Ethyl 2-hydr­oxy-5,11-dioxopyrrolo[2,1-c][1,4]benzodiazepine-10-acetate

Ourahou, S.; Chammache, M.; Zouihri, H.; Essassi, E.M.; Ng, S.W.

doi:10.1107/S1600536810006914

organic compounds

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ISSN: 2056-9890

Volume 66| Part 4| April 2010| Page o733

doi:10.1107/S1600536810006914

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Ethyl 2-hydroxy-5,11-dioxopyrrolo[2,1-c][1,4]benzodiazepine-10-acetate

S. Ourahou,^a M. Chammache,^a H. Zouihri,^b El Mokhtar Essassi ^a and Seik Weng Ng ^c ^*

^aLaboratoire de Chimie Organique Hétérocyclique, Pôle de Compétences Pharmacochimie, Université Mohammed V-Agdal, BP 1014 Avenue Ibn Batout, Rabat, Morocco, ^bCNRST, Division of UATRS Angle Allal Fassi/FAR, BP 8027 Hay Riad, 10000 Rabat, Morocco, and ^cDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
^*Correspondence e-mail: seikweng@um.edu.my

(Received 21 February 2010; accepted 23 February 2010; online 3 March 2010)

The title compound, C₁₆H₁₈N₂O₅, consists of a benzodiazepinedione system fused to a pyrrole system. The seven-membered ring adopts a boat-shaped conformation (with the methine C atom as the prow); the five-membered ring adopts an enveloped-shaped conformation (with the hydroxy-bearing C atom as the flap). The hydroxy group is hydrogen bonded to the carbonyl O atom of an adjacent molecule generating a zigzag chain in the crystal structure.

Related literature

Pyrrolo[2,1-c][1,4]benzodiazepines are potent antibiotics produced by Streptomyces species; see: Cargill et al. (1974 ). For the design of DNA inter-strand cross-linking as well as of conjugate agents to enhance the sequence selectivity and selectivity for tumor cells, see: Gregson et al. (2004 ).

Experimental

Crystal data

C₁₆H₁₈N₂O₅
M_r = 318.32
Orthorhombic, P 2₁ 2₁ 2₁
a = 8.5503 (2) Å
b = 9.6580 (2) Å
c = 18.2734 (4) Å
V = 1509.00 (6) Å³
Z = 4
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 293 K
0.3 × 0.3 × 0.3 mm

Data collection

Bruker APEXII diffractometer
11809 measured reflections
1907 independent reflections
1765 reflections with I > 2σ(I)
R_int = 0.024

Refinement

R[F² > 2σ(F²)] = 0.032
wR(F²) = 0.098
S = 1.04
1907 reflections
213 parameters
1 restraint
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.21 e Å⁻³
Δρ_min = −0.17 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O3—H3⋯O1ⁱ	0.84 (1)	2.02 (2)	2.810 (2)	157 (4)
Symmetry code: (i) $[-x, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

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: X-SEED (Barbour, 2001 ); software used to prepare material for publication: publCIF (Westrip, 2010 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810006914/bt5201sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536810006914/bt5201Isup2.hkl

checkCIF report

Related literature top

Pyrrolo[2,1-c][1,4]benzodiazepines are potent antibiotics produced by Streptomyces species; see: Cargill et al. (1974). For the design of DNA inter-strand cross-linking as well as of conjugate agents to enhance the sequence selectivity and selectivity for tumor cells, see: Gregson et al. (2004).

Experimental top

2-Hydroxy- pyrrolo[2,1-c][1,4]benzodiazepine-5,11-dione (0.5 g, 2.15 mmol), ethyl bromoacetate (0.45 ml, 4.3 mmol), potassium carbonate (0.6 g, 4.3 mmol) along with a catalytic amount of tetra-n-butyl ammonium bromide were stirred in N,N-dimethylformamide (20 ml) for 24 h. After the completion of the reaction (monitored by TLC), the solid material was removed by filtration and the solvent evaporated under vacuum. Dichloromethane (20 ml) was added and the solution filtered. The solvent was removed and the product purified by recrystallization from ethanol to afford colorless crystals in 80% yield.

