Diethyl 2,6-bis­(4-ethynylphen­yl)-4,8-dioxoperhydro-2,3a,4a,6,7a,8a-hexa­aza-cyclo­penta­[def]fluorene-8b,8c-dicarboxyl­ate

The mol­ecule of the title compound, C₃₀H₂₈N₆O₆, a glycoluril derivative, lies on a twofold rotation axis with two ethyl acetate groups bonded to the convex face of the glycoluril system. The dihedral angle between the imidazolone rings is 73.12 (3)°. Two symmetry-equivalent six-membered triazine rings are fused to the glycouril unit to form rigid side walls of a mol­ecular clip. The crystal structure is stabilized by weak inter­molecular C—H...O hydrogen bonds. The ethyl ester group is disordered over two sites of occupancy 0.539 (7) and 0.461 (7).

Key indicators

• Single-crystal X-ray study
• T = 294 K
• Mean [sigma](C-C) = 0.003 Å
• Disorder in main residue
• R factor = 0.053
• wR factor = 0.147
• Data-to-parameter ratio = 13.3

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for         O2
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        C13
PLAT301_ALERT_3_C Main Residue  Disorder .........................      16.00 Perc.
PLAT371_ALERT_2_C Long   C(sp2)-C(sp1) Bond  C2     -   C3     ...       1.44 Ang.

Alert level G
PLAT793_ALERT_1_G Check the Absolute Configuration of C12    = ...          R
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......         11

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   4 ALERT level C = Check and explain
   2 ALERT level G = General alerts; check

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   3 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

---

S1. Comment

Glycoluryl derivatives have been employed in many applications, including polymer cross-linking, explosives, stabilization of organic compounds against photo-degradation, textile waste, stream purfication, and comblinational chemistry (Witt et al., 2000). They are also used as building blocks for self assembly, molecular recognition, and catalysis (Rebek, 2005; Rowan et al., 1999). In this paper we report the crystal structure of the title glycoluryl derivative, (I)(Fig. 1), in which the dihedral angle between the imidazolone rings of the glycouril unit is 73.12 (3) ° and the dihedral angle between two phenyl ring is 16.82 (4)°. The molecule lies on a crystallographic twofold axis. In the crystal structure, molecules are connected by wek intermolecular C—H···O hydrogen bonds (Fig. 2).

Related literature

For related literature, see: Yin et al. (2006); Rebek (2005); Rowan et al. (1999); Witt et al. (2000).

S2. Experimental

The title compound was synthesized in analogy to the literature procedure of Yin et al. (2006), Crystals appropriate for data collection were obtained by slow evaporation from a methanol-chloroform solution (1:20 V/V) of (I).

S3. Refinement

The H atoms were constrained to an ideal geometry and constrained to ride on their parent atoms as follows: methylene H with d(C—H)=0.97 Å and U_iso(H) = 1.2U_eq(C); methine H with d(C—H)=0.98 Å and U_iso(H) = 1.2U_eq(C); aromatic H with d(C—H)=0.93 Å and U_iso(H) = 1.2U_eq(C). The unique ethyl acetate group is disorder over two sites; the site-occupancy factors for the two orientations were refined using the DFIX instruction in SHELXTL (Sheldrick, 2000) giving 0.539 (7) and 0.461 (7) for the major and minor components, respectively.

Computing details

Data collection: SMART (Bruker, 2001); cell refinement: SAINT-Plus (Bruker, 2001); data reduction: SAINT-Plus (Bruker, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Sheldrick, 2000); software used to prepare material for publication: SHELXTL (Sheldrick, 2000).

Figures

	Fig. 1. The molecular structure showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms atoms shown as circles of arbitrary radii.
	Fig. 2. The molecular packing of viewed along the b axis. Hydrogen bonds are shown as dashed lines

Diethyl 2,6-bis(4-ethynylphenyl)-4,8-dioxoperhydro- 2,3a,4a,6,7a,8a-hexaaza-cyclopenta[def]fluorene-8 b,8c-dicarboxylate

Crystal data

C30H28N6O6	F(000) = 1192
Mr = 568.58	Dx = 1.347 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 3199 reflections
a = 16.0226 (10) Å	θ = 2.2–22.7°
b = 14.0617 (9) Å	µ = 0.10 mm^−1
c = 13.7870 (9) Å	T = 294 K
β = 115.523 (1)°	Plate, colorless
V = 2803.1 (3) Å^3	0.30 × 0.20 × 0.04 mm
Z = 4

