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

Ma, P.-H.; Xiao, X.; Zhang, Y.-Q.; Xue, S.-F.; Tao, Z.

doi:10.1107/S160053680802429X

organic compounds

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1,3,5,7,9,11,13,15-Octaazapentacyclo[9.5.1.1^3,9.0^6,18.0^14,17]octadecane-4,8,12,16-tetrone monohydrate: a methylene-bridged glycoluril dimer

Pei-Hua Ma,^a Xin Xiao,^a Yun-Qian Zhang,^a Sai-Feng Xue ^b and Zhu Tao ^b ^*

^aKey Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, People's Republic of China, and ^bInstitute of Applied Chemistry, Guizhou University, Guiyang 550025, People's Republic of China.
^*Correspondence e-mail: sci.yqzhang@gzu.edu.cn

(Received 23 July 2008; accepted 30 July 2008; online 20 August 2008)

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 ); Zheng et al. (2005 ).

Experimental

Crystal data

C₁₀H₁₂N₈O₄·H₂O
M_r = 326.29
Orthorhombic, P m m n
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 ) 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[F² > 2σ(F²)] = 0.032
wR(F²) = 0.089
S = 1.11
616 reflections
59 parameters
H-atom parameters constrained
Δρ_max = 0.18 e Å⁻³
Δρ_min = −0.24 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1ⁱ	0.86	2.01	2.8417 (17)	164
O1W—H1WA⋯O1ⁱⁱ	0.86	2.36	3.0241 (17)	135
O1W—H1WA⋯O1	0.86	2.36	3.0241 (17)	135
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) $[x, -y+{\script{3\over 2}}, z]$ .

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

Supporting information

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

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

checkCIF report

Comment top

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).

Related literature top

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

Experimental top

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.

Computing details top

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

Figures top

	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.

1,3,5,7,9,11,13,15-Octaazapentacyclo[9.5.1.1^3,9.0^6,18.0^14,17]octadecane- 4,8,12,16-tetrone monohydrate top

Crystal data top

C₁₀H₁₂N₈O₄·H₂O	F(000) = 340
M_r = 326.29	D_x = 1.730 Mg m⁻³
Orthorhombic, Pmmn	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ab 2a	Cell parameters from 616 reflections
a = 10.292 (3) Å	θ = 2.6–25.1°
b = 12.286 (4) Å	µ = 0.14 mm⁻¹
c = 4.9530 (15) Å	T = 298 K
V = 626.2 (3) Å³	Prism, colorless
Z = 2	0.18 × 0.13 × 0.10 mm

Data collection top

Bruker APEXII CCD area-detector diffractometer	616 independent reflections
Radiation source: fine-focus sealed tube	528 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.026
ϕ and ω scans	θ_max = 25.1°, θ_min = 2.6°
Absorption correction: multi-scan (SADABS; Bruker, 2005)	h = −11→12
T_min = 0.975, T_max = 0.986	k = −14→14
3977 measured reflections	l = −5→5

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.032	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.089	H-atom parameters constrained
S = 1.11	w = 1/[σ²(F_o²) + (0.049P)² + 0.1538P] where P = (F_o² + 2F_c²)/3
616 reflections	(Δ/σ)_max < 0.001
59 parameters	Δρ_max = 0.18 e Å⁻³
0 restraints	Δρ_min = −0.24 e Å⁻³

Crystal data top

C₁₀H₁₂N₈O₄·H₂O	V = 626.2 (3) Å³
M_r = 326.29	Z = 2
Orthorhombic, Pmmn	Mo Kα radiation
a = 10.292 (3) Å	µ = 0.14 mm⁻¹
b = 12.286 (4) Å	T = 298 K
c = 4.9530 (15) Å	0.18 × 0.13 × 0.10 mm

Data collection top

Bruker APEXII CCD area-detector diffractometer	616 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2005)	528 reflections with I > 2σ(I)
T_min = 0.975, T_max = 0.986	R_int = 0.026
3977 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.032	0 restraints
wR(F²) = 0.089	H-atom parameters constrained
S = 1.11	Δρ_max = 0.18 e Å⁻³
616 reflections	Δρ_min = −0.24 e Å⁻³
59 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq
O1W	0.2500	0.7500	0.5795 (5)	0.0492 (7)
H1WA	0.3096	0.7500	0.4574	0.059*
C1	0.56573 (14)	0.59339 (12)	0.2017 (3)	0.0263 (4)
C2	0.7500	0.49067 (16)	0.0938 (4)	0.0272 (5)
H2	0.7500	0.4252	−0.0191	0.033*
C3	0.7500	0.59750 (16)	−0.0774 (4)	0.0254 (5)
H3	0.7500	0.5819	−0.2714	0.030*
C4	0.5795 (2)	0.7500	−0.1105 (4)	0.0265 (5)
H4A	0.5977	0.7500	−0.3027	0.032*
H4B	0.4859	0.7500	−0.0883	0.032*
N1	0.63278 (12)	0.50102 (10)	0.2503 (3)	0.0336 (4)
H1	0.6077	0.4527	0.3646	0.040*
N2	0.63117 (12)	0.65109 (9)	0.0058 (2)	0.0290 (4)
O1	0.46406 (10)	0.62196 (9)	0.3073 (2)	0.0341 (3)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1W	0.0359 (14)	0.0614 (16)	0.0504 (16)	0.000	0.000	0.000
C1	0.0257 (8)	0.0270 (8)	0.0263 (9)	−0.0046 (6)	−0.0020 (6)	−0.0024 (6)
C2	0.0257 (11)	0.0248 (10)	0.0312 (12)	0.000	0.000	−0.0036 (9)
C3	0.0239 (11)	0.0281 (10)	0.0241 (11)	0.000	0.000	−0.0033 (9)
C4	0.0243 (11)	0.0290 (10)	0.0262 (11)	0.000	−0.0049 (8)	0.000
N1	0.0328 (8)	0.0307 (7)	0.0374 (8)	0.0027 (6)	0.0088 (6)	0.0078 (5)
N2	0.0245 (7)	0.0306 (7)	0.0319 (7)	0.0024 (5)	0.0038 (6)	0.0038 (5)
O1	0.0291 (6)	0.0352 (6)	0.0380 (7)	0.0024 (5)	0.0081 (5)	0.0019 (5)

