A DMSO-capped dimeric glycoluril derivative

The crystal structure of the title compound, 1,2,3,4,8,13-hexa­hydro-4a,14-(iminomethano)-4aH,14H-benzimidazo­[1,7a-b][2,4]­benzodiazepine-6,15(5H)-dione di­methyl sulfoxide solvate, C₁₆H₁₈N₄O₂·C₂H₆OS, is reported. Unlike related glycoluril-derived compounds which form hydrogen-bonded tapes when crystallized from solvents of lower polarity, the title compound forms discrete hydrogen-bonded dimers in the crystal. Solvent mol­ecules cap these dimers by accepting hydrogen bonds from their edges and thus prevent further supramolecular assembly.

Key indicators

• Single-crystal X-ray study
• T = 193 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.041
• wR factor = 0.123
• Data-to-parameter ratio = 12.8

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT338_ALERT_2_C Small Average Tau in cyclohexane C2     -C8           34.31 Deg.

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

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

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Computing details

Data collection: SMART (Bruker , 2001); cell refinement: SMART; data reduction: SAINT (Bruker , 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Sheldrick, 1994); software used to prepare material for publication: SHELXTL.

(I)

Crystal data

C16H18N4O2·C2H6OS	F(000) = 800
Mr = 376.47	Dx = 1.357 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 5047 reflections
a = 6.6874 (2) Å	θ = 2.5–28.5°
b = 16.5431 (5) Å	µ = 0.20 mm^−1
c = 16.7931 (5) Å	T = 193 K
β = 97.363 (1)°	Block, colorless
V = 1842.51 (10) Å^3	0.41 × 0.26 × 0.13 mm
Z = 4

Data collection

Bruker SMART CCD area-detector diffractometer	4232 independent reflections
Radiation source: fine-focus sealed tube	3620 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.016
φ and ω scans	θmax = 27.5°, θmin = 1.7°
Absorption correction: empirical (using intensity measurements) (SADABS; Blessing, 1995; Sheldrick, 1996)	h = −6→8
Tmin = 0.932, Tmax = 0.975	k = −21→21
19374 measured reflections	l = −21→21

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: structure-invariant direct methods
R[F^2 > 2σ(F^2)] = 0.041	Hydrogen site location: difference Fourier map
wR(F^2) = 0.123	All H-atom parameters refined
S = 1.11	w = 1/[σ^2(Fo^2) + (0.0666P)^2 + 0.4304P] where P = (Fo^2 + 2Fc^2)/3
4232 reflections	(Δ/σ)max < 0.001
331 parameters	Δρmax = 0.45 e Å^−3
0 restraints	Δρmin = −0.42 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 > 2σ(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.

