Table of Contents
Organic Chemistry International
Volume 2011 (2011), Article ID 608165, 5 pages
http://dx.doi.org/10.1155/2011/608165
Review Article

Crystal Packing and Supramolecular Motifs in Four Phenoxyalkanoic Acid Herbicides—Low-Temperature Redeterminations

Institute of General and Ecological Chemistry, Technical University of Łódź, Żeromskiego 116, 90-924 Łódź, Poland

Received 30 September 2010; Revised 7 February 2011; Accepted 7 March 2011

Academic Editor: Ken Shimizu

Copyright © 2011 Lesław Sieroń et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

A low-temperature redetermination by X-ray crystallography of four phenoxyalkanoic acid herbicides, 4-chloro-2-methylphenoxyacetic acid (MCPA), rac-2-(4-chloro-2-methylphenoxy)propionic acid (MCPP), 2,4-dichlorophenoxyacetic acid (2,4-D), and 2,4-dichlorophenoxybutyric acid (2,4-DB), allowed the supramolecular structures of these compounds to be precisely described in terms of CO/C–H⋯π interactions. The geometric parameters of the redetermined structures agree with those previously reported, but with improved precision.

1. Introduction

Phenoxyalkanoic acids, having methyl and/or chlorine substituent groups in the ortho and meta positions of the benzene ring, are known selective herbicides, used to control broadleaf weeds in crop production. The first compound of this group, used already in 1944 in agriculture for weed control, was 2,4-dichlorophenoxyacetic acid (2,4-D). The physico- and biological properties of this group of compounds have been the subject of extensive studies [13]. As part of our wider study on metal complexes with herbicides of the phenoxyalkanoic acid series and on the herbicide-soil-plant interaction [4, 5], we report here structure redeterminations at 90 K of 4-chloro-2-methylphenoxyacetic acid (C9H9ClO3; MCPA; compound 1), rac-2-(4-chloro-2-methylphenoxy)propionic acid (C10H11ClO3; MCPP; compound 2), 2,4-dichlorophenoxyacetic acid (C8H6Cl2O3; 2,4-D; compound 3), and 2,4-dichlorophenoxybutyric acid (C10H10Cl2O3; 2,4-DB; compound 4). The structures of the compounds 13 were determined using X-ray diffraction data [69], collected at ambient temperature many years ago, with inaccurate refined or missing hydrogen atoms. The structure of 4 was previously determined at 173 K. In result, weak hydrogen interactions could not be precisely defined, and supramolecular structures have not been fully analyzed. These kind of bonds have been found to play an important role in many biological structures, as proteins, polypeptides, and drug-binding interactions [1012].

2. Experimental

Structures of the compounds 1–4 were determined by using single-crystal X-ray diffraction methods, using the Bruker AXS Smart APEX-II CCD 3-circle diffractometer with MonoCap capillary and monochromated Mo Kα radiation (λ = 0.71073 Å, 50 kV, 32 mA) at 90 K. Data collection and data reduction were done with the SMART [13] and SAINT-PLUS [14] programs. All structures were solved by direct methods and refined by the full-matrix least-squares methods on F2 with anisotropic thermal for all nonhydrogen atoms. All hydrogen atoms were located in difference Fourier syntheses and were refined freely. The final geometrical calculations were carried out using the PLATON program [15]. The relevant crystal data and experimental details are summarized in Table 1. Figures were drawn using Mercury [16] and SHELXTL [14] programs.

tab1
Table 1: Crystal data and structural refinement details for compounds 14.

3. Results

The unit-cell dimensions and atomic coordinates show that the phase is the same at both 90 K and ambient temperature for all redetermined structures. All described molecules associate via strong head-to-head carboxyl O–HO hydrogen bonds, forming typical carboxylic acid cyclic dimers about centres of symmetry into (8) rings [17, 18]. The compounds also crystallize with one independent molecule in the asymmetric unit.

The oxoacetic acid side chain in compound 1 adopts an extended planar conformation, with a C1–O3–C7–C8 torsion angle of 170.89(12)° (Figure 1).

608165.fig.001
Figure 1: A molecular diagram of 1, showing the atom numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are shown as small spheres of arbitrary radii.

Apart for the strong head-to-head hydrogen-bonded ring motif common to carboxylic acids [O1–H1O ], the molecules are also connected into dimers, forming 14-membered rings via C6–H6O interactions with symmetry-related molecules. The close contact between the Cl4 and the aryl methyl C9 group [Cl4C = 3.412(2) Å] is also observed (Figure 2). All three types of interactions are mutually coplanar and parallel to a crystallographic (1 1 −2) plane. A methylene group participates in a C7–H71⋯π interaction, with a benzene ring of an adjacent layer, and these serve to connect polymeric planes into a three-dimensional network.

608165.fig.002
Figure 2: A fragment of the structure of 1, showing the two-dimensional polymeric framework formed through the intermolecular O–HO hydrogen bonds and C–HO and C–ClC contacts, shown as dashed lines.

