Refinement. R[F 2 >2(F 2 )] = wr(f 2 ) = S = reflections 385 parameters

Transcription

1 organic compounds Acta Crystallographica Section E Structure Reports Online ISSN a,6a-Bis(ethoxycarbonyl)glycoluril (diethyl 2,5-dioxoperhydroimidazo- [4,5-d]imidazole-3a,6a-dicarboxylate) Yu-Zhou Wang, a * Zhi-Guo Wang b and Lin Li a a Key Laboratory of Pesticides & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan , People s Republic of China, and b School of Chemical and Materials Engineering, Huangshi Institute of Technology, Huangshi , People s Republic of China Correspondence yutian830@yahoo.com.cn Received 30 October 2007; accepted 6 November 2007 Key indicators: single-crystal X-ray study; T = 292 K; mean (C C) = Å; disorder in main residue; R factor = 0.068; wr factor = 0.197; data-to-parameter ratio = The title compound, C 10 H 14 N 4 O 6, crystallizes with two independent molecules in the asymmetric unit. An extensive network of N HO and C HO intermolecular hydrogen bonds stabilizes the crystal packing. One ethyl group is disordered over two positions; the site occupancy factors are 0.68 and Related literature For related literature, see: Burnett et al. (2003); Chen et al. (2007); Himes et al. (1978); Hof et al. (2002); Isaacs & Witt (2002); Kim et al. (2000); Li et al. (1994); Moon et al. (2003); Rowan et al. (1999); Wang et al. (2006, 2007); Wu et al. (2002). Experimental Crystal data C 10 H 14 N 4 O 6 M r = Orthorhombic, Pbca a = (13) Å b = (9) Å c = (2) Å Data collection Bruker SMART 4K CCD areadetector diffractometer V = (7) Å 3 Z =16 Mo K radiation = 0.12 mm 1 T = 292 (2) K mm Absorption correction: none measured reflections 4501 independent reflections 2784 reflections with I > 2(I) Refinement R[F 2 >2(F 2 )] = wr(f 2 ) = S = reflections 385 parameters Table 1 Hydrogen-bond geometry (Å, ). R int = restraints H-atom parameters constrained max = 0.37 e Å 3 min = 0.42 e Å 3 D HA D H HA DA D HA N1 H1O2 i (3) 158 N2 H2O7 ii (3) 162 N3 H3O1 iii (3) 161 N4 H4O8 iv (3) 134 N5 H5O1 iv (3) 133 N6 H6O7 v (3) 164 N7 H7O2 ii (3) 158 N8 H8O8 vi (3) 165 C16 H16CO3 vii (5) 119 C10 H10BO11 v (5) 146 Symmetry codes: (i) x; y 1 2 ; z þ 1 2 ; (ii) x þ 1 2 ; y 1 2 ; z; (iii) x; y þ 1 2 ; z þ 1 2 ; (iv) x þ 1 2 ; y þ 1 2 ; z; (v) x þ 1; y þ 1; z; (vi) x þ 1; y; z; (vii) x þ 1 2 ; y; z þ 1 2. Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 1999); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXTL (Bruker, 1997). The authors are grateful to Central China Normal University for support. Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CV2340). References Bruker (1997). SMART (Version 5.054) and SHELXTL (Version 5.10). Bruker AXS Inc., Madison, Wisconsin, USA. Bruker (1999). SAINT. Version Bruker AXS Inc., Madison, Wisconsin, USA. Burnett, C. A., Lagona, J., Wu, A. X., Shaw, J. A., Coady, D., Fettinger, J. C., Day, A. I. & Isaacs, L. (2003). Tetrahedron, 59, Chen, Y. F., She, N. F., Meng, X. G., Yin, G. D., Wu, A. X. & Isaacs, L. (2007). Org. Lett. 9, Himes, V. L., Hubbard, C. R., Mighell, A. D. & Fatiadi, A. J.(1978). Acta Cryst. B34, Hof, F., Craig, S. L., Nuckolls, C. & Rebek, J. Jr (2002). Angew. Chem. Int. Ed. 41, Isaacs, L. & Witt, D. (2002). Angew. Chem. Int. Ed. 41, Kim, J., Jung, I.-S., Kim, S.-Y., Lee, E., Kang, J.-K., Sakamoto, S., Yamaguchi, K. & Kim, K. (2000). J. Am. Chem. Soc. 122, Li, N., Maluendes, S., Blessing, R. H., Dupuis, M., Moss, G. R. & Detitta, G. T. (1994). J. Am. Chem. Soc. 116, Moon, K., Chen, W. Z., Ren, T. & Kaifer, A. E. (2003). CrystEngComm, 5, Rowan, A. E., Elemans, J. A. A. W. & Nolte, R. J. M. (1999). Acc. Chem. Res. 32, Sheldrick, G. M. (1997). SHELXL97 and SHELXS97. University of Göttingen, Germany. Spek, A. L. (2003). J. Appl. Cryst. 36, Wang, Y.-Z., Gao, M. & Cao, L.-P. (2007). Acta Cryst. E63, o3419. Wang, Z. G., Zhou, B. H., Chen, Y. F., Yin, G. D., Li, Y. T., Wu, A. X. & Isaacs, L. (2006). J. Org. Chem. 71, Wu, A. X., Fettinger, J. C. & Isaacs, L. (2002). Tetrahedron, 58, Acta Cryst. (2008). E64, o125 doi: /s # 2008 International Union of Crystallography o125