The final structure of (I) was refined to convergence [Δ/σ < 0.001] with R(F) = 4.83%, wR(F²) = 12.28%, GOF = 1.108 for all 4232 unique reflections [R(F) = 4.12%, wR(F²) = 11.69% for those 3620 data with F_o > 4σ(F_o)]. The final difference-Fourier map was featureless indicating that the structure is both correct and complete.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	0.6359 (2)	0.09979 (7)	0.46296 (7)	0.0320 (3)
N1	0.83158 (18)	0.25679 (6)	0.56403 (7)	0.0344 (2)
O1	0.49572 (16)	0.07349 (6)	0.41481 (6)	0.0405 (2)
C2	0.89146 (19)	0.18602 (7)	0.52140 (7)	0.0304 (3)
H2	0.775 (3)	0.1352 (11)	0.6908 (11)	0.045 (5)*
N2	0.7883 (2)	0.15698 (7)	0.64730 (7)	0.0396 (3)
C3	0.76470 (19)	0.23783 (8)	0.63595 (8)	0.0344 (3)
H3	0.655 (3)	0.0244 (11)	0.5549 (10)	0.041 (4)*
N3	0.70792 (19)	0.06634 (7)	0.53477 (7)	0.0387 (3)
O3	0.70014 (18)	0.28650 (6)	0.68126 (6)	0.0473 (3)
C4	0.86170 (18)	0.11529 (7)	0.58104 (7)	0.0302 (3)
N4	0.74885 (17)	0.16639 (6)	0.45117 (6)	0.0336 (2)
C5	1.0553 (2)	0.06868 (10)	0.60702 (9)	0.0418 (3)
H5A	1.087 (3)	0.0366 (12)	0.5583 (12)	0.059 (5)*
H5B	1.029 (3)	0.0320 (13)	0.6483 (13)	0.065 (6)*
C6	1.2291 (3)	0.12588 (16)	0.63536 (11)	0.0629 (5)
H6A	1.345 (4)	0.0958 (16)	0.6480 (15)	0.091 (8)*
H6B	1.208 (4)	0.1474 (15)	0.6842 (16)	0.082 (7)*
C7	1.2586 (2)	0.19334 (11)	0.57647 (13)	0.0548 (4)
H7A	1.252 (4)	0.2477 (17)	0.6017 (17)	0.098 (8)*
H7B	1.403 (4)	0.1918 (14)	0.5609 (15)	0.086 (7)*
C8	1.1076 (2)	0.19126 (10)	0.50119 (10)	0.0441 (3)
H8A	1.129 (3)	0.1425 (11)	0.4668 (10)	0.042 (4)*
H8B	1.121 (3)	0.2401 (12)	0.4707 (11)	0.051 (5)*
C9	0.6993 (2)	0.22307 (8)	0.38485 (8)	0.0389 (3)
C9A	0.5513 (2)	0.28799 (8)	0.40256 (8)	0.0374 (3)
H9A	0.643 (3)	0.1909 (11)	0.3360 (11)	0.050 (5)*
H9B	0.828 (3)	0.2488 (11)	0.3734 (11)	0.050 (5)*
C10	0.3721 (3)	0.29819 (10)	0.35129 (10)	0.0500 (4)
H10	0.345 (3)	0.2628 (11)	0.3078 (11)	0.044 (4)*
C11	0.2316 (3)	0.35680 (12)	0.36645 (13)	0.0599 (5)
H11	0.114 (4)	0.3629 (13)	0.3323 (13)	0.066 (6)*
C12	0.2691 (3)	0.40479 (11)	0.43322 (13)	0.0573 (5)
H12	0.174 (4)	0.4468 (13)	0.4442 (13)	0.067 (6)*
C13	0.4480 (3)	0.39593 (9)	0.48478 (10)	0.0471 (4)
C13A	0.5911 (2)	0.33871 (8)	0.46985 (8)	0.0369 (3)
H13	0.478 (3)	0.4318 (11)	0.5315 (11)	0.049 (5)*
C14	0.7898 (2)	0.33442 (8)	0.52454 (9)	0.0405 (3)
H14A	0.898 (3)	0.3475 (10)	0.4929 (11)	0.045 (4)*
H14B	0.788 (3)	0.3765 (11)	0.5671 (11)	0.050 (5)*
