Pyrrolo­[2,1-c][1,4]benzodiazepine-5,11-dithione

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

doi:10.1107/S1600536810021410

Pyrrolo[2,1-c][1,4]benzodiazepine-5,11-dithione

S. Ourahou, H. Zouihri, E. M. Essassi and S. W. Ng

The seven-membered fused-ring in the title compound, C₁₂H₁₂N₂S₂, adopts a boat conformation (with the two phenylene C atoms representing the stern and the methine C atom the prow). This methine C atom and the tertiary N atom also belong to a five-membered ring, which has an envelope conformation. In the crystal structure, molecules are linked about a center of inversion by pairs of N—H

S hydrogen bonds.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536810021410/xu2774sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536810021410/xu2774Isup2.hkl Contains datablock I

CCDC reference: 786590

checkCIF report

Key indicators

Single-crystal X-ray study
T = 200 K
Mean (C-C) = 0.003 Å
R factor = 0.042
wR factor = 0.107
Data-to-parameter ratio = 15.6

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT919_ALERT_3_B Reflection(s) # Likely Affected by the Beamstop           1

Alert level C
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600          3
PLAT912_ALERT_4_C Missing # of FCF Reflections Above STh/L=  0.600          5

Alert level G
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......         12
PLAT793_ALERT_4_G The Model has Chirality at C11     (Verify) ....          R

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

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

Comment top

Pyrrolo[2,1-c][1,4]benzodiazepine-5,11-dione is the homolog of a class of compounds that are active against mycobacterium tuberculosis (Kamal et al., 2007). Other C-2 aryl substituted derivatives are cytotoxic (Antonow et al., 2007). The crystal structure of the parent compound has not been reported although that the (11aS)-1,2,3,10,11,11a-hexahydro has bee published (Neidle et al., 1997). The structure of the parent compound is probably similar to that of the isoelectronic dithione (Scheme I, Fig. 1). The seven-membered fused-ring in C₁₂H₁₂N₂S₂ adopts a boat conformation (with the two phenylene carbons representing the stern and the methine carbon atom the prow). This methine C atom and the tertiary N atom also belong to a five-membered ring, which has an envelope shape. Two C₁₂H₁₂N₂O₂ molecules are linked about a center-of-inversion by N–H···O_carbonyl hydrogen bonds.

Related literature top

For pyrrolo[2,1-c][1,4]benzodiazepine-5,11-dione, see: Antonow et al. (2007); Kamal et al. (2007). For a related structure, Neidle et al. (1991).

Experimental top

Pyrrolo[2,1-c][1,4]benzodiazepine-5,11-dithione (1 g, 4.62 mmol) and phosphorus pentasulfide (2.05 g, 9.24 mmol) are heated in pyridine (60 ml) for 4 h. The pyridine was evaporated under reduced pressure and the residue heated in water (100 ml). The suspension was set aside for a day. The insoluble product was recrystallized from ethanol to furnish colorless crystals (90% yield).

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); 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. Thermal ellipsoid plot (Barbour, 2001) of the molecule of C₁₂H₁₂N₂S₂ at the 70% probability level; hydrogen atoms are drawn as spheres of arbitrary radius.

Pyrrolo[2,1-c][1,4]benzodiazepine-5,11-dithione top

Crystal data top

C₁₂H₁₂N₂S₂	F(000) = 520
M_r = 248.36	D_x = 1.436 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2753 reflections
a = 13.9831 (5) Å	θ = 2.5–26.5°
b = 10.0134 (3) Å	µ = 0.44 mm⁻¹
c = 8.2670 (3) Å	T = 200 K
β = 97.089 (1)°	Prism, colorless
V = 1148.68 (7) Å³	0.12 × 0.10 × 0.07 mm
Z = 4

Data collection top

Bruker X8 APEXII diffractometer	3017 independent reflections
Radiation source: fine-focus sealed tube	2117 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.055
ϕ and ω scans	θ_max = 28.9°, θ_min = 1.5°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −18→18
T_min = 0.950, T_max = 0.970	k = −12→13
14013 measured reflections	l = −11→11

