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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
Affiliation:
Laboratorio de Cristalografía-LNDRX, Departamento de Química, Facultad de Ciencias, Universidad de los Andes, Mérida 5101, Venezuela
Jacco van de Streek
Affiliation:
Avant-garde Materials Simulation, Alte Str. 2, Merzhausen D-79249, Germany
Graciela Díaz de Delgado
Affiliation:
Laboratorio de Cristalografía-LNDRX, Departamento de Química, Facultad de Ciencias, Universidad de los Andes, Mérida 5101, Venezuela
Alicja Rafalska-Lasocha
Affiliation:
Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland
José Miguel Delgado*
Affiliation:
Laboratorio de Cristalografía-LNDRX, Departamento de Química, Facultad de Ciencias, Universidad de los Andes, Mérida 5101, Venezuela
*
a)Author to whom correspondence should be addressed. Electronic mail: jmdq2000@gmail.com

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.

Information

Type
Technical Article
Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press on behalf of International Centre for Diffraction Data
Figure 0

Figure 1. Molecular diagram of 1-benzothiophene-2-carboxylic acid.

Figure 1

Figure 2. Rietveld plot obtained after the structure refinement of BTCA-Form II.

Figure 2

Figure 3. Molecular structure of BTCA-Form II with the labeling scheme for atoms and rings.

Figure 3

Figure 4. Superposition of the experimentally determined (red) and the energy-minimized (blue) structure for BTCA-Form II.

Figure 4

Table I. Crystal data, experimental parameters, and refinement results for 1-benzothiophene-2-carboxylic acid.

Figure 5

Figure 5. Graph set analysis of the intermolecular O–H⋯O and C–H⋯O hydrogen bonds in BTCA-Form II. The hydrogen bonded motifs are labeled as I: $\;\lpar \lsqb R_2^2 \lpar 8 \rpar \rsqb _{{\rm O}1}^{{\rm O}2} \rpar$; II:$\;\lsqb R_2^2 \lpar {10} \rpar \rsqb _{{\rm C}7}^{{\rm O}1}$; III:$\;\lsqb R_3^2 \lpar 8 \rpar \rsqb _{{\rm O}1\comma {\rm C}3\comma {\rm C}7}^{{\rm O}2\comma {\rm O}2\comma {\rm O}1}$.

Figure 6

Figure 6. Hydrogen-bonding scheme in BTCA-Form I (drawn using data from Jarczyk-Jędryka, 2013) seen along the a-axis.

Figure 7

Figure 7. (a) Geometry of π⋯π (magenta) and C–H⋯π (cyan) interactions; (b) sequence of head-to-tail π⋯π connected dimers and head-to-tail C–H⋯π connected dimers in BTCA-Form II; and (c) head-to-head π⋯π interactions in BTCA-Form I.

Figure 8

Figure 8. (a) Arrangement of molecules in BTCA-Form II connected by π⋯π (magenta) and C–H⋯π interactions (cyan); (b) head-to-head π⋯π interactions (magenta) in BTCA-Form I; and (c) dimers of BFCA molecules connected by π⋯π interactions (magenta).

Figure 9

Table II. Geometry of hydrogen bonds, π⋯π, C–H⋯π, and C–O⋯π interactions in (a) BTCA-Form II, (b) BTCA-Form I (Jarczyk-Jędryka, 2013), and (c) BFCA (Krishnaswamy et al., 2016).

Figure 10

Figure 9. (a–c) Packing arrangement of BTCA-Form II viewed down the a-, b-, and c-axes, respectively.

Figure 11

Figure 10. Fingerprint plots for BTCA-Form II. (a) All contacts, (b) H⋯C contacts, (c) H⋯H contacts, (d) H⋯O contacts, (e) H⋯S contacts, and (f) O⋯C contacts. The percent of the surface area included is shown for each plot (99.8%).

Figure 12

Figure 11. Fingerprint plots for BFCA. (a) All contacts, (b) H⋯O contacts, (c) H⋯H contacts, (d) H⋯C contacts, (e) C⋯C contacts, and (f) O⋯C contacts. The percent of the surface area included is shown for each plot (100.0%).

Figure 13

Figure 12. Comparison of the contribution of intermolecular contacts (%) to the Hirshfeld surface area for BTCA-Form II, BTCA-Form I, and BFCA.

Figure 14

Figure 13. Mapping of the dnorm parameter in the range −0.74 to 1.33 onto the Hirshfeld surface for (a) BTCA-Form II and (b) BFCA. The close contacts with neighboring molecules are shown for each compound.

Figure 15

Figure 14. Energy frameworks calculated for (a) BTCA-Form II viewed along the a-axis (3 × 3 × 3 unit cells); (b) BTCA-Form I viewed along the b-axis (3 × 5 × 5 unit cells); (c) BFCA viewed down the c-axis (2 × 1 × 3 unit cells). The radii of the cylinders were scaled to 80 arbitrary units with a cut-off value of 10 kJ mol−1. Eele, Edis, and Etot are represented in red, green, and blue, respectively.

Figure 16

Table III. Summary of calculated energies (kJ mol−1) for BTCA-form II (this work), BTCA-form I (Jarczyk-Jędryka, 2013), and BFCA (Krishnaswamy et al., 2016).

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