Received 10 August 2012
Helical supramolecular assembly of N2,N2'-bis[3-(morpholin-4-yl)propyl]-N1,N1'-(1,2-phenylene)dioxalamide dimethyl sulfoxide monosolvate
Juan Saulo González-González,a Itzia I. Padilla-Martínez,b Efrén V. García-Báez,b Olivia Franco-Hernándezb and Francisco J. Martínez-Martínezc*
aInstituto de Farmacobiologia, Universidad de la Cañada, Carretera Teotitlán-San Antonio Nanahuatipan Km 1.7 s/n, Paraje Titlacuatitla, CP 68540, Teotitlán de Flores Magon, Oaxaca, Mexico,bUnidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Avenida Acueducto s/n, Barrio La Laguna Ticomán, México DF 07340, Mexico, and cFacultad de Ciencias Químicas, Universidad de Colima, Carretera Coquimatlán-Colima, Coquimatlán Colima, Mexico 28400
In the title compound, C24H36N6O6·C2H6OS, the carbonyl groups are in an antiperiplanar conformation, with O=C-C=O torsion angles of 178.59 (15) and -172.08 (16)°. An intramolecular hydrogen-bonding pattern is depicted by four N-HO interactions, which form two adjacent S(5)S(5) motifs, and an N-HN interaction, which forms an S(6) ring motif. Intermolecular N-HO hydrogen bonding and C-HO soft interactions allow the formation of a meso-helix. The title compound is the first example of a helical 1,2-phenylenedioxalamide. The oxalamide traps one molecule of dimethyl sulfoxide through N-HO hydrogen bonding. C-HO soft interactions give rise to the two-dimensional structure.
In supramolecular chemistry, the design and synthesis of model molecules for donor-acceptor interaction studies continues to be an area of interest (Steed & Atwood, 2009). Hydrogen bonding (HB) is the most important noncovalent interaction used in the design of host-guest systems. HB is particularly important from a biological point of view because of its involvement in several biological processes, such as the stabilization of the double helix of DNA (Kool, 1997), peptide three-dimensional structures (helices, sheets or turns; Sewald & Hans-Dieter, 2002), enzyme-substrate interactions (Bugg, 2004), recognition among proteins (Keskin et al., 2008) and drug-acceptor interactions (Sarker & Nahar, 2007). The development of simple hydrogen-bonding motifs for anion recognition, that are easy to make and functionalize, has led to the design and synthesis of amide-, pyrrole- and urea-based hosts with conventional hydrogen-bond donors (Brooks et al., 2006, 2007). The supramolecular versatility of oxalamides has been demonstrated previously as formers of columns, sheets, tapes, helixes and layers (González-González, Martínez-Martínez, García-Báez et al., 2011; González-González, Martínez-Martínez, Peraza-Campos et al., 2011). In this context, the N-H and C=O groups of oxalamides can be exploited as recognition sites in the design of molecular hosts. In this contribution, we report the molecular structure and the helical supramolecular assembly of the complex, (I) (Fig. 1), formed between N2,N2'-bis[2-(morpholin-4-yl)propyl]-N1,N1'-(1,2-phenylene)dioxalamide and dimethyl sulfoxide (DMSO).
The title compound forms triclinic crystals (P, Z = 2). Selected bond lengths and angles are in the normal ranges found in related structures (Martínez-Martínez et al., 1998). The carbonyl groups are antiperiplanar, with O8-C8-C9-O9 and O28-C28-C29-O29 torsion angles of 178.59 (15) and -172.08 (16)°, respectively. The oxalamide group is almost planar, with N7-C8-C9-N10 and N27-C28-C29-N30 torsion angles of -177.62 (13) and -170.71 (14)°, respectively. These values are in agreement with those reported for oxalamides (Bernés et al., 2010). Both oxalyl arms are twisted from the mean plane of the phenylene ring and adopt an anticlinal conformation, with C6-C1-N7-C8 and C1-C6-N27-C28 torsion angles of -137.65 (16) and 125.88 (16)°, respectively. The N7-H and N27-H amide groups point towards the cavity; thus, the two oxalamide groups are cis-positioned between them, in relation to the mean plane of the phenylene ring. According to graph-set notation (Bernstein et al., 1995), four S(5) rings are formed between amide NH and carbonyl groups, through N7-H7O9, N10-H10O8, N27-H27O29 and N30-H30O28 interactions, and one S(6) ring is formed between an amide NH group and the N atom of one morpholine residue, through N30-H30N34 interactions, displaying only one N-H stretch maximum, at 3272 cm-1. NA distances and N-HA angles (A = O and N) are in the ranges of intramolecular HB (Taylor & Kennard, 1982; Desiraju, 1996), in agreement with similar structures (Desseyn et al., 2004; Martín et al., 2002; Blay et al., 2003) and also in agreement with values reported for intramolecular HB in other systems (Zhu et al., 2007; Yang & Gellman, 1998). The geometric parameters associated with HB interactions are summarized in Table 1. The S(5)S(5)S(6) intramolecular hydrogen-bonded side arm is twisted from the mean aromatic ring plane with N30-C31-C32-C33 and C31-C32-C33-N34 torsion angles of 54.54 (18) and -70.39 (18)°, respectively, whereas the S(5)S(5) side arm is twisted to the opposite side, with N10-C11-C12-C13 and C11-C12-C13-N14 torsion angles values of -168.49 (14) and 56.32 (19)°, respectively. One molecule of DMSO is located outside the cavity formed by the pair of oxalamide side arms and is bonded to the dioxalamide molecule by means of N7-H7O1i and N27-H27O1i HB interactions and C40-H40CO29i and C41-H41CO29i soft interactions to form a 1:1 complex (all symmetry codes are as in Table 1). C-HO interactions are weak HB interactions classified between electrostatic and van der Waals limits (Desiraju, 2002); herein they are called `soft interactions', as suggested by Desiraju (1996).