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)] = 0.042	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.107	All H-atom parameters refined
S = 1.01	w = 1/[σ²(F_o²) + (0.047P)² + 0.5062P] where P = (F_o² + 2F_c²)/3
3017 reflections	(Δ/σ)_max = 0.001
193 parameters	Δρ_max = 0.39 e Å⁻³
12 restraints	Δρ_min = −0.28 e Å⁻³

Crystal data top

C₁₂H₁₂N₂S₂	V = 1148.68 (7) Å³
M_r = 248.36	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 13.9831 (5) Å	µ = 0.44 mm⁻¹
b = 10.0134 (3) Å	T = 200 K
c = 8.2670 (3) Å	0.12 × 0.10 × 0.07 mm
β = 97.089 (1)°

Data collection top

Bruker X8 APEXII diffractometer	3017 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	2117 reflections with I > 2σ(I)
T_min = 0.950, T_max = 0.970	R_int = 0.055
14013 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.042	12 restraints
wR(F²) = 0.107	All H-atom parameters refined
S = 1.01	Δρ_max = 0.39 e Å⁻³
3017 reflections	Δρ_min = −0.28 e Å⁻³
193 parameters

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

	x	y	z	U_iso*/U_eq
S1	0.60817 (4)	0.35830 (6)	0.60020 (8)	0.02972 (16)
S2	0.92223 (4)	0.75918 (6)	0.51650 (7)	0.02991 (16)
N1	0.62240 (12)	0.61932 (18)	0.5884 (2)	0.0221 (4)
N2	0.82707 (11)	0.57256 (17)	0.6540 (2)	0.0196 (4)
C1	0.65476 (14)	0.7511 (2)	0.6273 (2)	0.0205 (4)
C2	0.58339 (16)	0.8462 (2)	0.6410 (3)	0.0277 (5)
C3	0.60718 (17)	0.9769 (2)	0.6798 (3)	0.0318 (5)
C4	0.70347 (18)	1.0143 (2)	0.7079 (3)	0.0307 (5)
C5	0.77396 (16)	0.9220 (2)	0.6894 (3)	0.0251 (5)
C6	0.75250 (14)	0.7891 (2)	0.6467 (2)	0.0191 (4)
C7	0.83258 (14)	0.7001 (2)	0.6109 (2)	0.0194 (4)
C8	0.90083 (16)	0.4717 (2)	0.6291 (3)	0.0274 (5)
C9	0.86119 (16)	0.3432 (2)	0.6929 (3)	0.0284 (5)
C10	0.80322 (16)	0.3926 (2)	0.8260 (3)	0.0251 (5)
C11	0.75591 (14)	0.5204 (2)	0.7555 (2)	0.0190 (4)
C12	0.66077 (14)	0.5040 (2)	0.6465 (2)	0.0205 (4)