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3 Acta Cryst. (2008). E64, o125 [ doi: /s ] 3,6 -Bis(ethoxycarbonyl)glycoluril (diethyl 2,5-dioxoperhydroimidazo[4,5-d]imidazole-3a,6a-dicarboxylate) Y.-Z. Wang, Z.-G. Wang and L. Li Comment Glycoluril skeleton moiety (Fig. 3) is an important building block for both molecular and supramolecular chemistry. Its derivatives have been used as the basis for molecular capsules (Hof et al., 2002), molecular clips (Rowan et al., 1999), self-complementary facial amphiphiles (Isaacs et al., 2002), and the cucurbit[n]uril (CB[n]) family (Kim et al., 2000), and its utilization has been explored as a platform for studies of crystal engineering (Wang et al., 2006; Chen et al., 2007). However, relatively few crystal structures are known for glycoluril derivatives without N-substituents. The crystal structures of the reported glycoluril with different substituents exhibit two H-bonded types (Fig. 4). The mode A was found for (R=H) (Li et al., 1994), (R=CH 3 ) (Himes et al., 1978), (I, R=Ph) (Wu et al., 2002), and so on, and the mode B was observed in the (R=Ph) (Moon et al., 2003), (R=COO-n-C 3 H 7 ) (Wang et al., 2007). Herein, we report the crystal structure of the title compound (I), which exhibits the mode A of hydrogen bonding (Fig. 4). The molecular structure of (I) (R=COOC 2 H 5 ) is shown in Fig. 1. Its crystal structure exhibits the eight-membered rings H-bonding motifs (Fig. 4), which are entirely made up of N H O=C(imidazolone rings) (Table 1). The two-dimension hydrogen bonding network is shown in Fig. 2, In addition, intermolecular C10 H10B O11, C16 H16C O3 interactions (Table 1) contribute to the crystal structure stability. Experimental The title compound was synthesized according to literature procedure (Burnett et al., 2003) in 62% isolated yield. Crystals appropriate for data collection were obtained by slow evaporation of CH 3 OH solution at room temperature. Refinement One ethyl group (C5 C6) was treted as disordered over two orientations with the occupancies refined to (15) / (15). All H-atoms were positioned geometrically (C H 0.96, 0.97 Å; N H 0.86 Å) and constrained to ride on their parent atoms, with U iso (H) = U eq (parent atom). Figures Fig. 1. The content of asymmetric unit of (I), showing the atom-labelling scheme and 50% probability displacement ellipsoids. Atoms of the minor disorder components are omitted for clarity. sup-1

4 Fig. 2. The partial hydrogen bonding network in the crystal structure of the title compound. H-bond drawn as dashed lines. 3α,6α- Diethoxylcarbonyl are omitted for simplicity. Fig. 3. The glycoluril skeleton moiety. Fig. 4. Hydrogen-bonding modes A and B. diethyl 2,5-dioxoperhydroimidazo[4,5-d]imidazole-3a,6a-dicarboxylate Crystal data C 10 H 14 N 4 O 6 F 000 = 2400 M r = Orthorhombic, Pbca Hall symbol: -P 2ac 2ab D x = Mg m 3 Mo Kα radiation λ = Å a = (13) Å θ = º b = (9) Å c = (2) Å V = (7) Å 3 Z = 16 Cell parameters from 2687 reflections µ = 0.12 mm 1 T = 292 (2) K Block, colourless mm Data collection Bruker SMART 4K CCD area-detector diffractometer Radiation source: fine-focus sealed tube R int = Monochromator: graphite θ max = 25.0º 2784 reflections with I > 2σ(I) sup-2

