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Ab initio crystal structure determination of two chain functionalized pyrroles from synchrotron X-ray powder diffraction data

Published online by Cambridge University Press:  17 August 2012

Iván da Silva ,
Sara López-Tosco ,
David Tejedor ,
Fernando García-Tellado  and
Javier González-Platas
Iván da Silva*
Affiliation:
SpLine Spanish CRG Beamline at the ESRF 6, Rue Jules Horowitz, BP 220, 38043 Grenoble Cedex 09, France Instituto de Ciencia de Materiales de Madrid-ICMM/CSIC, Cantoblanco, Madrid 28049, Spain
Sara López-Tosco
Affiliation:
Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
David Tejedor
Affiliation:
Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
Fernando García-Tellado
Affiliation:
Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
Javier González-Platas
Affiliation:
Servicio de Difracción de Rayos X, Departamento de Física Fundamental II, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, 38206 La Laguna, Tenerife, Spain
*
a)Author to whom correspondence should be addressed. Electronic mail: dasilvag@esrf.fr
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Abstract

The crystal structure of two chain functionalized pyrroles, methyl 1-benzyl-5-(1-(4-chlorobenzoyloxy)-2-methoxy-2-oxoethyl)-4-(4-chlorophenyl)-1H-pyrrole-2-carboxylate and methyl 1-benzyl-4-(biphenyl-4-yl)-5-(1-(4-biphenylcarbonyloxy)-2-methoxy-2-oxoethyl)-1H-pyrrole-2-carboxylate, which are both important active candidates as antitumoral agents, have been obtained ab initio from synchrotron X-ray powder diffraction data. Both compounds crystallize in the monoclinic system (space group P21/c), with a = 20.2544(3) Å, b = 6.80442(9) Å, c = 21.1981(3) Å, β = 111.6388(9)° and a = 29.7747(6) Å, b = 6.27495(14) Å, c = 18.8525(3) Å, β = 107.053(2)°, respectively. These structures were determined using a direct space approach, by means of Monte Carlo technique, followed by Rietveld refinement.

Keywords

pyrrolesstructure solvingpowder diffraction
Type
Technical Articles
Information
Powder Diffraction , Volume 27 , Issue 3 , September 2012 , pp. 172 - 178
Copyright
Copyright © International Centre for Diffraction Data 2012

I. INTRODUCTION

Chain functionalized pyrroles constitute a structural motif of particular interest in synthetic and medicinal chemistry, as it is the foundation of important medicines, natural products and synthetic materials (Jones, Reference Jones1992; Lehr, Reference Lehr1997; Le Quesne et al., Reference Le Quesne, Dong, Blythe and Pelletier1999; Boger and Hong, Reference Boger and Hong2001; Johnson et al., Reference Johnson, Li and Sames2002; Fürstner, Reference Fürstner2003; Walsh et al., Reference Walsh, Garneau-Tsodikova and Howard-Jones2006; Pfefferkorn et al., Reference Pfefferkorn, Bowles, Kissel, Boyles, Choi, Larsen, Song, Sun, Miller and Trivedi2007). In particular, tetrasubstituted pyrroles 5 can be considered as hybrid scaffolds (Mehta and Singh, Reference Mehta and Singh2002; Tietze et al., Reference Tietze, Bell and Chandrasekhar2003) comprising a structurally privileged pyrrole ring and a naturally occurring α-hydroxy acid motif (Abell and Nabbs, Reference Abell and Nabbs2001; Martyn et al., Reference Martyn, Vernall, Clark and Abell2003; Baran et al., Reference Baran, Richter and Lin2005; Gabriele et al., Reference Gabriele, Salerno, Fazio and Veltrid2006; Alcaide et al., Reference Alcaide, Almendros, Carrascosa and Redondo2008). The hybrid features five points of diversity (two chemo-differentiated ester groups, two chemo-differentiated R groups and one N-R1 group) and two differentiated points for complexity generation: one on the ring (sp2-linking point; C4-H) and the other on the chain (sp3-linking point; CH(OCOR)Z]. These molecules are ideal candidates for our wide research program aimed at developing new anti-tumoral agents (Padrón et al., Reference Padrón, Tejedor, Santos-Expósito, García-Tellado, Martín and Villar2005; Leon et al., Reference Leon, Rios-Luci, Tejedor, Perez-Roth, Montero, Pandiella, Garcia-Tellado and Padron2010).