H1	0.5667 (10)	0.611 (2)	0.534 (2)	0.027 (6)*
H2	0.5176 (8)	0.822 (2)	0.628 (3)	0.034 (7)*
H3	0.5592 (13)	1.0406 (19)	0.694 (3)	0.030 (6)*
H4	0.7233 (16)	1.1027 (13)	0.736 (3)	0.032 (7)*
H5	0.8403 (8)	0.948 (2)	0.708 (3)	0.021 (6)*
H81	0.9608 (11)	0.498 (2)	0.697 (2)	0.030 (6)*
H82	0.9116 (16)	0.471 (2)	0.5138 (14)	0.034 (7)*
H91	0.8196 (14)	0.296 (2)	0.606 (2)	0.029 (6)*
H92	0.9130 (13)	0.281 (2)	0.736 (3)	0.037 (7)*
H11	0.7457 (14)	0.5865 (16)	0.8397 (19)	0.017 (5)*
H101	0.8467 (13)	0.421 (2)	0.9245 (19)	0.029 (6)*
H102	0.7565 (13)	0.3271 (18)	0.859 (2)	0.025 (6)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0233 (3)	0.0180 (3)	0.0459 (3)	−0.0022 (2)	−0.0034 (2)	0.0011 (3)
S2	0.0248 (3)	0.0352 (4)	0.0300 (3)	−0.0034 (2)	0.0043 (2)	0.0035 (2)
N1	0.0172 (9)	0.0175 (10)	0.0299 (9)	−0.0008 (7)	−0.0039 (7)	−0.0007 (7)
N2	0.0172 (8)	0.0202 (10)	0.0211 (8)	0.0010 (7)	0.0012 (7)	−0.0007 (7)
C1	0.0238 (10)	0.0169 (11)	0.0202 (9)	0.0007 (8)	0.0004 (8)	−0.0004 (8)
C2	0.0244 (11)	0.0242 (12)	0.0344 (12)	0.0036 (9)	0.0037 (9)	−0.0019 (10)
C3	0.0360 (13)	0.0219 (13)	0.0382 (13)	0.0085 (10)	0.0074 (10)	−0.0027 (10)
C4	0.0455 (14)	0.0177 (12)	0.0289 (11)	−0.0002 (10)	0.0041 (10)	−0.0019 (9)
C5	0.0300 (12)	0.0222 (12)	0.0220 (10)	−0.0046 (9)	−0.0008 (9)	0.0023 (9)
C6	0.0232 (10)	0.0180 (11)	0.0157 (9)	0.0001 (8)	0.0013 (8)	0.0009 (8)
C7	0.0191 (10)	0.0229 (11)	0.0150 (9)	−0.0025 (8)	−0.0027 (7)	−0.0005 (8)
C8	0.0224 (11)	0.0276 (13)	0.0317 (12)	0.0081 (10)	0.0015 (9)	−0.0012 (10)
C9	0.0259 (11)	0.0223 (12)	0.0351 (12)	0.0073 (9)	−0.0042 (10)	−0.0028 (10)
C10	0.0296 (12)	0.0187 (11)	0.0254 (10)	0.0021 (9)	−0.0035 (9)	0.0012 (9)
C11	0.0221 (10)	0.0162 (10)	0.0184 (9)	0.0004 (8)	0.0016 (8)	0.0000 (8)
C12	0.0203 (10)	0.0197 (11)	0.0224 (10)	0.0019 (8)	0.0065 (8)	−0.0010 (8)

