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Acta Crystallogr Sect E Struct Rep Online. 2008 September 1; 64(Pt 9): o1795.
Published online 2008 August 20. doi:  10.1107/S160053680802429X
PMCID: PMC2960615

1,3,5,7,9,11,13,15-Octa­azapenta­cyclo­[9.5.1.13,9.06,18.014,17]octa­decane-4,8,12,16-tetrone monohydrate: a methyl­ene-bridged glycoluril dimer

Abstract

In the title compound, C10H12N8O4·H2O, prepared from the reaction of glycoluril with paraformaldehyde, the organic molecule has mm symmetry. The asymmetric unit comprises one quarter of the mol­ecule and a half-mol­ecule of water. The dimer is formed by bridging two glycoluril mol­ecules with methyl­ene groups at the 1 and 6 positions. In the crystal structure, mol­ecules are linked via N—H(...)O and O—H(...)O hydrogen bonds, forming a two-dimensional framework.

Related literature

For general background, see: Zhao et al. (2004 [triangle]); Zheng et al. (2005 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-o1795-scheme1.jpg

Experimental

Crystal data

  • C10H12N8O4·H2O
  • M r = 326.29
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1795-efi5.jpg
  • a = 10.292 (3) Å
  • b = 12.286 (4) Å
  • c = 4.9530 (15) Å
  • V = 626.2 (3) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.14 mm−1
  • T = 298 (2) K
  • 0.18 × 0.13 × 0.10 mm

Data collection

  • Bruker APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.975, T max = 0.986
  • 3977 measured reflections
  • 616 independent reflections
  • 528 reflections with I > 2σ(I)
  • R int = 0.026

Refinement

  • R[F 2 > 2σ(F 2)] = 0.032
  • wR(F 2) = 0.089
  • S = 1.11
  • 616 reflections
  • 59 parameters
  • H-atom parameters constrained
  • Δρmax = 0.18 e Å−3
  • Δρmin = −0.24 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053680802429X/sj2521sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680802429X/sj2521Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

We acknowledge the support of the National Natural Science Foundation of China (No. 20662003) and the Foundation of the Governor of Guizhou Province, China.

supplementary crystallographic information

Comment

In recent years, we have used different alkyl substituted glycolurils and glycoluril dimers as building blocks in the synthesis of partially alkyl substituted cucurbit[n]urils In this work, we report the crystal structure of the title compound, a glycoluril dimer, Fig 1.

The molecule comproses two glycoluril units linked by methylene bridges at the 1 and 6 positions. Molecules have mm crystallographic symmetry and the asymmetric unit comprises one quarter of the molecule and a half molecule of water. In the crystal structure, molecules are linked via N1—H1···O1i and O1W—H1WA···O1 hydrogen bonds forming a two-dimensional framework (Table 1 and Fig. 2).

Experimental

A solution of glycoluril (7.0 g, 0.05 mol) in H2SO4 (50 ml, 25%) was added to a stirred solution of paraformaldehyde (6.0 g, 0.2 mol) in H2SO4 (150 ml) and the mixture was kept at 40°C for 5 h. Glycoluril (14.2 g, 0.1 mol) and H2SO4 (100 ml, 25%) were added in small proportions to this reaction mixture and the solution held at 80°C on a water bath for 5 h. After cooling to room temperature, the mixture was filtered to remove the insoluble residue and the filtrate was neutralized with aqueous NH3 to pH 7. HCl (150 ml) was then added, the mixture, stirred for 10 min, then filtered again. The solid product was dissolved in 100 ml HCl, and then set aside for three weeks to form colourless crystals of I.

Refinement

The water H atoms were located in a difference Fourier map and refined as riding on the O atom in these positions with Uiso(H) = 1.2Ueq(O). All other H atoms were placed in calculated positions and refined as riding, with C—H = 0.97 Å (methylene) and 0.98 Å (methine), N—H = 0.86 Å, and Uiso(H) = 1.2Ueq(C,N).

Figures

Fig. 1.
The molecular structure of (I) showing the atom-labelling scheme (Symmetry codes: (A) -x + 3/2, y, z, (B) x, -y + 3/2, z, (C) -x + 3/2, -y + 3/2, z,). Displacement ellipsoids are drawn at the 50% probability level.
Fig. 2.
Packing diagram of (I). Hydrogen bonds are shown as dashed lines.

Crystal data

C10H12N8O4·H2OF000 = 340
Mr = 326.29Dx = 1.730 Mg m3
Orthorhombic, PmmnMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ab 2aCell parameters from 616 reflections
a = 10.292 (3) Åθ = 2.6–25.1º
b = 12.286 (4) ŵ = 0.14 mm1
c = 4.9530 (15) ÅT = 298 (2) K
V = 626.2 (3) Å3Prism, colorless
Z = 20.18 × 0.13 × 0.10 mm

Data collection

Bruker APEXII CCD area-detector diffractometer616 independent reflections
Radiation source: fine-focus sealed tube528 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.026
T = 298(2) Kθmax = 25.1º
[var phi] and ω scansθmin = 2.6º
Absorption correction: multi-scan(SADABS; Bruker, 2005)h = −11→12
Tmin = 0.975, Tmax = 0.986k = −14→14
3977 measured reflectionsl = −5→5

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.032H-atom parameters constrained
wR(F2) = 0.089  w = 1/[σ2(Fo2) + (0.049P)2 + 0.1538P] where P = (Fo2 + 2Fc2)/3
S = 1.11(Δ/σ)max < 0.001
616 reflectionsΔρmax = 0.18 e Å3
59 parametersΔρmin = −0.24 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