This paper reports the structure solution of the two organic compounds methyl 1-benzyl-5-(1-(4-chlorobenzoyloxy)-2-methoxy-2-oxoethyl)-4-(4-chlorophenyl)-1H-pyrrole-2-carboxylate (denoted 5EA) and methyl 1-benzyl-4-(biphenyl-4-yl)-5-(1-(4-biphenylcarbonyloxy)-2-methoxy-2-oxoethyl)-1H-pyrrole-2-carboxylate (denoted 5CA). As no suitable single crystals were obtained for single crystal X-ray analysis, both structures were solved by synchrotron X-ray powder diffraction analysis. The corresponding structures were determined by means of the Monte Carlo method and refined using the Rietveld method. The X-ray powder diffraction method, thanks to the recent experimental and software algorithms advances, shows to be a very promising technique when dealing with interesting pharmaceutical compounds, since many of them can only be obtained as powder samples, rather than single crystals (David et al., Reference David, Shankland and Shankland1998; Dinnebier et al., Reference Dinnebier, Sieger, Nar, Shankland and David2000; Harris and Cheung, Reference Harris and Cheung2004).

II. EXPERIMENTAL

A. Spectroscopic study

The structural identity, which is shown in Figure 1, of the studied compounds was determined spectroscopically (1H NMR, 13C NMR, IR spectroscopy and mass spectrometry). The details of this study, as well as information on the synthesis procedure of the compounds, can be found elsewhere (Tejedor et al., Reference Tejedor, López-Tosco, González-Platas and García-Tellado2009).

Figure 1. Structural fragments of 5EA (a) and 5CA (b) compounds.

B. X-ray diffraction

High resolution powder diffraction (HRPD) patterns were collected at SpLine beamline (BM25A) of the Spanish CRG at the European Synchrotron Radiation Facility (ESRF, Grenoble) using a fixed wavelength of 1.0323(1) Å, at room temperature. The powder samples were loaded inside 0.3-mm-diameter borosilicate glass capillaries, which were rotated during exposure, to reduce the effect of possible preferential orientations. Diffraction pattern recording for each compound was carried out in a 2θ-step scan mode with a step of 0.015°, counting 24 and 9 s of acquisition time per step, for 5EA and 5CA, respectively. The incoming beam was monitored to normalise the resulting data to the decay of the primary beam, while the diffracted beam was collected using a scintillation point detector. Data were collected in the range of 1–72° 2θ for both compounds.

III. STRUCTURE DETERMINATION AND RIETVELD REFINEMENT

For 5EA and 5CA diffraction patterns, angular positions of the first 20 reflections (up to about 15 13° 2θ, respectively) were determined using the peak search algorithm implemented in WinPLOTR program (Roisnel and Rodriguez-Carvajal, Reference Roisnel and Rodriguez-Carvajal2001). These positions were used to index both patterns using DicVOL06 program (Boultif and Louër, Reference Boultif and Louër2004) into the monoclinic system, yielding cells with figures of merit (De Wolff, Reference De Wolff1968) of M(20) = 21.6 and 23.0, for compounds 5EA and 5CA, respectively. For space group determination, EXPO2004 program (Altomare et al., Reference Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni and Rizzi2004) was used, using the statistical algorithm implemented to determine the most probable extinction group (Altomare et al., Reference Altomare, Camalli, Cuocci, da Silva, Giacovazzo, Moliterni and Rizzi2005). In this case, the found extinction group with the highest probability was P21/c, for both crystal cells, which was confirmed by visual inspection of systematic absences.

Structures of 5EA and 5CA compounds were solved, by means of Monte Carlo calculations, using the parallel tempering algorithm implemented in FOX program (Favre-Nicolin and Cerný, Reference Favre-Nicolin and Cerný2002). Templates of the structural fragments were previously built using the software package ChemBio Office (version 11.0), which were introduced in FOX program. During the calculations, the observed and calculated intensities were compared only in the 2θ range from 1 to 25° and the molecules could translate and rotate randomly; different torsion angles could also change and the aromatic rings were treated as rigid fragments. After 15 million trials, the agreement factors were R wp = 0.055, GoF = 17.078 and R wp = 0.1018, GoF = 14.323.