O21	0.1800 (3)	−0.05242 (9)	0.21689 (8)	0.0733 (4)
S21	0.25130 (8)	0.02180 (3)	0.17891 (2)	0.06110 (17)
C22	0.5102 (3)	0.03347 (12)	0.21644 (12)	0.0587 (5)
H22A	0.527 (3)	0.0328 (13)	0.2736 (14)	0.066 (6)*
H22B	0.561 (4)	0.0848 (15)	0.1975 (14)	0.078 (7)*
H22C	0.584 (4)	−0.0117 (15)	0.1949 (15)	0.079 (7)*
C23	0.1626 (5)	0.10608 (18)	0.23081 (19)	0.0865 (8)
H23A	0.027 (5)	0.1049 (18)	0.2180 (18)	0.105 (10)*
H23B	0.209 (5)	0.153 (2)	0.2079 (19)	0.107 (10)*
H23C	0.214 (4)	0.1018 (16)	0.2906 (17)	0.086 (7)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0355 (6)	0.0305 (6)	0.0300 (6)	0.0001 (5)	0.0045 (5)	−0.0017 (5)
N1	0.0408 (6)	0.0294 (5)	0.0324 (5)	0.0012 (4)	0.0029 (4)	−0.0037 (4)
O1	0.0467 (6)	0.0393 (5)	0.0332 (5)	−0.0075 (4)	−0.0043 (4)	−0.0012 (4)
C2	0.0306 (6)	0.0299 (6)	0.0307 (6)	−0.0003 (5)	0.0042 (5)	−0.0017 (5)
N2	0.0504 (7)	0.0376 (6)	0.0338 (6)	0.0022 (5)	0.0167 (5)	−0.0007 (5)
C3	0.0311 (6)	0.0368 (6)	0.0349 (6)	−0.0014 (5)	0.0027 (5)	−0.0073 (5)
N3	0.0431 (6)	0.0359 (6)	0.0345 (6)	−0.0108 (5)	−0.0048 (5)	0.0059 (5)
O3	0.0543 (6)	0.0444 (6)	0.0448 (6)	0.0030 (5)	0.0122 (5)	−0.0142 (4)
C4	0.0303 (6)	0.0315 (6)	0.0288 (6)	0.0002 (5)	0.0042 (4)	−0.0016 (4)
N4	0.0416 (6)	0.0312 (5)	0.0273 (5)	−0.0027 (4)	0.0022 (4)	0.0002 (4)
C5	0.0362 (7)	0.0464 (8)	0.0426 (7)	0.0088 (6)	0.0046 (6)	0.0082 (6)
C6	0.0349 (8)	0.1043 (16)	0.0471 (9)	−0.0106 (9)	−0.0038 (7)	0.0088 (10)
C7	0.0323 (8)	0.0505 (9)	0.0794 (12)	−0.0016 (6)	−0.0007 (7)	−0.0050 (8)
C8	0.0356 (7)	0.0464 (8)	0.0525 (8)	0.0006 (6)	0.0141 (6)	0.0082 (7)
C9	0.0529 (8)	0.0363 (7)	0.0277 (6)	−0.0025 (6)	0.0062 (6)	0.0026 (5)
C9A	0.0440 (7)	0.0340 (6)	0.0338 (6)	−0.0031 (5)	0.0038 (5)	0.0100 (5)
C10	0.0579 (10)	0.0459 (8)	0.0431 (8)	−0.0065 (7)	−0.0060 (7)	0.0171 (7)
C11	0.0462 (9)	0.0591 (10)	0.0715 (12)	0.0015 (8)	−0.0030 (8)	0.0359 (9)
C12	0.0531 (10)	0.0476 (9)	0.0746 (12)	0.0132 (7)	0.0209 (9)	0.0289 (9)
C13	0.0592 (9)	0.0347 (7)	0.0506 (8)	0.0077 (6)	0.0187 (7)	0.0127 (6)
C13A	0.0441 (7)	0.0296 (6)	0.0380 (7)	−0.0001 (5)	0.0088 (5)	0.0071 (5)
C14	0.0489 (8)	0.0289 (6)	0.0430 (7)	−0.0027 (6)	0.0028 (6)	−0.0027 (5)
O21	0.0928 (11)	0.0696 (8)	0.0548 (7)	−0.0407 (8)	−0.0004 (7)	0.0151 (6)
S21	0.0855 (4)	0.0587 (3)	0.0359 (2)	−0.0266 (2)	−0.0044 (2)	0.01075 (17)
C22	0.0736 (12)	0.0551 (10)	0.0500 (10)	−0.0155 (9)	0.0185 (9)	−0.0047 (8)
C23	0.0872 (19)	0.0778 (16)	0.0880 (18)	0.0202 (14)	−0.0131 (14)	0.0134 (13)