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: X-SEED (Barbour, 2001); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top

Fig. 1. Anisotropic displacement ellipsoid plot (Barbour, 2001) of C₁₆H₁₈N₂O₅ at the 50% probability level; hydrogen atoms are drawn as arbitrary radius.

Ethyl 2-hydroxy-5,11-dioxopyrrolo[2,1-c][1,4]benzodiazepine-10-acetate top

Crystal data top

C₁₆H₁₈N₂O₅	F(000) = 672
M_r = 318.32	D_x = 1.401 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 6127 reflections
a = 8.5503 (2) Å	θ = 2.2–32.7°
b = 9.6580 (2) Å	µ = 0.11 mm⁻¹
c = 18.2734 (4) Å	T = 293 K
V = 1509.00 (6) Å³	Block, colorless
Z = 4	0.3 × 0.3 × 0.3 mm

Data collection top

Bruker APEXII diffractometer	1765 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.024
Graphite monochromator	θ_max = 27.5°, θ_min = 3.1°
ϕ and ω scans	h = −10→9
11809 measured reflections	k = −12→12
1907 independent reflections	l = −23→23

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) = 0.098	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	w = 1/[σ²(F_o²) + (0.0709P)² + 0.1392P] where P = (F_o² + 2F_c²)/3
1907 reflections	(Δ/σ)_max = 0.001
213 parameters	Δρ_max = 0.21 e Å⁻³
1 restraint	Δρ_min = −0.17 e Å⁻³

Crystal data top

C₁₆H₁₈N₂O₅	V = 1509.00 (6) Å³
M_r = 318.32	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 8.5503 (2) Å	µ = 0.11 mm⁻¹
b = 9.6580 (2) Å	T = 293 K
c = 18.2734 (4) Å	0.3 × 0.3 × 0.3 mm

Data collection top

Bruker APEXII diffractometer	1765 reflections with I > 2σ(I)
11809 measured reflections	R_int = 0.024
1907 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.032	1 restraint
wR(F²) = 0.098	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	Δρ_max = 0.21 e Å⁻³
1907 reflections	Δρ_min = −0.17 e Å⁻³
213 parameters