Refinements of the structures found by FOX program were carried out by the Rietveld method (Rietveld, Reference Rietveld1969), using FullProf program (Rodriguez-Carvajal, Reference Rodriguez-Carvajal2001) in the 2θ range from 1 to 50° for both diffraction patterns, as the diffracted signal-to-noise ratios were very low for both patterns at 2θ angles above 50°. Atomic coordinates of all atoms were included in the refinement but, in order to ensure the convergence of the process, phenyl rings were treated as rigid bodies and restraints on the other bond lengths and angles were introduced, thus limiting the number of free parameters. The values for the bond lengths and angles were taken from similar molecules and molecular fragments in the CCDC database (codes: QOQGAF, BOPSEE11, ABEFOD, ACERAC and ADAGUI) and the mean-square deviations of assigned values were 0.02 Å and 1°, respectively. An overall isotropic temperature factor was introduced for each structure refinement. The peak function used for fitting the experimental data was the Thompson–Cox–Hastings Pseudo–Voigt (Thompson et al., Reference Thompson, Cox and Hastings1987), which can take into account the experimental resolution and the broadening due to size and strain effects, often present in this type of organic powder samples; axial divergence asymmetry of peaks was modelled using the Finger's treatment (Finger et al., Reference Finger, Cox and Jephcoat1994); 44 and 56 points were chosen regularly distributed on the experimental patterns to model the background through a linear interpolation made between two successive points. Hydrogen atoms for 5EA and 5CA molecules were introduced in FullProf at their calculated positions with Olex2 program (Dolomanov et al., Reference Dolomanov, Bourhis, Gildea, Howard and Puschmann2009). During the Rietveld refinements, the position of H atoms was restrained to that of their riding atom. Owing to the possibility of deformation or rotation of both molecules, the positions of H atoms were recalculated several times during the refinement procedure before it converged.

On the final Rietveld fits, there were 79 and 86 adjustable parameters for 5EA and 5CA, respectively (scale factor, zero-shift, atomic coordinates, overall temperature factor, unit-cell parameters and peak-shape parameters), taking into account the introduced constraints. In Figure 2, the plot of the final fits for both compounds are given. Crystallographic and refinement-related data are reported in Table I, while atomic coordinates and displacement parameters for non-H atoms are reported in Table II.

Figure 2. Final Rietveld refinement plots for 5EA (a) and 5CA (b), showing the experimental (red circles), calculated (black line) and difference profiles (blue line); green tick marks indicate reflection positions. From dotted vertical line: intensity scale 5-times multiplied for clarity.

TABLE I. Crystallographic data and Rietveld refinement summary for compounds 5EA and 5CA.

TABLE II. Fractional atomic coordinates and isotropic displacement parameters (Å2) for compounds 5EA and 5CA.

