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Crystal structure from laboratory X-ray powder diffraction data, DFT-D calculations, Hirshfeld surface analysis, and energy frameworks of a new polymorph of 1-benzothiophene-2-carboxylic acid

Published online by Cambridge University Press:  14 January 2021

Analio J. Dugarte-Dugarte Open the ORCID record for Analio J. Dugarte-Dugarte [Opens in a new window] ,
Jacco van de Streek ,
Graciela Díaz de Delgado Open the ORCID record for Graciela Díaz de Delgado [Opens in a new window] ,
Alicja Rafalska-Lasocha Open the ORCID record for Alicja Rafalska-Lasocha [Opens in a new window]  and
José Miguel Delgado Open the ORCID record for José Miguel Delgado [Opens in a new window]
Analio J. Dugarte-Dugarte
Affiliation:
Laboratorio de Cristalografía-LNDRX, Departamento de Química, Facultad de Ciencias, Universidad de los Andes, Mérida5101, Venezuela
Jacco van de Streek
Affiliation:
Avant-garde Materials Simulation, Alte Str. 2, MerzhausenD-79249, Germany
Graciela Díaz de Delgado
Affiliation:
Laboratorio de Cristalografía-LNDRX, Departamento de Química, Facultad de Ciencias, Universidad de los Andes, Mérida5101, Venezuela
Alicja Rafalska-Lasocha
Affiliation:
Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow30-387, Poland
José Miguel Delgado*
Affiliation:
Laboratorio de Cristalografía-LNDRX, Departamento de Química, Facultad de Ciencias, Universidad de los Andes, Mérida5101, Venezuela
*
a)Author to whom correspondence should be addressed. Electronic mail: jmdq2000@gmail.com
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Abstract

Several benzothiophene-based compounds, including 1-benzothiophene-2-carboxylic acid, exhibit a wide variety of pharmacological activities. They have been extensively used to treat various types of diseases with high therapeutic effectiveness. In this contribution, the crystal structure of a new polymorph of 1-benzothiophene-2-carboxylic acid (BTCA) was determined from laboratory X-ray powder diffraction data with DASH, refined by the Rietveld method with TOPAS-Academic, and optimized using DFT-D calculations. The new form of 1-benzothiophene-2-carboxylic acid crystallizes in space group C2/c (No. 15) with a = 14.635(4), b = 5.8543(9), c = 19.347(3) Å, β = 103.95(1)°, V = 1608.8(6) Å3, and Z = 8. The structure is a complex 3D arrangement which can be described in terms of hydrogen-bonded dimers of BTCA molecules, joined by the acid–acid homosynthon, which interact through C–H⋯O hydrogen bonds to produce tapes further connected through head-to-tail π⋯π and edge-to-face C–H⋯π interactions. A comparison with a previously reported triclinic polymorph and with the related 1-benzofuran-2-carboxylic acid (BFCA) is also presented.

Keywords

1-benzothiophene-2-carboxylic acidthionaphthene-2-carboxylic acidstructure determinationDFT-D calculationsHirshfeld surface analysis
Type
Technical Article
Information
Powder Diffraction , Volume 36 , Issue 1 , March 2021 , pp. 2 - 13
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Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press on behalf of International Centre for Diffraction Data