Data collection

Bruker SMART CCD area-detector diffractometer	1952 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.055
Graphite monochromator	θmax = 27.0°, θmin = 2.0°
/f and /w scans	h = −20→20
12898 measured reflections	k = −17→17
3057 independent reflections	l = −16→17

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.053	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.147	H-atom parameters constrained
S = 1.05	w = 1/[σ^2(Fo^2) + (0.0768P)^2] where P = (Fo^2 + 2Fc^2)/3
3057 reflections	(Δ/σ)max = 0.001
229 parameters	Δρmax = 0.16 e Å^−3
11 restraints	Δρmin = −0.18 e Å^−3

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 (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
C1	0.1661 (2)	1.5590 (2)	0.3141 (2)	0.1019 (9)
H1	0.1691	1.6246	0.3076	0.122*
C2	0.16248 (15)	1.47641 (18)	0.32223 (18)	0.0773 (6)
C3	0.16116 (13)	1.37528 (14)	0.33657 (15)	0.0638 (5)
C4	0.22584 (14)	1.31674 (15)	0.32419 (17)	0.0687 (6)
H4	0.2685	1.3429	0.3027	0.082*
C5	0.22749 (13)	1.22119 (14)	0.34323 (17)	0.0668 (5)
H5	0.2722	1.1837	0.3357	0.080*
C6	0.16372 (12)	1.17853 (13)	0.37371 (14)	0.0581 (5)
C7	0.09803 (13)	1.23665 (15)	0.38301 (17)	0.0692 (6)
H7	0.0535	1.2102	0.4013	0.083*
C8	0.09754 (14)	1.33303 (16)	0.36569 (18)	0.0715 (6)
H8	0.0532	1.3707	0.3738	0.086*
C9	0.19180 (13)	1.01352 (14)	0.33255 (17)	0.0676 (5)
H9A	0.2329	0.9646	0.3778	0.081*
H9B	0.2233	1.0459	0.2958	0.081*
C10	0.05180 (13)	1.02199 (11)	0.16204 (14)	0.0521 (4)
C11	−0.11956 (15)	1.03730 (15)	0.04899 (15)	0.0683 (6)
H11A	−0.1018	1.0856	0.0112	0.082*
H11B	−0.1581	0.9911	−0.0034	0.082*
C12	−0.04897 (13)	0.92670 (11)	0.20293 (14)	0.0525 (4)
C13	−0.08516 (16)	0.82917 (14)	0.15162 (19)	0.0730 (6)
N1	0.17227 (11)	1.08128 (11)	0.39963 (13)	0.0654 (5)
N2	0.10735 (10)	0.96859 (9)	0.25254 (12)	0.0535 (4)
N3	−0.03683 (10)	0.99023 (9)	0.12713 (11)	0.0528 (4)
O1	0.07893 (9)	1.08330 (8)	0.12080 (11)	0.0660 (4)
C14	−0.0932 (6)	0.7206 (4)	0.0159 (6)	0.101 (2)	0.539 (7)
H14A	−0.1119	0.7359	−0.0592	0.121*	0.539 (7)
H14B	−0.1472	0.6988	0.0242	0.121*	0.539 (7)
C15	−0.0228 (4)	0.6458 (4)	0.0495 (6)	0.118 (3)	0.539 (7)
H15A	0.0320	0.6694	0.0460	0.176*	0.539 (7)
H15B	−0.0459	0.5920	0.0027	0.176*	0.539 (7)
H15C	−0.0085	0.6271	0.1219	0.176*	0.539 (7)
O2	−0.0548 (5)	0.8049 (4)	0.0821 (6)	0.107 (3)	0.539 (7)
O3	−0.1358 (6)	0.7852 (5)	0.1785 (7)	0.097 (2)	0.539 (7)