Geometric parameters (Å, º) top

O1W—H1WA	0.8616	C3—N2ⁱ	1.4487 (16)
C1—O1	1.2214 (17)	C3—N2	1.4487 (16)
C1—N1	1.350 (2)	C3—H3	0.9800
C1—N2	1.3774 (19)	C4—N2ⁱⁱ	1.4461 (16)
C2—N1ⁱ	1.4395 (17)	C4—N2	1.4461 (16)
C2—N1	1.4395 (17)	C4—H4A	0.9700
C2—C3	1.563 (3)	C4—H4B	0.9700
C2—H2	0.9800	N1—H1	0.8600

O1—C1—N1	127.08 (14)	C2—C3—H3	111.6
O1—C1—N2	124.95 (14)	N2ⁱⁱ—C4—N2	114.35 (17)
N1—C1—N2	107.97 (13)	N2ⁱⁱ—C4—H4A	108.7
N1ⁱ—C2—N1	113.86 (18)	N2—C4—H4A	108.7
N1ⁱ—C2—C3	102.59 (11)	N2ⁱⁱ—C4—H4B	108.7
N1—C2—C3	102.59 (11)	N2—C4—H4B	108.7
N1ⁱ—C2—H2	112.3	H4A—C4—H4B	107.6
N1—C2—H2	112.3	C1—N1—C2	113.98 (14)
C3—C2—H2	112.3	C1—N1—H1	123.0
N2ⁱ—C3—N2	115.16 (17)	C2—N1—H1	123.0
N2ⁱ—C3—C2	103.14 (11)	C1—N2—C4	122.23 (14)
N2—C3—C2	103.14 (11)	C1—N2—C3	112.29 (13)
N2ⁱ—C3—H3	111.6	C4—N2—C3	125.37 (15)
N2—C3—H3	111.6

N1ⁱ—C2—C3—N2ⁱ	0.93 (16)	N1—C1—N2—C4	174.54 (13)
N1—C2—C3—N2ⁱ	119.26 (13)	O1—C1—N2—C3	179.04 (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—C1	98.33 (19)
O1—C1—N1—C2	−179.74 (14)	N2ⁱⁱ—C4—N2—C3	−85.8 (2)
N2—C1—N1—C2	1.10 (18)	N2ⁱ—C3—N2—C1	−109.90 (16)
N1ⁱ—C2—N1—C1	110.00 (16)	C2—C3—N2—C1	1.67 (17)
C3—C2—N1—C1	−0.06 (18)	N2ⁱ—C3—N2—C4	73.9 (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, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1ⁱⁱⁱ	0.86	2.01	2.8417 (17)	164
O1W—H1WA···O1ⁱⁱ	0.86	2.36	3.0241 (17)	135
O1W—H1WA···O1	0.86	2.36	3.0241 (17)	135

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

Experimental details

Crystal data
Chemical formula	C₁₀H₁₂N₈O₄·H₂O
M_r	326.29
Crystal system, space group	Orthorhombic, Pmmn
Temperature (K)	298
a, b, c (Å)	10.292 (3), 12.286 (4), 4.9530 (15)
V (Å³)	626.2 (3)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.14
Crystal size (mm)	0.18 × 0.13 × 0.10

Data collection
Diffractometer	Bruker APEXII CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2005)
T_min, T_max	0.975, 0.986
No. of measured, independent and observed [I > 2σ(I)] reflections	3977, 616, 528
R_int	0.026
(sin θ/λ)_max (Å⁻¹)	0.597

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.032, 0.089, 1.11
No. of reflections	616
No. of parameters	59
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.18, −0.24

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1ⁱ	0.86	2.01	2.8417 (17)	163.5
O1W—H1WA···O1ⁱⁱ	0.86	2.36	3.0241 (17)	134.6
O1W—H1WA···O1	0.86	2.36	3.0241 (17)	134.6

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

Acknowledgements

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

References

Bruker, (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565. CrossRef IUCr Journals Google Scholar
Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838. CrossRef CAS IUCr Journals Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
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. Web of Science CSD CrossRef CAS Google Scholar
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. CAS Google Scholar

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doi:10.1107/S160053680802429X

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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

Related literature

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

1,3,5,7,9,11,13,15-Octaazapentacyclo[9.5.1.1^3,9.0^6,18.0^14,17]octadecane-4,8,12,16-tetrone monohydrate: a methylene-bridged glycoluril dimer