5 T = 292(2) K θ min = 1.9º φ and ω scans h = Absorption correction: none k = measured reflections l = independent reflections Refinement Refinement on F 2 Least-squares matrix: full R[F 2 > 2σ(F 2 )] = wr(f 2 ) = 0.197? Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained S = 1.00 (Δ/σ) max < reflections Δρ max = 0.37 e Å parameters Δρ min = 0.42 e Å 3 6 restraints Extinction correction: none Primary atom site location: structure-invariant direct methods Special details Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wr and goodness of fit S are based on F 2, conventional R-factors R are based on F, with F set to zero for negative F 2. The threshold expression of F 2 > σ(f 2 ) is used only for calculating R- factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å 2 ) x y z U iso */U eq Occ. (<1) C (19) (3) (10) (8) C (2) (3) (10) (8) C (2) (2) (10) (7) C (2) (3) (12) (9) C (3) (8) (3) (2) (15) H5A * (15) H5B * (15) C (4) (8) (4) (3) (15) H6A * (15) H6B * (15) H6C * (15) C5' (6) (2) (7) (7) (15) H5' * (15) sup-3

6 H5' * (15) C6' (8) (2) (9) (12) (15) H6' * (15) H6' * (15) H6' * (15) C (2) (2) (10) (8) C (2) (3) (13) (10) C (3) (4) (16) (15) H9A * H9B * C (3) (4) (17) (17) H10A * H10B * H10C * C (2) (3) (11) (8) C (19) (3) (10) (7) C (19) (2) (10) (7) C (2) (3) (12) (9) C (3) (4) (16) (14) H15A * H15B * C (3) (4) (17) (16) H16A * H16B * H16C * C (2) (2) (10) (7) C (2) (3) (11) (8) C (2) (4) (19) (16) H19A * H19B * C (3) (4) (17) (16) H20A * H20B * H20C * N (16) (2) (8) (7) H * N (17) (2) (8) (7) H * N (17) (2) (9) (7) H * N (17) (2) (9) (7) H * N (16) (2) (9) (7) H * N (17) (2) (9) (7) H * N (16) (2) (8) (7) H * N (16) (2) (8) (7) sup-4

7 H * O (15) (18) (7) (6) O (16) (19) (7) (6) O (19) (3) (10) (9) O (15) (3) (10) (8) O (17) (2) (9) (8) O (3) (2) (13) (18) O (16) (19) (8) (7) O (15) (18) (7) (6) O (2) (2) (10) (10) O (17) (2) (9) (8) O (17) (2) (10) (9) O (14) (2) (10) (8) Atomic displacement parameters (Å 2 ) U 11 U 22 U 33 U 12 U 13 U 23 C (18) (18) (18) (15) (14) (14) C (2) (18) (18) (15) (15) (14) C (19) (16) (17) (14) (14) (13) C (2) (2) (2) (2) (17) (18) C (3) (5) (4) (3) (3) (4) C (4) (6) (6) (3) (4) (5) C5' (15) (12) (14) (11) (11) (11) C6' 0.16 (2) (18) 0.14 (2) (16) (16) (18) C (19) (16) (18) (14) (14) (13) C (3) (18) (2) (18) (2) (17) C (3) (3) (3) (3) (3) (3) C (4) (4) (3) (3) (3) (3) C (2) (18) (18) (16) (15) (14) C (18) (17) (17) (14) (14) (13) C (19) (16) (16) (14) (14) (13) C (2) (17) (2) (17) (18) (16) C (3) (3) (3) (3) (2) (3) C (5) (3) (3) (3) (3) (3) C (18) (16) (17) (14) (14) (12) C (2) (2) (2) (17) (16) (16) C (3) (3) (4) (2) (3) (3) C (3) (4) (4) (3) (2) (3) N (17) (14) (13) (12) (12) (11) N (19) (14) (14) (13) (13) (11) N (18) (16) (15) (14) (13) (12) N (18) (15) (14) (13) (13) (12) N (17) (15) (15) (13) (12) (12) N (18) (15) (15) (13) (13) (12) N (18) (14) (13) (13) (12) (11) N (17) (14) (13) (12) (12) (11) O (17) (12) (13) (11) (11) (10) sup-5