C14'	−0.0331 (5)	0.6950 (4)	0.0815 (5)	0.0825 (19)	0.461 (7)
H14C	0.0255	0.6739	0.0841	0.099*	0.461 (7)
H14D	−0.0503	0.6516	0.1245	0.099*	0.461 (7)
C15'	−0.1034 (6)	0.6932 (6)	−0.0291 (5)	0.097 (3)	0.461 (7)
H15D	−0.1621	0.7105	−0.0312	0.145*	0.461 (7)
H15E	−0.1073	0.6304	−0.0580	0.145*	0.461 (7)
H15F	−0.0873	0.7376	−0.0712	0.145*	0.461 (7)
O2'	−0.0227 (4)	0.7905 (4)	0.1261 (6)	0.084 (2)	0.461 (7)
O3'	−0.1586 (6)	0.7929 (7)	0.1352 (9)	0.109 (4)	0.461 (7)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.127 (2)	0.0702 (16)	0.137 (2)	0.0139 (15)	0.085 (2)	0.0180 (16)
C2	0.0842 (14)	0.0712 (16)	0.0856 (16)	0.0025 (12)	0.0453 (13)	0.0057 (12)
C3	0.0683 (12)	0.0612 (12)	0.0584 (12)	−0.0044 (9)	0.0239 (10)	0.0000 (10)
C4	0.0735 (12)	0.0670 (13)	0.0736 (14)	−0.0136 (10)	0.0392 (11)	−0.0070 (10)
C5	0.0659 (11)	0.0654 (13)	0.0750 (14)	−0.0075 (10)	0.0360 (11)	−0.0087 (10)
C6	0.0621 (11)	0.0605 (12)	0.0471 (11)	−0.0111 (9)	0.0192 (9)	−0.0062 (9)
C7	0.0709 (12)	0.0709 (14)	0.0740 (14)	−0.0071 (10)	0.0390 (11)	−0.0002 (11)
C8	0.0704 (12)	0.0725 (14)	0.0779 (14)	0.0019 (10)	0.0380 (12)	−0.0010 (11)
C9	0.0668 (12)	0.0601 (12)	0.0805 (14)	0.0043 (9)	0.0362 (11)	0.0062 (11)
C10	0.0793 (12)	0.0375 (9)	0.0562 (11)	0.0047 (8)	0.0449 (10)	−0.0012 (8)
C11	0.0872 (14)	0.0668 (13)	0.0500 (11)	0.0066 (10)	0.0287 (11)	−0.0030 (9)
C12	0.0731 (10)	0.0372 (9)	0.0579 (11)	−0.0034 (8)	0.0385 (9)	−0.0049 (7)
C13	0.1027 (17)	0.0463 (11)	0.0882 (16)	−0.0129 (11)	0.0583 (15)	−0.0129 (11)
N1	0.0766 (10)	0.0620 (10)	0.0602 (10)	−0.0104 (8)	0.0319 (9)	−0.0036 (8)
N2	0.0677 (9)	0.0414 (8)	0.0615 (10)	0.0025 (7)	0.0375 (8)	0.0033 (7)
N3	0.0726 (10)	0.0453 (8)	0.0467 (8)	0.0002 (7)	0.0315 (8)	−0.0002 (6)
O1	0.0950 (10)	0.0526 (8)	0.0732 (9)	0.0010 (6)	0.0577 (8)	0.0087 (6)
C14	0.153 (7)	0.064 (4)	0.090 (6)	−0.026 (4)	0.057 (6)	−0.038 (4)
C15	0.140 (5)	0.085 (4)	0.148 (6)	−0.007 (4)	0.081 (5)	−0.030 (4)
O2	0.190 (6)	0.073 (3)	0.103 (5)	−0.056 (4)	0.106 (5)	−0.048 (3)
O3	0.163 (5)	0.051 (2)	0.115 (6)	−0.044 (2)	0.096 (4)	−0.038 (3)
C14'	0.111 (5)	0.057 (4)	0.086 (5)	−0.002 (4)	0.048 (4)	−0.025 (3)
C15'	0.129 (6)	0.078 (6)	0.085 (5)	−0.032 (5)	0.047 (4)	−0.023 (4)
O2'	0.125 (4)	0.055 (2)	0.094 (5)	−0.006 (2)	0.069 (4)	−0.030 (3)
O3'	0.141 (5)	0.101 (5)	0.128 (8)	−0.063 (4)	0.100 (6)	−0.057 (5)

Geometric parameters (Å, º)