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References

Bernstein, J., Davis, R. E., Shimoni, L., and Chang, N.-L. (1995). “Patterns in hydrogen bonding: functionality and graph set analysis in crystals,” Angew. Chem. Int. Ed. Engl. 34, 1555–1573.CrossRefGoogle Scholar
Biswas, S., Mandal, L., Shen, Y., and Yamashita, M. (2019). “Exploration of SMM behavior of Ln2 complexes derived from thianaphthene-2-carboxylic acid,” Dalton Trans. 48, 14096–14102.CrossRefGoogle ScholarPubMed
Blanton, J. R., Papoular, R. J., and Louër, D. (2019). “PreDICT: a graphical user interface to the DICVOL14 indexing software program for powder diffraction data,” Powd. Diffr. 34, 233–241.CrossRefGoogle Scholar
Brandenburg, K. (1999). DIAMOND, Version 3.0 (Crystal Impact GbR, Bonn, Germany).Google Scholar
Bruno, I. J., Cole, J. C., Kessler, M., Luo, J., Motherwell, W. D. S., Purkis, L. H., Smith, B. R., Taylor, R., Cooper, R. I., Harris, S. E., and Orpen, A. G. (2004). “Retrieval of crystallographically-derived molecular geometry information,” J. Chem. Inf. Comput. Sci. 44, 2133–2144.CrossRefGoogle ScholarPubMed
Coelho, A. A. (2016). TOPAS-Academic Version 6, Program for Crystal Structure Refinement (Coelho Software, Brisbane, Australia).Google Scholar
David, W. I. F., Shankland, K., van de Streek, J., Pidcock, E., Motherwell, W. D. S., and Cole, J. C. (2006). “DASH: a program for crystal structure determination from powder diffraction data,” J. Appl. Crystallogr. 39, 910–915.CrossRefGoogle Scholar
Decker, J. E., Morrison, N. E., Lorenzo, J. A., Samour, C. M., McCarron, B. A., and Raisz, L. G. (1989). “The effect of thionapthene-2-carboxylic acid-lysine on the hypercalcemia of malignancy in the rat,” Calcif. Tissue Int. 44, 61–64.CrossRefGoogle Scholar
de Wolff, P. M. (1968). “A simplified criterion for the reliability of a powder pattern indexing,” J. Appl. Crystallogr. 1, 108–113.CrossRefGoogle Scholar
Esmaeili, A., Kamiyama, T., and Oishi-Tomiyasu, R. (2017). “New functions and graphical user interface attached to powder indexing software CONOGRAPH,” J. Appl. Crystallogr. 50, 651–659.CrossRefGoogle Scholar
Etter, M. C., MacDonald, J. C., and Bernstein, J. (1990). “Graph-set analysis of hydrogen-bond patterns in organic crystals,” Acta Crystallogr. B 46, 256–262.CrossRefGoogle ScholarPubMed
Friberg, A., Vigil, D., Zhao, B., Daniels, R. N., Burke, J. P., Garcia-Barrantes, P. M., Camper, D., Chauder, B. A., Lee, T., Olejniczak, E. T., and Fesik, S. W. (2013). “Discovery of potent myeloid cell leukemia 1 (Mcl-1) inhibitors using fragment-based methods and structure-based design,” J. Med. Chem. 56, 15–30.CrossRefGoogle ScholarPubMed
Gates-Rector, S. and Blanton, T. (2019). “The powder diffraction file: a quality materials characterization database,” Powd. Diffr. 34, 352–360.CrossRefGoogle Scholar
Gronowitz, S., Herslof, M., Svenson, R., Bondesson, G., and Magnusson, O. (1978). “Potential hypolipidemic agents. XX: Synthesis and lipid-lowering properties of annealed thiophenecarboxylic acids,” Acta Pharm. Suec. 15, 368–381.Google Scholar
Groom, C. R., Bruno, I. J., Lightfoot, M. P., and Ward, S. C. (2016). “The Cambridge structural database,” Acta Crystallogr. B. 72, 171–179.CrossRefGoogle ScholarPubMed
Hige, S., Shiota, N., Kobayashi, Y., Wakabayashi, T., Sato, T., and Imai, Y. (2012). “Control of release properties of guest molecules by the type of benzoheterocyclic ring in supramolecular host complexes,” Tetrahedron 68, 9999–10004.CrossRefGoogle Scholar
Jarczyk-Jędryka, A. (2013). Efekty temperaturowe i efekty dichroizmu liniowego w widmach wiązania wodorowego w zakresie podczerwieni, kryształów kwasów karboksylowych z cyklicznymi dimerami w sieci (Praca doktorska. Uniwersytet Śląski, Katowice, Polska).Google Scholar
Johannesson, A. J., Onkelinx, C., Rodan, G. A., and Raisz, L. G. (1985). “Thionapthene-2-carboxylic acid: a new antihypercalcemic agent,” Endocrinology 117, 1508–1511.CrossRefGoogle ScholarPubMed
Keri, R. S., Chand, K., Budagumpi, S., Balappa Somappa, S., Patil, S. A., and Nagaraja, B. M. (2017). “An overview of benzo[b]thiophene-based medicinal chemistry,” Eur. J. Med. Chem. 138, 1002–1033.CrossRefGoogle ScholarPubMed