Geometric parameters (Å, º) top

S1—C12	1.657 (2)	C4—H4	0.947 (10)
S2—C7	1.665 (2)	C5—C6	1.400 (3)
N1—C12	1.337 (3)	C5—H5	0.956 (9)
N1—C1	1.419 (3)	C6—C7	1.489 (3)
N1—H1	0.855 (10)	C8—C9	1.520 (3)
N2—C7	1.330 (3)	C8—H81	0.984 (10)
N2—C11	1.474 (2)	C8—H82	0.984 (9)
N2—C8	1.476 (3)	C9—C10	1.527 (3)
C1—C2	1.394 (3)	C9—H91	0.986 (10)
C1—C6	1.409 (3)	C9—H92	0.986 (10)
C2—C3	1.379 (3)	C10—C11	1.523 (3)
C2—H2	0.944 (10)	C10—H101	0.996 (10)
C3—C4	1.389 (3)	C10—H102	0.986 (9)
C3—H3	0.942 (10)	C11—C12	1.521 (3)
C4—C5	1.374 (3)	C11—H11	0.984 (9)

C12—N1—C1	128.23 (17)	N2—C8—C9	103.87 (17)
C12—N1—H1	113.8 (16)	N2—C8—H81	107.5 (14)
C1—N1—H1	117.1 (16)	C9—C8—H81	110.5 (14)
C7—N2—C11	123.94 (16)	N2—C8—H82	109.3 (14)
C7—N2—C8	123.70 (17)	C9—C8—H82	116.0 (15)
C11—N2—C8	111.65 (16)	H81—C8—H82	109.2 (19)
C2—C1—C6	120.0 (2)	C8—C9—C10	102.99 (18)
C2—C1—N1	116.23 (18)	C8—C9—H91	110.8 (14)
C6—C1—N1	123.69 (18)	C10—C9—H91	111.3 (13)
C3—C2—C1	120.8 (2)	C8—C9—H92	112.0 (14)
C3—C2—H2	118.2 (16)	C10—C9—H92	112.0 (14)
C1—C2—H2	120.9 (16)	H91—C9—H92	108 (2)
C2—C3—C4	119.7 (2)	C11—C10—C9	103.89 (17)
C2—C3—H3	121.1 (15)	C11—C10—H101	105.2 (14)
C4—C3—H3	119.1 (15)	C9—C10—H101	111.0 (13)
C5—C4—C3	119.6 (2)	C11—C10—H102	113.1 (13)
C5—C4—H4	117.6 (15)	C9—C10—H102	114.2 (13)
C3—C4—H4	122.8 (15)	H101—C10—H102	109.0 (18)
C4—C5—C6	122.2 (2)	N2—C11—C12	107.68 (15)
C4—C5—H5	119.9 (14)	N2—C11—C10	102.94 (16)
C6—C5—H5	117.9 (14)	C12—C11—C10	116.32 (17)
C5—C6—C1	117.39 (19)	N2—C11—H11	109.3 (12)
C5—C6—C7	118.44 (18)	C12—C11—H11	107.4 (12)
C1—C6—C7	123.96 (19)	C10—C11—H11	112.9 (12)
N2—C7—C6	116.84 (17)	N1—C12—C11	113.76 (17)
N2—C7—S2	122.59 (16)	N1—C12—S1	122.01 (15)
C6—C7—S2	120.55 (16)	C11—C12—S1	124.22 (15)

C12—N1—C1—C2	−140.9 (2)	C5—C6—C7—S2	−36.1 (2)
C12—N1—C1—C6	41.2 (3)	C1—C6—C7—S2	138.49 (17)
C6—C1—C2—C3	−2.6 (3)	C7—N2—C8—C9	−178.51 (18)
N1—C1—C2—C3	179.4 (2)	C11—N2—C8—C9	10.8 (2)
C1—C2—C3—C4	−0.9 (3)	N2—C8—C9—C10	−30.2 (2)
C2—C3—C4—C5	3.0 (3)	C8—C9—C10—C11	38.8 (2)
C3—C4—C5—C6	−1.6 (3)	C7—N2—C11—C12	79.1 (2)
C4—C5—C6—C1	−1.8 (3)	C8—N2—C11—C12	−110.28 (18)
C4—C5—C6—C7	173.16 (19)	C7—N2—C11—C10	−157.51 (18)
C2—C1—C6—C5	3.8 (3)	C8—N2—C11—C10	13.1 (2)
N1—C1—C6—C5	−178.33 (18)	C9—C10—C11—N2	−31.7 (2)
C2—C1—C6—C7	−170.78 (19)	C9—C10—C11—C12	85.7 (2)
N1—C1—C6—C7	7.0 (3)	C1—N1—C12—C11	−6.1 (3)
C11—N2—C7—C6	−9.7 (3)	C1—N1—C12—S1	174.50 (16)
C8—N2—C7—C6	−179.26 (17)	N2—C11—C12—N1	−65.3 (2)
C11—N2—C7—S2	171.99 (14)	C10—C11—C12—N1	179.85 (18)
C8—N2—C7—S2	2.5 (3)	N2—C11—C12—S1	114.07 (17)
C5—C6—C7—N2	145.61 (19)	C10—C11—C12—S1	−0.8 (3)
C1—C6—C7—N2	−39.8 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···S1ⁱ	0.86 (1)	2.58 (1)	3.411 (2)	166 (2)

Symmetry code: (i) −x+1, −y+1, −z+1.

Experimental details

Crystal data
Chemical formula	C₁₂H₁₂N₂S₂
M_r	248.36
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	200
a, b, c (Å)	13.9831 (5), 10.0134 (3), 8.2670 (3)
β (°)	97.089 (1)
V (Å³)	1148.68 (7)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.44
Crystal size (mm)	0.12 × 0.10 × 0.07

Data collection
Diffractometer	Bruker X8 APEXII diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.950, 0.970
No. of measured, independent and observed [I > 2σ(I)] reflections	14013, 3017, 2117
R_int	0.055
(sin θ/λ)_max (Å⁻¹)	0.680

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.042, 0.107, 1.01
No. of reflections	3017
No. of parameters	193
No. of restraints	12
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.39, −0.28

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