The zero-dimensional array is obtained by pairing of two dioxalamide molecules (Fig. 2) through self-complementary strong N10-H10O8ii hydrogen bonding, to form the R22(10) motif characteristic of oxalamides. This motif is developed as a one-dimensional meso-helix by C35-H35AO29iv soft interaction, forming an R22(18) ring motif along the (001) direction. In the crystal lattice, a perfect alignment of the helical molecules of the same chirality in the meso-helix is observed (Fig. 3).
The turn of the helix, measured as the spacing between the aromatic rings on neighbouring homochiral molecules, is 16.328 (2) Å, which matches the exact value of the lattice c parameter. Adjacent meso-helices are interlinked through C4-H4O37iii soft interactions to form an infinite sheet on the  family of planes separated by 5.329 (2) Å. DMSO molecules not only act as a template to form the cavity between the two oxalamide arms, but also facilitate the development of the two-dimensional structure, linking the meso-helices through C40-H40BO28(-x + 1, -y + 1, -z + 1) soft interactions, and fill the voids left between the layers.
The softness of DMSO is not capable of interrupting the formation of the typical R22(10) (N-HO) ring motif of oxalamides, in contrast to that observed with the use of 2-(4-nitrophenyl)acetic acid (Arman et al., 2012). As a final remark, it is worth mentioning that a search of the Cambridge Structural Database (CSD, Version 5.33, November 2011; Allen, 2002) for the 1,2-fenilenedioxalyl moiety produced only one hit, viz. for ethyl 1,2-fenilenedioxalamate (Martín et al., 2002). Thus, the title compound is the first example of a 1,2-fenilenedioxalamide crystal structure which, in addition, presents a meso-helix supramolecular architecture.
| || Figure 1 |
The molecular structure of the title DMSO-solvated complex, (I), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii.
| || Figure 2 |
Two molecules of the title DMSO-solvated complex are paired through self-complementary strong N10-H10O8(-x + 1, -y + 1, -z) hydrogen bonding to form the R22(10) motif characteristic of oxalamides.
| || Figure 3 |
The linkage of the title DMSO-solvated complex dimer through C35-H35AO29iv soft interactions developing a meso-helix along the c-axis direction. H atoms and the DMSO solvent molecule have been omitted for clarity.
A solution of diethyl 1,2-phenylenedioxalamate (0.5 g, 1.6 mmol) in methanol (30 ml) and 3-(morpholin-4-yl)propylamine (0.474 ml, 3.2 mmol) was refluxed for 24 h. The suspension was filtered off and the resulting solid was washed with acetone (3 ml) and dried to yield 0.49 g (61%) of a white solid (m.p. 438-440 K). Good quality crystals were grown from a DMSO solution by slow evaporation. IR (neat) (cm-1): 3272 (N-H), 1667 (C=O). 1H NMR (300 MHz, DMSO-d6): 7.27 (m, 2H), 7.59 (m, 2H), 10.52 (s, 2H, Ar-NH), 8.87 (t, 2H, NH-CH2), 3.24 (m, 4H, NH-CH2), 1.64 (m, 4H, NH-CH2-CH2), 2.32 (m, 4H, CH2-N), 2.30 [m, 8H, N-(CH2)2], 3.56 [m, 8H, O-(CH2)2]. 13C NMR (75.46 MHz, DMSO-d6): 130.5 (C1,6), 126.2 (C2,5), 126.8 (C3,4), 159.3 (C8), 160.1 (C9), 38.9 (C11), 25.6 (C12), 57.0 (C13), 53.9 (N-CH2), 66.8 (CH2-O). ESI-MS (m/z): calculated 504.27, found 526.9 [M + Na]+.