Kresse, G. and Furthmüller, J. (1996). “Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set,” Phys. Rev. B. 54, 11169–11186.CrossRefGoogle ScholarPubMed
Krishnaswamy, G., Desai, N. R., Potla, K. M., Suchetan, P. A., and Arunakumar, D. B. (2016). “Synthesis, characterization, crystal structure and DFT calculations of 1-benzofuran-2-carboxylic acid,” Der Pharma Chem. 8, 46–54.Google Scholar
Loots, L. and Barbour, L. J. (2012). “A rudimentary method for classification of π…π packing motifs for aromatic molecules,” in The Importance of Pi-Interactions in Crystal Engineering, edited by Tiekink, E. R. T. and Zukerman-Schpector, J. (John Wiley & Sons, Chichester, UK), pp. 109–124.CrossRefGoogle Scholar
Louër, D. and Boultif, A. (2014). “Some further considerations in powder diffraction pattern indexing with the dichotomy method,” Powd. Diffr. 29, S7–S12.CrossRefGoogle Scholar
Malone, J. F., Murray, C. M., Charlton, M. H., Docherty, R., and Lavery, A. J. (1997). “X-H⋯π(phenyl) interactions theoretical and crystallographic observations,” J. Chem. Soc., Faraday Trans. 93, 3429–3436.CrossRefGoogle Scholar
Markvardsen, A. J., David, W. I. F., Johnson, J. C., and Shankland, K. (2001). “A probabilistic approach to space-group determination from powder diffraction data” Acta Crystallogr. A 57, 47–54.CrossRefGoogle ScholarPubMed
Netsuwan, P., Sriwichai, S., Phanichphant, S., Baba, A., Shinbo, K., Kato, K., and Kaneko, F. (2013). “Fabrication of carboxylated conducting polymer/CNTs composites thin films for immunosensor application,” Mol. Cryst. Liq. Cryst. 580, 7–14.CrossRefGoogle Scholar
Neumann, M. A. (2002). GRACE has been developed by Avant-garde Materials Simulation since 2002.Google Scholar
Neumann, M. A. and Perrin, M.-A. (2005). “Energy ranking of molecular crystals using density functional theory calculations and an empirical van der Waals correction,” J. Phys. Chem. B 109, 15531–15541.CrossRefGoogle Scholar
Nyska, M., Nyska, A., Waner, T., and Wolter, K. (1992). “The effect of thionaphthene-2-carboxylic acid (TNCA) on bone structure in the rat: a histomorphometric study,” Int. J. Exp. Pathol. 73, 733–740.Google Scholar
Oishi-Tomiyasu, R. (2013). “Reversed de Wolff figure of merit and its application to powder indexing solutions,” J. Appl. Crystallogr. 46, 1277–1282.CrossRefGoogle Scholar
Perdew, J. P., Burke, K., and Ernzerhof, M. (1996). “Generalized gradient approximation made simple,” Phys. Rev. Lett. 77, 3865–3868.CrossRefGoogle ScholarPubMed
Ramos, F., Flores, H., Rojas, A., Hernández-Pérez, J. M., Camarillo, E. A., and Amador, M. P. (2016). “Experimental and computational thermochemical study of benzofuran, benzothiophene and indole derivatives,” J. Chem. Thermodyn. 97, 304–313.CrossRefGoogle Scholar
Robin, J. C., Brown, M. J., Weinfeld, N., and Dziak, R. M. (1984). “Benzo(B)thiophene-2-carboxylic acid: calcium uptake and cyclic AMP production in isolated bone cells,” Calcif. Tissue Int. 36, 194–199.CrossRefGoogle ScholarPubMed
Sagaama, A. and Issaoui, N. (2020). “Design, molecular docking analysis of an anti-inflammatory drug, computational analysis and intermolecular interactions energy studies of 1-benzothiophene-2-carboxylic acid,” Comput. Biol. Chem. 88, 107348.CrossRefGoogle ScholarPubMed
Spackman, M. A. and Jayatilaka, D. (2009). “Hirshfeld surface analysis,” CrystEngComm 11, 19–32.CrossRefGoogle Scholar
Stewart, J. J. P. (2013). “Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters,” J. Mol. Model 19, 1–32.CrossRefGoogle ScholarPubMed
Stewart, J. J. P. (2016). MOPAC2016 (Stewart Computational Chemistry, Colorado Springs, CO, USA).Google Scholar
Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D., and Spackman, M. A. (2017). CrystalExplorer 17.5 (The University of Western Australia, Crawley, WA, Australia).Google Scholar
Vallcorba, O., Rius, J., Frontera, C., Peral, I., and Miravitlles, C. (2012). “DAJUST: a suite of computer programs for pattern matching, space-group determination and intensity extraction from powder diffraction data,” J. Appl. Crystallogr. 45, 844–848.CrossRefGoogle Scholar
van de Streek, J. and Neumann, M. (2014). “Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D),” Acta Crystallogr. B70, 1020–1032.Google Scholar
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