C1—C2	1.170 (3)	C12—N2^i	1.447 (2)
C1—H1	0.9300	C12—N3	1.450 (2)
C2—C3	1.437 (3)	C12—C13	1.538 (3)
C3—C8	1.381 (3)	C12—C12^i	1.547 (4)
C3—C4	1.390 (3)	C13—O3	1.200 (5)
C4—C5	1.367 (3)	C13—O3'	1.211 (6)
C4—H4	0.9300	C13—O2	1.294 (4)
C5—C6	1.397 (2)	C13—O2'	1.314 (5)
C5—H5	0.9300	N1—C11^i	1.454 (2)
C6—C7	1.381 (3)	N2—C12^i	1.447 (2)
C6—N1	1.405 (2)	C14—O2	1.460 (6)
C7—C8	1.376 (3)	C14—C15	1.463 (7)
C7—H7	0.9300	C14—H14A	0.9700
C8—H8	0.9300	C14—H14B	0.9700
C9—N1	1.453 (2)	C15—H15A	0.9600
C9—N2	1.470 (2)	C15—H15B	0.9600
C9—H9A	0.9700	C15—H15C	0.9600
C9—H9B	0.9700	C14'—C15'	1.455 (7)
C10—O1	1.2118 (19)	C14'—O2'	1.456 (6)
C10—N3	1.363 (2)	C14'—H14C	0.9700
C10—N2	1.399 (2)	C14'—H14D	0.9700
C11—N1^i	1.454 (2)	C15'—H15D	0.9600
C11—N3	1.458 (2)	C15'—H15E	0.9600
C11—H11A	0.9700	C15'—H15F	0.9600
C11—H11B	0.9700
C2—C1—H1	180.0	N3—C12—C12^i	101.66 (14)
C1—C2—C3	177.6 (3)	C13—C12—C12^i	115.55 (12)
C8—C3—C4	117.63 (19)	O3—C13—O2	127.8 (4)
C8—C3—C2	121.48 (18)	O3'—C13—O2	113.3 (5)
C4—C3—C2	120.86 (17)	O3—C13—O2'	124.3 (5)
C5—C4—C3	120.80 (18)	O3'—C13—O2'	124.5 (5)
C5—C4—H4	119.6	O3—C13—C12	119.3 (3)
C3—C4—H4	119.6	O3'—C13—C12	127.3 (4)
C4—C5—C6	121.58 (18)	O2—C13—C12	112.9 (3)
C4—C5—H5	119.2	O2'—C13—C12	108.2 (3)
C6—C5—H5	119.2	C6—N1—C9	120.04 (15)
C7—C6—C5	117.35 (18)	C6—N1—C11^i	121.63 (16)
C7—C6—N1	123.15 (16)	C9—N1—C11^i	111.16 (15)
C5—C6—N1	119.38 (17)	C10—N2—C12^i	108.53 (14)
C8—C7—C6	120.95 (17)	C10—N2—C9	117.71 (15)
C8—C7—H7	119.5	C12^i—N2—C9	114.26 (14)
C6—C7—H7	119.5	C10—N3—C12	112.96 (14)
C7—C8—C3	121.65 (19)	C10—N3—C11	126.10 (15)
C7—C8—H8	119.2	C12—N3—C11	116.78 (15)
C3—C8—H8	119.2	O2—C14—C15	109.0 (6)
N1—C9—N2	112.24 (14)	O2—C14—H14A	109.9
N1—C9—H9A	109.2	C15—C14—H14A	109.9
N2—C9—H9A	109.2	O2—C14—H14B	109.9
N1—C9—H9B	109.2	C15—C14—H14B	109.9
N2—C9—H9B	109.2	H14A—C14—H14B	108.3
H9A—C9—H9B	107.9	C13—O2—C14	119.1 (5)
O1—C10—N3	126.66 (17)	C15'—C14'—O2'	110.8 (6)
O1—C10—N2	125.56 (17)	C15'—C14'—H14C	109.5
N3—C10—N2	107.74 (14)	O2'—C14'—H14C	109.5
N1^i—C11—N3	111.55 (14)	C15'—C14'—H14D	109.5
N1^i—C11—H11A	109.3	O2'—C14'—H14D	109.5
N3—C11—H11A	109.3	H14C—C14'—H14D	108.1
N1^i—C11—H11B	109.3	C14'—C15'—H15D	109.5
N3—C11—H11B	109.3	C14'—C15'—H15E	109.5
H11A—C11—H11B	108.0	H15D—C15'—H15E	109.5
N2^i—C12—N3	111.53 (13)	C14'—C15'—H15F	109.5
N2^i—C12—C13	111.95 (14)	H15D—C15'—H15F	109.5
N3—C12—C13	111.03 (14)	H15E—C15'—H15F	109.5
N2^i—C12—C12^i	104.58 (15)	C13—O2'—C14'	122.2 (5)

Symmetry code: (i) −x, y, −z+1/2.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1···O3^ii	0.93	2.35	3.226 (7)	158

Symmetry code: (ii) −x, y+1, −z+1/2.