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	−0.0674 (2)	1.16444 (16)	−0.01855 (9)	0.0502 (4)
O2	0.1577 (2)	1.04456 (15)	0.23744 (7)	0.0480 (4)
O3	0.2180 (2)	1.50177 (16)	0.09188 (10)	0.0577 (5)
H3	0.277 (3)	1.452 (3)	0.0664 (16)	0.077 (10)*
O4	0.25606 (19)	0.66847 (14)	0.26892 (8)	0.0426 (4)
O5	0.4250 (2)	0.8107 (2)	0.21372 (11)	0.0677 (6)
N1	0.0805 (2)	1.20584 (14)	0.08027 (8)	0.0306 (4)
N2	0.1825 (2)	0.92800 (14)	0.13177 (7)	0.0299 (3)
C1	0.2136 (2)	0.92042 (17)	0.05498 (9)	0.0275 (4)
C2	0.3094 (3)	0.81259 (19)	0.03067 (10)	0.0386 (4)
H2	0.3605	0.7567	0.0645	0.046*
C3	0.3287 (3)	0.7885 (2)	−0.04302 (12)	0.0478 (6)
H3A	0.3932	0.7168	−0.0586	0.057*
C4	0.2530 (3)	0.8699 (2)	−0.09410 (11)	0.0495 (6)
H4	0.2638	0.8517	−0.1438	0.059*
C5	0.1614 (3)	0.9784 (2)	−0.07053 (9)	0.0395 (5)
H5	0.1116	1.0338	−0.1050	0.047*
C6	0.1411 (2)	1.00772 (17)	0.00397 (8)	0.0289 (4)
C7	0.0428 (2)	1.13048 (18)	0.02157 (9)	0.0325 (4)
C8	0.0024 (3)	1.33736 (19)	0.09788 (12)	0.0403 (4)
H8A	−0.0890	1.3219	0.1282	0.048*
H8B	−0.0292	1.3855	0.0537	0.048*
C9	0.1259 (3)	1.41889 (18)	0.13900 (11)	0.0385 (5)
H9	0.0747	1.4784	0.1752	0.046*
C10	0.2186 (3)	1.30721 (18)	0.17856 (11)	0.0383 (4)
H10A	0.1717	1.2869	0.2257	0.046*
H10B	0.3256	1.3371	0.1863	0.046*
C11	0.2141 (2)	1.17906 (16)	0.12901 (9)	0.0270 (3)
H11	0.3111	1.1711	0.1008	0.032*
C12	0.1830 (2)	1.04664 (17)	0.17179 (8)	0.0292 (4)
C13	0.1586 (3)	0.79979 (17)	0.17246 (10)	0.0333 (4)
H13A	0.1398	0.7249	0.1382	0.040*
H13B	0.0663	0.8092	0.2029	0.040*
C14	0.2970 (3)	0.76303 (19)	0.22022 (10)	0.0353 (4)
C15	0.3801 (3)	0.6167 (3)	0.31610 (14)	0.0548 (6)
H15A	0.4280	0.6929	0.3425	0.066*
H15B	0.4602	0.5718	0.2869	0.066*
C16	0.3116 (4)	0.5171 (3)	0.36799 (15)	0.0711 (9)
H16A	0.3933	0.4765	0.3970	0.107*
H16B	0.2580	0.4457	0.3414	0.107*
H16C	0.2390	0.5641	0.3994	0.107*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0530 (10)	0.0443 (7)	0.0533 (8)	0.0063 (8)	−0.0280 (8)	0.0017 (7)
O2	0.0756 (12)	0.0458 (7)	0.0226 (6)	−0.0069 (8)	0.0034 (6)	0.0001 (5)
O3	0.0718 (13)	0.0293 (6)	0.0720 (11)	−0.0031 (8)	0.0311 (10)	0.0004 (7)
O4	0.0435 (9)	0.0418 (7)	0.0425 (7)	−0.0019 (7)	−0.0044 (6)	0.0179 (6)
O5	0.0443 (10)	0.0727 (12)	0.0861 (13)	−0.0162 (10)	−0.0148 (9)	0.0430 (10)
N1	0.0319 (9)	0.0271 (7)	0.0328 (7)	0.0039 (6)	−0.0047 (6)	0.0007 (5)
N2	0.0402 (10)	0.0256 (6)	0.0240 (6)	−0.0003 (6)	0.0007 (6)	0.0043 (5)
C1	0.0333 (10)	0.0243 (7)	0.0250 (7)	−0.0037 (7)	0.0014 (6)	−0.0006 (6)
C2	0.0468 (13)	0.0303 (8)	0.0387 (9)	0.0031 (9)	0.0036 (9)	−0.0004 (7)
C3	0.0591 (16)	0.0382 (9)	0.0462 (11)	0.0012 (10)	0.0159 (11)	−0.0116 (8)
C4	0.0744 (17)	0.0461 (10)	0.0279 (8)	−0.0115 (11)	0.0115 (10)	−0.0091 (8)
C5	0.0553 (14)	0.0376 (9)	0.0255 (8)	−0.0098 (9)	−0.0031 (8)	0.0026 (7)
C6	0.0348 (10)	0.0267 (7)	0.0250 (7)	−0.0057 (7)	−0.0024 (7)	0.0008 (6)
C7	0.0371 (11)	0.0287 (8)	0.0316 (8)	−0.0007 (7)	−0.0070 (7)	0.0061 (6)
C8	0.0391 (12)	0.0301 (8)	0.0516 (10)	0.0083 (8)	0.0007 (9)	0.0006 (8)
C9	0.0464 (13)	0.0264 (8)	0.0428 (10)	0.0008 (8)	0.0135 (9)	−0.0059 (7)
C10	0.0432 (12)	0.0319 (8)	0.0398 (9)	−0.0016 (8)	0.0003 (9)	−0.0115 (7)
C11	0.0292 (10)	0.0258 (7)	0.0259 (7)	−0.0001 (7)	−0.0024 (6)	−0.0019 (6)
C12	0.0322 (10)	0.0314 (7)	0.0239 (7)	−0.0010 (7)	−0.0028 (7)	0.0007 (6)
C13	0.0387 (11)	0.0300 (8)	0.0311 (8)	−0.0042 (7)	−0.0018 (7)	0.0077 (6)
C14	0.0365 (12)	0.0328 (8)	0.0366 (9)	−0.0016 (8)	−0.0015 (8)	0.0095 (7)
C15	0.0501 (15)	0.0564 (12)	0.0579 (13)	0.0070 (12)	−0.0091 (11)	0.0248 (11)
C16	0.080 (2)	0.0770 (17)	0.0566 (14)	0.0242 (17)	0.0073 (14)	0.0332 (13)