In the structure of compound 2, the side chain C1–O3–C7–C8 torsion angle of 84.6(2)° indicates a synclinal conformation of the chain (Figure 3).

608165.fig.003
Figure 3: A molecular diagram of 2, showing the atom numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are shown as small spheres of arbitrary radii.

The main intermolecular interactions are the (8) dimers involving strong hydrogen bonds O1–H1O between the carboxyl groups of adjacent molecules. Another hydrogen-bonding interaction involves a methine H7 atom that is engaged in bifurcated symmetrical C7–H7O contacts to carboxyl O1 and ether O3 atoms of neighbouring molecule, and making a graph-set motif of C21(3)[ (5)], running along a axis (Figure 4). A bifurcation is confirmed by the sum of angles about atom H7, which is 359.7(10)° [19].

608165.fig.004
Figure 4: The molecular packing of the compound 2, showing atoms of a neighbouring molecule, making a C21(3)[ (5)] graph set motif, running along the a axis. Dashed lines indicate the hydrogen-bonding interactions. All the hydrogens except for the methine H7 have been removed for clarity.

Replacement of the 2-methyl ring substituent group in 1 by a chlorine atom in 3 results in a different conformation of the chain that is synclinal, with a C1–O3–C7–C8 torsion angle of 81.02(13)° (Figure 5).

608165.fig.005
Figure 5: A molecular diagram of 3, showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are shown as small spheres of arbitrary radii.

A methylene group is engaged here in two relatively strong C–HO interactions with carboxyl O1 and ether O3 atoms, forming in effect two centrosymmetric (6) and (8) rings (Figure 6). The C3–H3O contact and its symmetry-related counterpart join two another molecules, generating an (14) graph-set motif. The structure shows also a significant contact between adjacent benzene rings with a centroid separation distance of 3.6505(7) Å, and the C2–Cl2⋯Cg [Cg1 is the centroid of ring C(1–6)] contact with a Cl⋯π separation of 3.5610(6) Å.

608165.fig.006
Figure 6: The molecular packing of the compound 3, showing the alternating (6) and (8) rings, running along the b axis. Dashed lines indicate the hydrogen-bonding interactions. All the hydrogens except H71 and H72 have been removed for clarity.

Compound 4 is conformationally similar to 1 and adopts the planar conformation, confirmed by the torsion angles of C1–O3–C7–C8 = 179.20(10), O3–C7–C8–C9 = −178.25(9), and C7–C8–C9–C10 = 173.83(11)° (Figure 7).

608165.fig.007
Figure 7: A molecular diagram of 4, showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are shown as small spheres of arbitrary radii.

The neighbouring molecules are connected via O1–H1O , C5–H5O C6–H6O hydrogen bonds and a short Cl2Cl nonbonding interaction of 3.2976(4) Å which are mutually coplanar and parallel to crystallographic plane (2 2 1). Further interactions in the crystal structure of C7–H71Cl , C8–H81O and C8–H82⋯Cg [Cg1 is the centroid of ring C(1–6)] connect adjacent polymeric layers into a three-dimensional supramolecular network (Figure 8).

608165.fig.008
Figure 8: The intermolecular O–HO, C–HO, C–H⋯π and ClCl contacts in compound 4, shown as dashed lines. All the hydrogens except those not involved in interactions have been removed for clarity.

The comparison of the all analyzed structures shows that the C2–Cl2 bond lengths of 1.7323(11) and 1.7371(10)° in 3 and 4 are distinctly shorter than C4–Cl4, ranging from 1.7416(11) to 1.746(2)° in 14. The bond lengths in the carboxylic acid group range from 1.2171(13) to 1.2211(18) Å and from 1.313(2) to 1.3250(13) Å for C=O and C–OH, respectively. Selected bond distances and torsion angles are listed in Table 2. Hydrogen-bonding geometries are listed in Table 3.

tab2
Table 2: Selected bond lengths (Å) and angles (°) for compounds 14.
tab3
Table 3: Close contacts of hydrogen bond type [Å and °] for compounds 14.

4. Conclusion

A low-temperature redetermination by X-ray crystallography of four phenoxyalkanoic acids have been carried out. Investigations of the interactions shown the typical carboxylic acid cyclic O–HO hydrogen bonds between adjacent molecules. However, their conformations and molecular packing in the crystals are quite different, which can be explained by the influence of significant C–HO, C–H⋯π, C–ClC intermolecular contacts, forming supramolecular structures. The additional contacts of the π⋯π and C–Cl⋯π type have been observed in compound 3, and the ClCl type in compound 4.

