energy approximation with correct asymptotic behaviour,” Phys. Rev. A. 38, 30983100.Google Scholar
Berger, R., Resnati, G., Metrangolo, P., Weber, E., and Hulliger, J. (2011). “Organic fluorine compounds: a great opportunity for enhanced materials properties,” Chem. Soc. Rev. 40, 34963508.Google Scholar
Bernstein, J. (2011). “Polymorphism−A perspective,” Cryst. Growth Des. 11, 632650.Google Scholar
Bernstein, J., Dunitz, J. D., and Gavezzotti, A. (2008). “Polymorphic perversity: crystal structures with many symmetry-independent molecules in the unit cell,” Cryst. Growth Des. 8, 20112018.Google Scholar
Brock, C. P. (2016). “High-Z′ structures of organic molecules: their diversity and organizing principles,” Acta Cryst. B72, 807821.Google Scholar
Caruso, F., Raimondi, M. V., Daidone, G., Pettinari, C., and Rossi, M. (2009). “5-Amino-1-phenyl-3-trifluoromethyl-1H-pyrazole-4-carboxylic acid,” Acta Crystallogr. Sect E. 65, o2173o2173.Google Scholar
Chatterjee, P., Dey, T., Pal, S., and Mukherjee, A. K. (2017). “Two mefenamic acid derivatives: structural study using powder X-ray diffraction, Hirshfeld surface and molecular electrostatic potential calculations,” Z. Kristallogr. 232, 385394.Google Scholar
Das, D., Banerjee, R., Mondal, R., Howard, J. A. K., Boese, R., and Desiraju, G. R. (2006). “Synthon evolution and unit cell evolution during crystallisation. A study of symmetry-independent molecules (Z′>1) in crystals of some hydroxy compounds,” Chem. Commun., 555557.1)+in+crystals+of+some+hydroxy+compounds,”+Chem.+Commun.,+555–557.>Google Scholar
Das, U., Chattopadhyay, B., Hazra, D. K., Sureshbabu, V. V., and Mukherjee, A. K. (2016). “Two carbamate derivatives with Z′ = 2 and 3: an interplay of strong and weak hydrogen bonds,” J. Mol. Str. 1122, 290298.Google Scholar
David, W. I. F., and Shankland, K. (2008). “Structure determination from powder diffraction data,” Acta Crystallogr. A. 64, 5264.Google Scholar
Delley, B. (1990). “An all-electron numerical method for solving the local density functional for polyatomic molecules,” J. Chem. Phys. 92, 508517.Google Scholar
Desiraju, G. R. (2007). “On the presence of multiple molecules in the crystal asymmetric unit (Z′>1),” CrystEngComm. 9, 9192.1),”+CrystEngComm.+9,+91–92.>Google Scholar
Favre-Nicolin, V., and Cerný, R. (2004). “A better FOX: using flexible modelling and maximum likelihood to improve direct-space ab initio structure determination from powder diffraction,” Z. Krist. - Cryst. Mat. 219, 847856.Google Scholar
Hao, X., Siegler, M. A., Parkin, S., and Brock, C. P. (2005a). “[M(H2O)2(15-crown-5)](NO3)2: A system rich in polymorphic and modulated phases,” Cryst.Growth Des. 5, 22252232.Google Scholar
Hao, X., Chen, J., Cammers, A., Parkin, S., and Brock, C. P. (2005b). “A helical structure with Z′ = 10,” Acta Cryst. B61, 218226.Google Scholar
Harris, K. D. M., and Cheung, E. Y. (2004). “How to determine structures when single crystals cannot be grown: opportunities for structure determination of molecular materials using powder diffraction data,” Chem. Soc. Rev. 33, 526.Google Scholar
Harris, K. D. M., Tremayne, M., and Kariuki, B. M. (2001). “Contemporary advances in the Use of powder X-Ray diffraction for structure determination,” Angew. Chem. Int. Ed. 40, 16261651.Google Scholar
Jelsch, C., Ejsmont, K., and Huder, L. (2014). “The enrichment ratio of atomic contacts in crystals, an indicator derived from the Hirshfeld surface analysis,” IUCr J. 1, 119128.Google Scholar
Johnstone, R. D. L., Ieva, M., Lennie, A. R., McNab, H., Pidcock, E., Warren, J. E., and Parsons, S. (2010). “Pressure as a tool in crystal engineering: inducing a phase transition in a high-Z′ structure,” CrystEngComm. 12, 25202523.Google Scholar
Larson, A. C., and Von Dreele, R. B. (2000). “General Structure Analysis System (GSAS), Los Alamos Laboratory Report, LAUR,” 86–784.Google Scholar
Lee, C., Yang, W., and Parr, R. G. (1988). “Development of the colle-salvetti correlation-energy formula into a functional of the electron density,” Phys. Rev. B. 37, 785789.Google Scholar
Lehmler, H.-J., Parlin, S., and Brock, C. P. (2004). “Packing conflicts in the Z′ = 5 structure of CF3(CF2)3(CH2)10COOH,” Acta Cryst. B60, 325332.Google Scholar