Geometric parameters (Å, º) top

O1—C7	1.238 (2)	C5—H5	0.9300
O2—C12	1.219 (2)	C6—C7	1.489 (3)
O3—C9	1.415 (2)	C8—C9	1.517 (3)
O3—H3	0.841 (10)	C8—H8A	0.9700
O4—C14	1.322 (2)	C8—H8B	0.9700
O4—C15	1.455 (3)	C9—C10	1.521 (3)
O5—C14	1.193 (3)	C9—H9	0.9800
N1—C7	1.336 (2)	C10—C11	1.534 (2)
N1—C11	1.471 (2)	C10—H10A	0.9700
N1—C8	1.471 (2)	C10—H10B	0.9700
N2—C12	1.359 (2)	C11—C12	1.522 (2)
N2—C1	1.430 (2)	C11—H11	0.9800
N2—C13	1.459 (2)	C13—C14	1.513 (3)
C1—C2	1.397 (3)	C13—H13A	0.9700
C1—C6	1.402 (2)	C13—H13B	0.9700
C2—C3	1.376 (3)	C15—C16	1.472 (3)
C2—H2	0.9300	C15—H15A	0.9700
C3—C4	1.381 (3)	C15—H15B	0.9700
C3—H3A	0.9300	C16—H16A	0.9600
C4—C5	1.377 (3)	C16—H16B	0.9600
C4—H4	0.9300	C16—H16C	0.9600
C5—C6	1.401 (2)

C9—O3—H3	110 (2)	C8—C9—H9	109.1
C14—O4—C15	116.28 (18)	C10—C9—H9	109.1
C7—N1—C11	125.27 (15)	C9—C10—C11	106.17 (15)
C7—N1—C8	122.48 (16)	C9—C10—H10A	110.5
C11—N1—C8	111.83 (14)	C11—C10—H10A	110.5
C12—N2—C1	124.78 (13)	C9—C10—H10B	110.5
C12—N2—C13	116.22 (13)	C11—C10—H10B	110.5
C1—N2—C13	118.86 (13)	H10A—C10—H10B	108.7
C2—C1—C6	119.74 (15)	N1—C11—C12	108.85 (15)
C2—C1—N2	117.34 (16)	N1—C11—C10	103.58 (14)
C6—C1—N2	122.65 (16)	C12—C11—C10	112.28 (13)
C3—C2—C1	120.47 (19)	N1—C11—H11	110.6
C3—C2—H2	119.8	C12—C11—H11	110.6
C1—C2—H2	119.8	C10—C11—H11	110.6
C4—C3—C2	120.6 (2)	O2—C12—N2	120.99 (15)
C4—C3—H3A	119.7	O2—C12—C11	123.37 (15)
C2—C3—H3A	119.7	N2—C12—C11	115.62 (13)
C3—C4—C5	119.21 (18)	N2—C13—C14	112.56 (16)
C3—C4—H4	120.4	N2—C13—H13A	109.1
C5—C4—H4	120.4	C14—C13—H13A	109.1
C4—C5—C6	121.87 (19)	N2—C13—H13B	109.1
C4—C5—H5	119.1	C14—C13—H13B	109.1
C6—C5—H5	119.1	H13A—C13—H13B	107.8
C5—C6—C1	118.02 (17)	O5—C14—O4	125.18 (19)
C5—C6—C7	116.15 (16)	O5—C14—C13	124.73 (17)
C1—C6—C7	125.82 (14)	O4—C14—C13	110.08 (18)
O1—C7—N1	120.98 (18)	O4—C15—C16	108.4 (2)
O1—C7—C6	120.85 (16)	O4—C15—H15A	110.0
N1—C7—C6	118.12 (16)	C16—C15—H15A	110.0
N1—C8—C9	103.94 (16)	O4—C15—H15B	110.0
N1—C8—H8A	111.0	C16—C15—H15B	110.0
C9—C8—H8A	111.0	H15A—C15—H15B	108.4
N1—C8—H8B	111.0	C15—C16—H16A	109.5
C9—C8—H8B	111.0	C15—C16—H16B	109.5
H8A—C8—H8B	109.0	H16A—C16—H16B	109.5
O3—C9—C8	112.32 (18)	C15—C16—H16C	109.5
O3—C9—C10	113.62 (19)	H16A—C16—H16C	109.5
C8—C9—C10	103.30 (14)	H16B—C16—H16C	109.5
O3—C9—H9	109.1