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 F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 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 (Å2)

xyzUiso*/Ueq
O1W0.25000.75000.5795 (5)0.0492 (7)
H1WA0.30960.75000.45740.059*
C10.56573 (14)0.59339 (12)0.2017 (3)0.0263 (4)
C20.75000.49067 (16)0.0938 (4)0.0272 (5)
H20.75000.4252−0.01910.033*
C30.75000.59750 (16)−0.0774 (4)0.0254 (5)
H30.75000.5819−0.27140.030*
C40.5795 (2)0.7500−0.1105 (4)0.0265 (5)
H4A0.59770.7500−0.30270.032*
H4B0.48590.7500−0.08830.032*
N10.63278 (12)0.50102 (10)0.2503 (3)0.0336 (4)
H10.60770.45270.36460.040*
N20.63117 (12)0.65109 (9)0.0058 (2)0.0290 (4)
O10.46406 (10)0.62196 (9)0.3073 (2)0.0341 (3)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O1W0.0359 (14)0.0614 (16)0.0504 (16)0.0000.0000.000
C10.0257 (8)0.0270 (8)0.0263 (9)−0.0046 (6)−0.0020 (6)−0.0024 (6)
C20.0257 (11)0.0248 (10)0.0312 (12)0.0000.000−0.0036 (9)
C30.0239 (11)0.0281 (10)0.0241 (11)0.0000.000−0.0033 (9)
C40.0243 (11)0.0290 (10)0.0262 (11)0.000−0.0049 (8)0.000
N10.0328 (8)0.0307 (7)0.0374 (8)0.0027 (6)0.0088 (6)0.0078 (5)
N20.0245 (7)0.0306 (7)0.0319 (7)0.0024 (5)0.0038 (6)0.0038 (5)
O10.0291 (6)0.0352 (6)0.0380 (7)0.0024 (5)0.0081 (5)0.0019 (5)

Geometric parameters (Å, °)

O1W—H1WA0.8616C3—N2i1.4487 (16)
C1—O11.2214 (17)C3—N21.4487 (16)
C1—N11.350 (2)C3—H30.9800
C1—N21.3774 (19)C4—N2ii1.4461 (16)
C2—N1i1.4395 (17)C4—N21.4461 (16)
C2—N11.4395 (17)C4—H4A0.9700
C2—C31.563 (3)C4—H4B0.9700
C2—H20.9800N1—H10.8600
O1—C1—N1127.08 (14)C2—C3—H3111.6
O1—C1—N2124.95 (14)N2ii—C4—N2114.35 (17)
N1—C1—N2107.97 (13)N2ii—C4—H4A108.7
N1i—C2—N1113.86 (18)N2—C4—H4A108.7
N1i—C2—C3102.59 (11)N2ii—C4—H4B108.7
N1—C2—C3102.59 (11)N2—C4—H4B108.7
N1i—C2—H2112.3H4A—C4—H4B107.6
N1—C2—H2112.3C1—N1—C2113.98 (14)
C3—C2—H2112.3C1—N1—H1123.0
N2i—C3—N2115.16 (17)C2—N1—H1123.0
N2i—C3—C2103.14 (11)C1—N2—C4122.23 (14)
N2—C3—C2103.14 (11)C1—N2—C3112.29 (13)
N2i—C3—H3111.6C4—N2—C3125.37 (15)
N2—C3—H3111.6
N1i—C2—C3—N2i0.93 (16)N1—C1—N2—C4174.54 (13)
N1—C2—C3—N2i119.26 (13)O1—C1—N2—C3179.04 (14)
N1i—C2—C3—N2−119.26 (13)N1—C1—N2—C3−1.78 (18)
N1—C2—C3—N2−0.93 (16)N2ii—C4—N2—C198.33 (19)
O1—C1—N1—C2−179.74 (14)N2ii—C4—N2—C3−85.8 (2)
N2—C1—N1—C21.10 (18)N2i—C3—N2—C1−109.90 (16)
N1i—C2—N1—C1110.00 (16)C2—C3—N2—C11.67 (17)
C3—C2—N1—C1−0.06 (18)N2i—C3—N2—C473.9 (2)
O1—C1—N2—C4−4.6 (2)C2—C3—N2—C4−174.51 (14)

Symmetry codes: (i) −x+3/2, y, z; (ii) x, −y+3/2, z.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O1iii0.862.012.8417 (17)164
O1W—H1WA···O1ii0.862.363.0241 (17)135
O1W—H1WA···O10.862.363.0241 (17)135

Symmetry codes: (iii) −x+1, −y+1, −z+1; (ii) x, −y+3/2, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: SJ2521).

References

  • Bruker, (2005). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Farrugia, L. J. (1999). J. Appl. Cryst.32, 837–838.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Zhao, Y. J., Xue, S. F., Zhu, Q. J., Tao, Z., Zhang, J. X., Wei, Z. B., Long, L. S., Hu, M. L., Xiao, H. P. & Day, A. I. (2004). Chin. Sci. Bull.49, 1111–1116.
  • Zheng, L. M., Zhu, J. N., Zhang, Y. Q., Tao, Z., Xue, S. F., Zhu, Q. J., Wei, Z. B. & Long, L. S. (2005). Chin. J. Inorg. Chem.21, 1583–1588.

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