All H atoms were found by Fourier difference synthesis and refined. The DMSO molecule is disordered over two orientations, although the S atom could be located and refined to occupancies of 0.931 (2) (for S1A) and 0.0692 (2) (for S1B). The C and O atoms bonded to the very low-occupancy minor-orientation S1B atom were omitted from the model.
Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008) and WinGX (Farrugia, 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2006); software used to prepare material for publication: PLATON (Spek, 2009).
Supplementary data for this paper are available from the IUCr electronic archives (Reference: SF3181 ). Services for accessing these data are described at the back of the journal.
This work was supported by CONACYT grant 83378, SIP-IPN (Secretaría de Investigación y Postgrado del Instituto Politécnico Nacional) and FRABA Universidad de Colima 797/12.
Allen, F. H. (2002). Acta Cryst. B58, 380-388.
Arman, H. D., Kaulgud, T., Miller, T., Poplaukhin, P. & Tiekink, E. R. T. (2012). J. Chem. Crystallogr. 42, 673-679.
Bernés, S., Hernández, G., Vázquez, J., Tovar, A. & Gutiérrez, R. (2010). Acta Cryst. E66, o2988.
Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.
Blay, G., Fernández, I., Pedro, J. R., Ruiz-García, R., Muñoz, M. C., Cano, J. & Carrasco, R. (2003). Eur. J. Org. Chem. pp. 1627-1630.
Brooks, S. J., Edwards, P. R., Gale, P. A. & Light, M. E. (2006). New J. Chem. 30, 65-70.
Brooks, S., García-Garrido, S. E. & Light, M. E. (2007). Chem. Eur. J. 13, 3320-3329.
Bruker (2004). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.
Bugg, T. (2004). Introduction to Enzyme and Coenzyme Chemistry, pp. 20-21. Oxford: Blackwell Publishing Ltd.
Desiraju, G. R. (1996). Acc. Chem. Res. 29, 441-449.
Desiraju, G. R. (2002). Acc. Chem. Res. 35, 565-573.
Desseyn, H. O., Perlepes, S. P., Clou, K., Blaton, N., Veken, B. J., Dommisse, R. & Hansen, P. E. (2004). J. Phys. Chem. A, 108, 5175-5182.
Dwiggins, C. W. (1975). Acta Cryst. A31, 146-148.
Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.
Gonzalez-Gonzalez, J. S., Martínez-Martínez, F. J., García-Báez, E. V., Franco-Hernández, O. M. & Padilla-Martínez, I. I. (2011). Acta Cryst. E67, o398.
González-González, J. S., Martínez-Martínez, F. J., Peraza-Campos, A. L., Rosales-Hoz, M. J., García-Báez, E. V. & Padilla-Martínez, I. I. (2011). CrystEngComm, 13, 4748-4761.
Keskin, O., Gursoy, A., Ma, B. & Nussinov, R. (2008). Chem. Rev. 108, 1225-1244.
Kool, E. T. (1997). Chem. Rev. 97, 1473-1487.
Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.
Martín, S., Beitia, J. I., Ugalde, M., Vitoria, P. & Cortés, R. (2002). Acta Cryst. E58, o913-o915.
Martínez-Martínez, F. J., Padilla-Martínez, I. I., Brito, M. A., Geniz, E. D., Rojas, R. C., Saavedra, J. B. R., Höpfl, H., Tlahuextl, M. & Contreras, R. (1998). J. Chem. Soc. Perkin Trans. 2, pp. 401-406.
Sarker, S. D. & Nahar, L. (2007). Chemistry for Pharmacy Students: General, Organic and Natural Product Chemistry, pp. 30-31. London: John Wiley & Sons Ltd.
Sewald, N. & Hans-Dieter, J. (2002). Peptides: Chemistry and Biology, pp. 36-38. Germany: Wiley-VCH Verlag GmbH.
Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.
Spek, A. L. (2009). Acta Cryst. D65, 148-155.
Steed, J. W. & Atwood, J. L. (2009). Supramolecular Chemistry, 2nd ed., pp. 27-36. Wiltshire: John Wiley & Sons Ltd.
Taylor, R. & Kennard, O. (1982). J. Am. Chem. Soc. 104, 5063-5070.
Yang, J. & Gellman, S. H. (1998). J. Am. Chem. Soc. 120, 9090-9091.
Zhu, Y.-Y., Wu, J., Li, C., Zhu, J., Hou, J.-H., Li, C.-Z., Jiang, X.-K. & Li, Z.-T. (2007). Cryst. Growth Des. 7, 1490-1496.