References

  1. G. G. Bond and R. Rossbacher, “A review of potential human carcinogenicity of the chlorophenoxy herbicides MCPA, MCPP, and 2,4-DP,” British Journal of Industrial Medicine, vol. 50, no. 4, pp. 340–348, 1993. View at Google Scholar · View at Scopus
  2. P. Mai, O. Stig Jacobsen, and J. Aamand, “Mineralization and co-metabolic degradation of phenoxyalkanoic acid herbicides by a pure bacterial culture isolated from an aquifer,” Applied Microbiology and Biotechnology, vol. 56, no. 3-4, pp. 486–490, 2001. View at Publisher · View at Google Scholar · View at Scopus
  3. J. R. de Lipthay, S. R. Sørensen, and J. Aamand, “Effect of herbicide concentration and organic and inorganic nutrient amendment on the mineralization of mecoprop, 2,4-D and 2,4,5-T in soil and aquifer samples,” Environmental Pollution, vol. 148, no. 1, pp. 83–93, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  4. J. Kobyłecka and A. Turek, “Complexes of lead(II), copper(II), zinc(II) and cadmium(II) with 2,4-dichlorophenoxyacetic acid,” Annals of the Polish Chemical Society, vol. 2, pp. 462–466, 2003. View at Google Scholar
  5. J. Kobyłecka, B. Ptaszyński, R. Rogaczewski, and A. Turek, “Phenoxyalkanoic acid complexes. Part I. Complexes of lead(II), cadmium(II) and copper(II) with 4-chloro-2-methylphenoxyacetic acid (MCPA),” Thermochimica Acta, vol. 407, no. 1-2, pp. 25–31, 2003. View at Publisher · View at Google Scholar · View at Scopus
  6. G. Smith and C. H. L. Kennard, “4-Chloro-2-methylphenoxyacetic acid,” Structure Communications, vol. 10, pp. 295–299, 1981. View at Google Scholar
  7. G. Smith, C. H. L. Kennard, A. H. White, and P. G. Hodgson, “(+-)-2-(4-Chloro-2-methylphenoxy)propionic acid (mecoprop),” Acta Crystallographica Section B, vol. 36, pp. 992–994, 1980. View at Publisher · View at Google Scholar
  8. G. Smith, C. H. L. Kennard, and A. H. White, “Herbicides. Part I. Crystal structure of 2,4-D (2,4-dichlorophenoxy-acetic acid),” Journal of the Chemical Society, Perkin Transactions 2, no. 7, pp. 791–792, 1976. View at Publisher · View at Google Scholar · View at Scopus
  9. G. Smith, S. M. Shariff, E. J. O'Reilly, and C. H. L. Kennard, “γ-phenoxybutanoic acids and their metal(II) complexes. The crystal structures of 4-(4-chlorophenoxy)butanoic acid, 4-(2,4-dichlorophenoxy)butanoic acid, diaquabis [4-phenoxybutanoato]nickel(II), and cobalt(II) and diaquabis[4-(4-chlorophenoxy)butanoato]nickel(II),” Polyhedron, vol. 8, no. 1, pp. 39–43, 1989. View at Google Scholar · View at Scopus
  10. Z. S. Derewenda, L. Lee, and U. Derewenda, “The occurrence of C–H···O hydrogen bonds in proteins,” Journal of Molecular Biology, vol. 252, no. 2, pp. 248–262, 1995. View at Publisher · View at Google Scholar · View at Scopus
  11. G. R. Desiraju and T. Steiner, The Weak Hydrogen Bond in Structural Chemistry and Biology, Oxford University Press, Oxford, UK, 1999.
  12. M. Brandl, M. S. Weiss, A. Jabs, J. Sühnel, and R. Hilgenfeld, “C–H···π-interactions in proteins,” Journal of Molecular Biology, vol. 307, no. 1, pp. 357–377, 2001. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  13. Bruker, SMART for WNT/2000, Version 5.630, Bruker AXS Inc., Madison, Wis, USA, 2002.
  14. Bruker, SAINT-Plus (Version 6.45) and SHELXTL (Version 6.14), Bruker AXS Inc., Madison, Wis, USA, 2003.
  15. A. L. Spek, “Single-crystal structure validation with the program PLATON,” Journal of Applied Crystallography, vol. 36, no. 1, pp. 7–13, 2003. View at Publisher · View at Google Scholar · View at Scopus
  16. C. F. Macrae, P. R. Edgington, P. McCabe et al., “Mercury: visualization and analysis of crystal structures,” Journal of Applied Crystallography, vol. 39, no. 3, pp. 453–457, 2006. View at Publisher · View at Google Scholar · View at Scopus
  17. M. C. Etter, J. C. MacDonald, and J. Bernstein, “Graph-set analysis of hydrogen-bond patterns in organic crystals,” Acta Crystallographica Section B, vol. 46, pp. 2–262, 1990. View at Publisher · View at Google Scholar · View at Scopus
  18. L. Leiserowitz, “Molecular packing modes. Carboxylic acids,” Acta Crystallographica Section B, vol. 32, pp. 775–802, 1976. View at Publisher · View at Google Scholar
  19. G. A. Jeffrey and W. Saenger, Hydrogen Bonding in Biological Structures, Springer, New York, NY, USA, 1991.