C12—N2—C1—C2	137.2 (2)	N1—C8—C9—O3	90.74 (19)
C13—N2—C1—C2	−38.4 (3)	N1—C8—C9—C10	−32.09 (19)
C12—N2—C1—C6	−48.8 (3)	O3—C9—C10—C11	−90.0 (2)
C13—N2—C1—C6	135.63 (19)	C8—C9—C10—C11	32.0 (2)
C6—C1—C2—C3	−2.3 (3)	C7—N1—C11—C12	−69.2 (2)
N2—C1—C2—C3	171.88 (19)	C8—N1—C11—C12	118.12 (16)
C1—C2—C3—C4	−0.4 (3)	C7—N1—C11—C10	171.13 (18)
C2—C3—C4—C5	1.9 (4)	C8—N1—C11—C10	−1.53 (19)
C3—C4—C5—C6	−0.8 (3)	C9—C10—C11—N1	−19.1 (2)
C4—C5—C6—C1	−1.8 (3)	C9—C10—C11—C12	−136.39 (17)
C4—C5—C6—C7	178.27 (19)	C1—N2—C12—O2	−178.8 (2)
C2—C1—C6—C5	3.3 (3)	C13—N2—C12—O2	−3.2 (3)
N2—C1—C6—C5	−170.55 (18)	C1—N2—C12—C11	2.2 (3)
C2—C1—C6—C7	−176.78 (18)	C13—N2—C12—C11	177.84 (17)
N2—C1—C6—C7	9.4 (3)	N1—C11—C12—O2	−111.0 (2)
C11—N1—C7—O1	−176.41 (17)	C10—C11—C12—O2	3.1 (3)
C8—N1—C7—O1	−4.5 (3)	N1—C11—C12—N2	68.0 (2)
C11—N1—C7—C6	1.1 (3)	C10—C11—C12—N2	−177.93 (18)
C8—N1—C7—C6	173.01 (16)	C12—N2—C13—C14	−69.9 (2)
C5—C6—C7—O1	32.0 (3)	C1—N2—C13—C14	106.03 (19)
C1—C6—C7—O1	−147.9 (2)	C15—O4—C14—O5	−2.1 (3)
C5—C6—C7—N1	−145.53 (19)	C15—O4—C14—C13	176.49 (19)
C1—C6—C7—N1	34.6 (3)	N2—C13—C14—O5	−17.2 (3)
C7—N1—C8—C9	−151.47 (18)	N2—C13—C14—O4	164.23 (16)
C11—N1—C8—C9	21.4 (2)	C14—O4—C15—C16	177.9 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3···O1ⁱ	0.84 (1)	1.95 (1)	2.782 (2)	173 (4)

Symmetry code: (i) x+1/2, −y+5/2, −z.

Experimental details

Crystal data
Chemical formula	C₁₆H₁₈N₂O₅
M_r	318.32
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	293
a, b, c (Å)	8.5503 (2), 9.6580 (2), 18.2734 (4)
V (Å³)	1509.00 (6)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.3 × 0.3 × 0.3

Data collection
Diffractometer	Bruker APEXII diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	11809, 1907, 1765
R_int	0.024
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.032, 0.098, 1.04
No. of reflections	1907
No. of parameters	213
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.21, −0.17

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), X-SEED (Barbour, 2001), publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3···O1ⁱ	0.84 (1)	1.95 (1)	2.782 (2)	173 (4)

Symmetry code: (i) x+1/2, −y+5/2, −z.

Acknowledgements

We thank Université Mohammed V-Agdaland the University of Malaya for supporting this study.

References

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