Lodochnikova, O. A., Startseav, V. A., Nikitana, L. E., Bodrov, A. V., Klimovitskii, A. E., Klimovitskii, E. N., and Litvinov, I. A. (2014). “When two symmetrically independent molecules must be different: “crystallization-induced diastereomerization” of chiral pinanyl sulfone,” CrystEngComm. 16, 43144321.Google Scholar
Martin, T., Fleissner, J., Milius, W., and Breu, J. (2016). “Behind crime scenes: the crystal structure of commercial luminol,” Cryst. Growth Des. 16, 30143018.Google Scholar
McKinnon, J. J., Jayatilaka, D., and Spackman, M. A. (2007). “Towards quantitative analysis of intermolecular interactions with Hirshfeld surfaces,” Chem. Commun., 38143816.Google Scholar
Nichol, G. S., and Clegg, W. (2006). “The importance of weak C − H···O bonds and π···π stacking interactions in the formation of organic 1,8-Bis(dimethylamino)naphthalene complexes with Z‘>1,” Cryst. Growth Des. 6, 451460.1,”+Cryst.+Growth+Des.+6,+451–460.>Google Scholar
Owczarzak, A. M., Samshuddin, S., Narayana, B., Yathirajan, H. S., and Kubicki, M. (2013). “Pseudosymmetry, polymorphism and weak interactions: 4,4′′-difluoro-5′-hydroxy-1,1′:3′,1′′-terphenyl-4′-carboxylic acid and its derivatives,” CrystEngComm. 15, 98939898.Google Scholar
Pagola, S., Stephens, P. W., Bohle, D. S., Kosar, A. D., and Madsen, S. K. (2000). “The structure of malaria pigment β-haematin,” Nature. 404, 307310.Google Scholar
Perdew, J. P., Burke, K., and Ernzerhof, M. (1996). “Generalized gradient approximation made simple,” Phys. Rev. Lett. 77, 38653868.Google Scholar
Platteau, C., Lefebvre, J., Hemon, S., Baehtz, C., Danede, F., and Prevost, D. (2005). “Structure determination of forms I and II of phenobarbital from X-ray powder diffraction,” Acta Cryst B. 61, 8088.Google Scholar
Politzer, P., and Murray, J. S. (2015). “Quantitative analyses of molecular surface electrostatic potentials in relation to hydrogen bonding and Co-crystallization,” Cryst. Growth Des. 15, 37673774.Google Scholar
Pramanik, S., Dey, T., and Mukherjee, A. K. (2019). “Five benzoic acid derivatives: crystallographic study using X-ray powder diffraction, electronic structure and molecular electrostatic potential calculation,” J. Mol. Str. 1175, 185207.Google Scholar
Rehman, M. Z., Elsegood, M. R. J., Akbar, N., and Saleem, R. S. Z. (2008). “5-Amino-1-phenyl-1H-pyrazole-4-carboxylic acid,” Acta Crystallogr. Sec E. 64, 1312.Google Scholar
Rietveld, H. (1967). “Line profiles of neutron powder-diffraction peaks for structure refinement,” Acta Crystallogr. 22, 151152.Google Scholar
Rohl, A. L., Moret, M., Kaminsky, W., Claborn, K., McKinnon, J. J., and Kahr, B. (2008). “Hirshfeld surfaces identify inadequacies in computations of intermolecular interactions in crystals: pentamorphic 1,8-dihydroxyanthraquinone,” Cryst. Growth Des. 8, 45174525.Google Scholar
Spackman, M. A., and McKinnon, J. J. (2002). “Fingerprinting intermolecular interactions in molecular crystals,” CrystEngComm. 4, 378392.Google Scholar
Steed, K. M., and Steed, J. W. (2015). “Packing problems: high Z' crystal structures and their relationship to co-crystals, inclusion compounds, and polymorphism,” Chem. Rev. 115, 28952933.Google Scholar
Stewart, J. J. P. (2007). “Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements,” J. Mol. Model. 13, 11731213.Google Scholar
Thompson, P., Cox, D. E., and Hastings, J. B. (1987). “Rietveld refinement of Debye-Scherrer synchrotron X-ray data from Al2O3,” J. Appl. Crystallogr. 20, 7983.Google Scholar
Watts, A. E., Maruyoshi, K., Hughes, C. E., Brown, S. P., and Harris, K. D. M. (2016). “Combining the advantages of powder X-ray diffraction and NMR crystallography in structure determination of the pharmaceutical material cimetidine hydrochloride,” Cryst.Growth Des. 16, 17981804.Google Scholar
Wen, H.-L., Kang, J.-J., Dai, B., Deng, R.-H., and Hu. Chin, H.-W. (2015) “Syntheses, crystal structures and antibacterial activities of 5-chloro-3-m ethyl-1-phenyl-1H-pyrazole-4-carboxylic acid and its copper(II) compound,” J. Struct. Chem. 34, 33.Google Scholar
Werner, P. E., Eriksson, L., and Westdahl, M. (1985). “TREOR, a semi-ex-haustive trial-and-error powder indexing program for all symmetries,” J. Appl. Cryst. 18, 367370.Google Scholar
Wolff, S. K., Grimwood, D. J., McKinnon, J. J., Turner, M. J., Jayatilaka, D., and Spackman, M. A. (2012). Crystal Explorer 3.1 (University of Western Australia, Perth, Australia).Google Scholar
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