8 O (16) (13) (14) (12) (11) (10) O (2) (19) (2) (17) (17) (17) O (15) (2) (2) (15) (14) (17) O (19) (16) (16) (14) (14) (13) O (4) (2) (3) (2) (3) (2) O (18) (14) (13) (13) (12) (11) O (16) (13) (12) (11) (11) (10) O (3) (17) (19) (17) (19) (14) O (19) (18) (15) (16) (14) (14) O (19) (2) (19) (16) (15) (16) O (16) (15) (2) (12) (14) (15) Geometric parameters (Å, ) C1 O (4) C11 N (4) C1 N (4) C11 N (4) C1 N (4) C12 O (3) C2 O (4) C12 N (4) C2 N (4) C12 N (4) C2 N (4) C13 N (3) C3 N (4) C13 N (4) C3 N (3) C13 C (4) C3 C (5) C13 C (4) C3 C (4) C14 O (4) C4 O (4) C14 O (4) C4 O (4) C15 C (6) C5 O (5) C15 O (4) C5 C (7) C15 H15A C5 H5A C15 H15B C5 H5B C16 H16A C6 H6A C16 H16B C6 H6B C16 H16C C6 H6C C17 N (4) C5' O (9) C17 N (3) C5' C6' (10) C17 C (5) C5' H5' C18 O (4) C5' H5' C18 O (4) C6' H6' C19 O (4) C6' H6' C19 C (6) C6' H6' C19 H19A C7 N (3) C19 H19B C7 N (4) C20 H20A C7 C (4) C20 H20B C8 O (4) C20 H20C C8 O (4) N1 H C9 C (6) N2 H C9 O (4) N3 H C9 H9A N4 H C9 H9B N5 H sup-6

9 C10 H10A N6 H C10 H10B N7 H C10 H10C N8 H C11 O (4) O1 C1 N (3) O9 C14 O (3) O1 C1 N (3) O9 C14 C (3) N2 C1 N (3) O10 C14 C (3) O2 C2 N (3) C16 C15 O (4) O2 C2 N (3) C16 C15 H15A N3 C2 N (3) O10 C15 H15A N3 C3 N (3) C16 C15 H15B N3 C3 C (3) O10 C15 H15B N1 C3 C (3) H15A C15 H15B N3 C3 C (2) C15 C16 H16A N1 C3 C (2) C15 C16 H16B C4 C3 C (2) H16A C16 H16B O3 C4 O (4) C15 C16 H16C O3 C4 C (3) H16A C16 H16C O4 C4 C (3) H16B C16 H16C O4 C5 C (5) N6 C17 N (2) O4 C5 H5A N6 C17 C (3) C6 C5 H5A N8 C17 C (2) O4 C5 H5B N6 C17 C (2) C6 C5 H5B N8 C17 C (2) H5A C5 H5B C18 C17 C (2) O4 C5' C6' (9) O11 C18 O (3) O4 C5' H5' O11 C18 C (3) C6' C5' H5' O12 C18 C (3) O4 C5' H5' O12 C19 C (4) C6' C5' H5' O12 C19 H19A H5'1 C5' H5' C20 C19 H19A C5' C6' H6' O12 C19 H19B C5' C6' H6' C20 C19 H19B H6'1 C6' H6' H19A C19 H19B C5' C6' H6' C19 C20 H20A H6'1 C6' H6' C19 C20 H20B H6'2 C6' H6' H20A C20 H20B N2 C7 N (3) C19 C20 H20C N2 C7 C (3) H20A C20 H20C N4 C7 C (2) H20B C20 H20C N2 C7 C (2) C1 N1 C (2) N4 C7 C (2) C1 N1 H C8 C7 C (3) C3 N1 H O6 C8 O (3) C1 N2 C (2) O6 C8 C (3) C1 N2 H O5 C8 C (3) C7 N2 H C10 C9 O (4) C2 N3 C (2) C10 C9 H9A C2 N3 H O5 C9 H9A C3 N3 H sup-7