IV. DISCUSSION

The final molecular structures and crystal packings are shown in Figures 3 and 4, respectively. The structures of 5EA and 5CA are very similar; both molecules contain a pyrrol ring as central part, two ester groups (methyl ethanoate and methyl methanoate) and one toluene group with a torsional angle (N1-C6-C7-C8) of 15.14(6)° and 32.8(3)° respectively, being the main difference between them. However, the angle defined by the planes formed between the pyrrol ring and the benzenic ring were quite similar, 86.92(2)° for 5EA and 85.34(10)° for 5CA. The main difference between 5EA and 5CA is the substitution in the same relative position, containing a 4-chlorobenzoic acid and a 4-biphenylcarboxylic acid, respectively. In the last case, this group has a slight torsional angle between the rings [39.12(9)° and 36.12(9)°], being these values similar to others found in the literature for this type of group (Brown et al., Reference Brown, Freeman and Walter1977; Busetti, Reference Busetti1982). No classical hydrogen bonds were found in both structures. The molecules in 5EA are linked by weak π–π stacking interactions (Cg…Cg) with distances of 4.3081(2) Å [Cg4…Cg4 i; Cg4 = C25–C30; symmetry code: (i) −x, 1 − y, −z; perpendicular distance of 3.6660(2) Å with slippage of 2.263 Å] and 4.5049(3) Å [Cg3…Cg3 ii; Cg3 = C15–C20; symmetry code: (ii) 1 − x, 1 − y, −z; perpendicular distance of 3.5655(2) Å with slippage of 2.753 Å] (see Figure 4a). Also C–H…O intermolecular contacts exists (Table III). The packing in 5CA is stabilized by very weak π–π interactions where (Cg…Cg) distances are from 4.5631(11) Å [Cg4…Cg3 i; Cg4 = C21–C26; Cg3 = C15–C20; symmetry code: (i) 1 − x, −y, 1 − z] to 4.8148(10) Å [Cg6…Cg6 ii; Cg6 = C37–C42; symmetry code: (ii) −x, −y, −z] as significant distances. Also C–O…Cg (π-ring) interaction is present [3.8948(14) Å for O…Cg, 4.591(2) Å for C…Cg and 118.56(11)° for C–O…Cg angle] (see Figure 4b). As in 5EA molecule, C–H…O intermolecular contacts are also present in 5CA (Table III).

Figure 3. Molecular structures of 5EA (a) and 5CA (b) compounds, showing the atom-numbering scheme.

Figure 4. Crystal structures of 5EA (a) and 5CA (b) viewed along the b-axis. Intermolecular contacts are shown as dotted lines.

TABLE III. Geometry of intermolecular C-H…O contacts of compounds 5EA and 5CA.

aSymmetry code: x, y − 1, z.

bSymmetry code: −x, 1 − y, −z.

cSymmetry code: x, 1 + y, z.

dSymmetry code: −x + 1, −y + 1, −z + 1.

eSymmetry code: x, y + 1, z.

V. CONCLUSION

In this work we report the structure determination of methyl 1-benzyl-5-(1-(4-chlorobenzoyloxy)-2-methoxy-2-oxoethyl)-4-(4-chlorophenyl)-1H-pyrrole-2-carboxylate and methyl 1-benzyl-4-(biphenyl-4-yl)-5-(1-(4-biphenylcarbonyloxy)-2-methoxy-2-oxoethyl)-1H-pyrrole-2-carboxylate compounds from synchrotron radiation X-ray powder diffraction data applying the Monte Carlo and Rietveld methods. For both cases, the crystal packing was stabilized by very weak π–π stacking interactions, C–H…O and C–O…Cg (π-ring) intermolecular contacts.

CCDC 851218 and 851219 contain the supplementary crystallographic data for this paper. These data can be obtained free of charge via www.ccdc.cam.ac.uk/data_request/cif or by emailing , or by contacting The Cambridge Crystallographic Data Centre, 12, Union Road, Cambridge CB2 1EZ, UK; fax: +44 1223 336033.

ACKNOWLEDGMENTS

We thank the SpLine staff for their assistance in using BM25A-SpLine beamline. The financial support from the Spanish Ministerio de Ciencia e Innovación (PI201060E013) is also acknowledged.

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Figure 0

Figure 1. Structural fragments of 5EA (a) and 5CA (b) compounds.

Figure 1

Figure 2. Final Rietveld refinement plots for 5EA (a) and 5CA (b), showing the experimental (red circles), calculated (black line) and difference profiles (blue line); green tick marks indicate reflection positions. From dotted vertical line: intensity scale 5-times multiplied for clarity.

Figure 2

TABLE I. Crystallographic data and Rietveld refinement summary for compounds 5EA and 5CA.

Figure 3

TABLE II. Fractional atomic coordinates and isotropic displacement parameters (Å2) for compounds 5EA and 5CA.

Figure 4

Figure 3. Molecular structures of 5EA (a) and 5CA (b) compounds, showing the atom-numbering scheme.

Figure 5

Figure 4. Crystal structures of 5EA (a) and 5CA (b) viewed along the b-axis. Intermolecular contacts are shown as dotted lines.

Figure 6

TABLE III. Geometry of intermolecular C-H…O contacts of compounds 5EA and 5CA.