Geometric parameters (Å, º)

C1—O1	1.2358 (16)	C8—H8B	0.97 (2)
C1—N3	1.3578 (17)	C9—C9A	1.516 (2)
C1—N4	1.3647 (16)	C9—H9A	1.010 (19)
N1—C3	1.3767 (17)	C9—H9B	1.002 (19)
N1—C2	1.4550 (16)	C9A—C10	1.393 (2)
N1—C14	1.4559 (17)	C9A—C13A	1.405 (2)
C2—N4	1.4553 (16)	C10—C11	1.397 (3)
C2—C8	1.5287 (19)	C10—H10	0.936 (18)
C2—C4	1.5694 (17)	C11—C12	1.370 (3)
N2—C3	1.3574 (18)	C11—H11	0.92 (2)
N2—C4	1.4474 (16)	C12—C13	1.392 (3)
N2—H2	0.829 (19)	C12—H12	0.98 (2)
C3—O3	1.2239 (16)	C13—C13A	1.392 (2)
N3—C4	1.4533 (16)	C13—H13	0.984 (19)
N3—H3	0.869 (18)	C13A—C14	1.517 (2)
C4—C5	1.5219 (18)	C14—H14A	0.977 (19)
N4—C9	1.4610 (17)	C14—H14B	0.998 (19)
C5—C6	1.527 (3)	O21—S21	1.4900 (13)
C5—H5A	1.02 (2)	S21—C22	1.776 (2)
C5—H5B	0.95 (2)	S21—C23	1.786 (3)
C6—C7	1.521 (3)	C22—H22A	0.95 (2)
C6—H6A	0.92 (3)	C22—H22B	0.98 (2)
C6—H6B	0.92 (3)	C22—H22C	0.99 (3)
C7—C8	1.514 (2)	C23—H23A	0.91 (3)
C7—H7A	1.00 (3)	C23—H23B	0.93 (3)
C7—H7B	1.03 (3)	C23—H23C	1.02 (3)
C8—H8A	1.013 (17)
O1—C1—N3	126.21 (12)	C2—C8—H8A	106.9 (10)
O1—C1—N4	125.23 (12)	C7—C8—H8B	109.1 (11)
N3—C1—N4	108.53 (11)	C2—C8—H8B	108.5 (11)
C3—N1—C2	112.90 (10)	H8A—C8—H8B	109.5 (14)
C3—N1—C14	122.39 (11)	N4—C9—C9A	113.29 (11)
C2—N1—C14	122.31 (11)	N4—C9—H9A	107.8 (10)
N1—C2—N4	112.66 (10)	C9A—C9—H9A	110.2 (11)
N1—C2—C8	113.04 (11)	N4—C9—H9B	107.6 (11)
N4—C2—C8	111.88 (11)	C9A—C9—H9B	109.6 (11)
N1—C2—C4	102.74 (9)	H9A—C9—H9B	108.2 (15)
N4—C2—C4	103.14 (9)	C10—C9A—C13A	118.95 (14)
C8—C2—C4	112.63 (11)	C10—C9A—C9	119.74 (14)
C3—N2—C4	113.97 (11)	C13A—C9A—C9	121.31 (13)
C3—N2—H2	121.8 (12)	C9A—C10—C11	121.14 (17)
C4—N2—H2	123.8 (12)	C9A—C10—H10	118.3 (11)
O3—C3—N2	127.21 (13)	C11—C10—H10	120.5 (11)
O3—C3—N1	125.15 (13)	C12—C11—C10	119.64 (17)
N2—C3—N1	107.63 (11)	C12—C11—H11	120.0 (14)
C1—N3—C4	113.21 (11)	C10—C11—H11	120.4 (14)
C1—N3—H3	123.7 (12)	C11—C12—C13	120.04 (17)
C4—N3—H3	122.4 (12)	C11—C12—H12	120.8 (14)
N2—C4—N3	112.96 (11)	C13—C12—H12	119.1 (14)
N2—C4—C5	112.39 (11)	C13A—C13—C12	121.06 (17)
N3—C4—C5	112.87 (11)	C13A—C13—H13	118.8 (11)
N2—C4—C2	102.63 (10)	C12—C13—H13	120.1 (11)
N3—C4—C2	102.31 (10)	C13—C13A—C9A	119.16 (14)
C5—C4—C2	112.82 (11)	C13—C13A—C14	119.48 (14)
C1—N4—C2	112.34 (10)	C9A—C13A—C14	121.32 (13)
C1—N4—C9	123.57 (11)	N1—C14—C13A	114.78 (11)
C2—N4—C9	122.39 (11)	N1—C14—H14A	109.3 (10)
C4—C5—C6	111.16 (15)	C13A—C14—H14A	108.4 (11)
C4—C5—H5A	107.0 (12)	N1—C14—H14B	107.9 (10)
C6—C5—H5A	110.0 (12)	C13A—C14—H14B	108.2 (11)
C4—C5—H5B	107.4 (13)	H14A—C14—H14B	108.1 (15)
C6—C5—H5B	111.9 (13)	O21—S21—C22	106.78 (10)
H5A—C5—H5B	109.2 (17)	O21—S21—C23	106.85 (14)
C7—C6—C5	114.15 (14)	C22—S21—C23	96.41 (13)
C7—C6—H6A	111.6 (17)	S21—C22—H22A	109.9 (13)
C5—C6—H6A	108.8 (17)	S21—C22—H22B	109.9 (15)
C7—C6—H6B	110.0 (16)	H22A—C22—H22B	109.6 (19)
C5—C6—H6B	108.7 (16)	S21—C22—H22C	107.2 (15)
H6A—C6—H6B	103 (2)	H22A—C22—H22C	111 (2)
C8—C7—C6	113.46 (14)	H22B—C22—H22C	109.0 (19)
C8—C7—H7A	108.3 (16)	S21—C23—H23A	105 (2)
C6—C7—H7A	111.7 (16)	S21—C23—H23B	107 (2)
C8—C7—H7B	109.4 (14)	H23A—C23—H23B	107 (3)
C6—C7—H7B	110.5 (14)	S21—C23—H23C	109.6 (15)
H7A—C7—H7B	102.9 (19)	H23A—C23—H23C	116 (2)
C7—C8—C2	111.36 (13)	H23B—C23—H23C	112 (2)
C7—C8—H8A	111.4 (10)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···O21^i	0.829 (19)	2.062 (19)	2.8484 (18)	158.2 (17)
N3—H3···O1^i	0.869 (18)	2.005 (19)	2.8667 (15)	171.2 (17)

Symmetry code: (i) −x+1, −y, −z+1.