10 C10 C9 H9B C2 N4 C (3) O5 C9 H9B C2 N4 H H9A C9 H9B C7 N4 H C9 C10 H10A C11 N5 C (2) C9 C10 H10B C11 N5 H H10A C10 H10B C13 N5 H C9 C10 H10C C11 N6 C (2) H10A C10 H10C C11 N6 H H10B C10 H10C C17 N6 H O7 C11 N (3) C12 N7 C (2) O7 C11 N (3) C12 N7 H N6 C11 N (3) C13 N7 H O8 C12 N (3) C12 N8 C (2) O8 C12 N (3) C12 N8 H N8 C12 N (2) C17 N8 H N7 C13 N (3) C4 O4 C5' (10) N7 C13 C (2) C4 O4 C (4) N5 C13 C (2) C5' O4 C (7) N7 C13 C (2) C8 O5 C (3) N5 C13 C (2) C14 O10 C (3) C14 C13 C (3) C18 O12 C (3) N3 C3 C4 O3 4.5 (5) C8 C7 N2 C (3) N1 C3 C4 O (3) C3 C7 N2 C1 1.5 (3) C7 C3 C4 O (4) O2 C2 N3 C (3) N3 C3 C4 O (3) N4 C2 N3 C3 9.1 (4) N1 C3 C4 O (4) N1 C3 N3 C (3) C7 C3 C4 O (4) C4 C3 N3 C (3) N3 C3 C7 N (2) C7 C3 N3 C2 2.8 (3) N1 C3 C7 N2 3.6 (3) O2 C2 N4 C (3) C4 C3 C7 N (3) N3 C2 N4 C (4) N3 C3 C7 N4 4.0 (3) N2 C7 N4 C (3) N1 C3 C7 N (2) C8 C7 N4 C (3) C4 C3 C7 N (3) C3 C7 N4 C2 9.8 (3) N3 C3 C7 C (3) O7 C11 N5 C (3) N1 C3 C7 C (3) N6 C11 N5 C (4) C4 C3 C7 C8 4.1 (4) N7 C13 N5 C (3) N2 C7 C8 O (5) C14 C13 N5 C (3) N4 C7 C8 O (5) C17 C13 N5 C (3) C3 C7 C8 O (4) O7 C11 N6 C (3) N2 C7 C8 O (3) N5 C11 N6 C (4) N4 C7 C8 O (4) N8 C17 N6 C (3) C3 C7 C8 O (4) C18 C17 N6 C (3) N7 C13 C14 O (4) C13 C17 N6 C (3) N5 C13 C14 O (4) O8 C12 N7 C (3) C17 C13 C14 O (3) N8 C12 N7 C (3) N7 C13 C14 O (3) N5 C13 N7 C (3) N5 C13 C14 O (3) C14 C13 N7 C (3) C17 C13 C14 O (4) C17 C13 N7 C (3) N7 C13 C17 N (2) O8 C12 N8 C (3) sup-8

11 N5 C13 C17 N (3) N7 C12 N8 C (4) C14 C13 C17 N (3) N6 C17 N8 C (3) N7 C13 C17 N (3) C18 C17 N8 C (3) N5 C13 C17 N (2) C13 C17 N8 C (3) C14 C13 C17 N (3) O3 C4 O4 C5' 18.8 (11) N7 C13 C17 C (3) C3 C4 O4 C5' (9) N5 C13 C17 C (3) O3 C4 O4 C5 3.3 (6) C14 C13 C17 C (4) C3 C4 O4 C (4) N6 C17 C18 O (4) C6' C5' O4 C4 96 (2) N8 C17 C18 O (3) C6' C5' O4 C (16) C13 C17 C18 O (4) C6 C5 O4 C (7) N6 C17 C18 O (3) C6 C5 O4 C5' 47.1 (14) N8 C17 C18 O (3) O6 C8 O5 C9 2.7 (7) C13 C17 C18 O (3) C7 C8 O5 C (3) O1 C1 N1 C (3) C10 C9 O5 C (5) N2 C1 N1 C3 4.2 (4) O9 C14 O10 C (6) N3 C3 N1 C (3) C13 C14 O10 C (3) C4 C3 N1 C (3) C16 C15 O10 C (4) C7 C3 N1 C1 4.8 (3) O11 C18 O12 C (5) O1 C1 N2 C (3) C17 C18 O12 C (3) N1 C1 N2 C7 1.4 (4) C20 C19 O12 C (5) N4 C7 N2 C (3) Hydrogen-bond geometry (Å, ) D H A D H H A D A D H A N1 H1 O2 i (3) 158 N2 H2 O7 ii (3) 162 N3 H3 O1 iii (3) 161 N4 H4 O8 iv (3) 134 N5 H5 O1 iv (3) 133 N6 H6 O7 v (3) 164 N7 H7 O2 ii (3) 158 N8 H8 O8 vi (3) 165 C16 H16C O3 vii (5) 119 C10 H10B O11 v (5) 146 Symmetry codes: (i) x, y 1/2, z+1/2; (ii) x+1/2, y 1/2, z; (iii) x, y+1/2, z+1/2; (iv) x+1/2, y+1/2, z; (v) x+1, y+1, z; (vi) x+1, y, z; (vii) x+1/2, y, z+1/2. sup-9

12 Fig. 1 sup-10

13 Fig. 2 sup-11

14 Fig. 3 sup-12

15 Fig. 4 sup-13