Buy article online - an online subscription or single-article purchase is required to access this article.
Download citation
Download citation
link to html
The title compound (RS 1350), C11H9ClN4, was recently synthesized by a Smiles rearrangement of 1-[(5-chloro-2-nitro­phenyl)­sulfonyl]-1H-pyrrole-2-carbohydrazide or 1-(5-chloro-2-nitro­phenyl)-1H-pyrrole-2-carbohydrazide in pow­der­ed iron-glacial acetic acid medium. From the crystallographic analysis, it is observed that, in the title compound, the benz­imidazole moiety is planar and forms a dihedral angle of 3.8 (2)° with the pyrrole ring. The near planarity of the two rings indicates an extended conjugation.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536801010856/ci6034sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536801010856/ci6034Isup2.hkl
Contains datablock I

CCDC reference: 172199

Key indicators

  • Single-crystal X-ray study
  • T = 293 K
  • Mean [sigma](C-C) = 0.006 Å
  • R factor = 0.042
  • wR factor = 0.070
  • Data-to-parameter ratio = 8.2

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


Yellow Alert Alert Level C:
REFNR_01 Alert C Ratio of reflections to parameters is < 10 for a centrosymmetric structure sine(theta)/lambda 0.8085 Proportion of unique data used 0.2557 Ratio reflections to parameters 8.2345 PLAT_420 Alert C D-H Without Acceptor N(2) - H(1B) ?
0 Alert Level A = Potentially serious problem
0 Alert Level B = Potential problem
2 Alert Level C = Please check

Comment top

HIV-1 Reverse transcriptase (RT), the enzyme which catalyses the transcription of viral single-stranded RNA into double-stranded DNA, is the most investigated target in searching for anti-AIDS drugs. In the last decade, many RT inhibitors were synthesized and some were selected as lead compounds for clinical trials (Artico, 1996; Pedersen et al., 1999). Two classes of RT inhibitors were identified (Vandamme et al., 1998). The nucleoside analogues (NRTIs) act as competitive inhibitors or DNA chain terminator. The non-nucleoside analogues (NNRTIs) are allosteric inhibitors of the RT enzyme which bind to an hydrophobic pocket in the enzyme-DNA complex close to the active site (Spence et al., 1995; Vandamme et al., 1998; De Clercq, 1998). Despite their different structures, NNRTIs adopt a common `butterfly-like' active conformation, having two π-electron-donor regions between a lipophilic site (Schaefer et al., 1993). The major problem related to NNRTIs concerns the rapid development of mutations in the RT, with failure of therapy. The synthesis of NNRTIs active on a wide panel of viral resistant mutants useful in anti-AIDS drug combination strategies is a very actual goal. Our engagement in the field of anti-AIDS chemotherapy (Silvestri et al., 1994, 1995, 1997, 1998; Silvestri, Artico et al., 2000; Silvestri, Pifferi et al., 2000; Artico et al., 1994, 1995, 2000; Artico, Silvestri, Massa et al., 1996; Artico, Silvestri, Pagnozzi, Stefancich, Massa & La Colla, 1996; Ettorre et al., 2001) led to the discovery of the pyrrolo[1,2-b][1,2,5]benzothiadiazepin-10(11H)ones (PBTDs), a novel class of NNRTIs endowed with anti-HIV-1 RT activity comparable with that of nevirapine (Artico, Silvestri, Pagnozzi, Stefancich, Massa, Loi et al., 1996). Pursuing our research on novel PBTDs active toward resistant mutants, we planned the synthesis of 7-chloro-11-hydrazinopyrrolo[1,2-b][1,2,5]benzothiadiazepin-10(11H)one 5,5-dioxide, (IV), by iron powder–acetic acid reduction of 1-[(5-chloro-2-nitrophenyl)sulfonyl]-1H-pyrrole-2-carbohydrazide, (II) (Silvestri, Pifferi et al., 2000). Unexpectedly instead of (IV), the reaction furnished 1-amino-6-chloro-2-(1H-pyrrol-2-yl)benzimidazole, (I), as the sole product. We supposed that (II) underwent Smiles rearrangement to give (I). In fact, 1-[(5-chloro-2-nitrophenyl)sulfonyl]-1H-pyrrole-2-carbohydrazide, (II), possesses the structural features required to achieve Smiles rearrangement, i.e. (i) a strongly electron-withdrawing ortho-nitro group activating the aromatic ring; (ii) the sulfonyl group as a good leaving group; (iii) the nucleofilicity; (iv) the acidity of CONHNH2 entering group (Truce et al., 1971).

We decided to confirm unambiguously the structure of (I) by the crystallographic analysis here reported. The benzimidazole moiety is planar, with Cl1 and N2 deviating from it by -0.030 (2) and 0.038 (3) Å, respectively. The angle between the planar benzimidazole moiety and the pyrrole ring is 3.8 (2)°. No unusual feactures were found in the geometry of the rings. The near planarity of the benzimidazole and the pyrrol rings indicate extended conjugation. The NH2 group adopts a pyramidal configuration.

Experimental top

The title compound was synthesized according to Silvestri, Pifferi et al. (2000).

Refinement top

The crystal diffracted quite weakly at room temperature which reduced the number of reflections with significant intensities. The position of the H atoms were calculated geometrically at a distance of 0.96 Å from the corrosponding C or N atom, and a riding model was used during their refinement.

Computing details top

Data collection: R3m/V (Siemens, 1989); cell refinement: R3m/V; data reduction: XDISK (Siemens, 1989); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: CAOS (Camalli & Spagna, 1994); molecular graphics: CAOS; software used to prepare material for publication: CAOS.

Figures top
[Figure 1] Fig. 1. The molecular structure of (I). Displacement ellipsoids are shown at the 50% probability level.
(I) top
Crystal data top
C11H9ClN4Dx = 1.460 Mg m3
Mr = 232.67Mo Kα radiation, λ = 0.71069 Å
Orthorhombic, PbcaCell parameters from 32 reflections
a = 10.065 (2) Åθ = 2.9–16.0°
b = 23.178 (4) ŵ = 0.34 mm1
c = 9.077 (3) ÅT = 293 K
V = 2117.5 (9) Å3Prism, brown
Z = 80.3 × 0.2 × 0.15 mm
F(000) = 960
Data collection top
Siemens P3 automatic four circle
diffractometer
Rint = 0.063
Radiation source: X-ray tubeθmax = 35.1°, θmin = 1.8°
Graphite monochromatorh = 016
θ/2θ scansk = 037
5213 measured reflectionsl = 014
4669 independent reflections3 standard reflections every 97 reflections
1194 reflections with F > 3σ(F) intensity decay: none
Refinement top
Refinement on F145 parameters
Least-squares matrix: FullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.042 w = 1/(0.2 + F + 0.0792F2)
wR(F2) = 0.070(Δ/σ)max = 0.001
S = 0.97Δρmax = 0.26 e Å3
1194 reflectionsΔρmin = 0.24 e Å3
Crystal data top
C11H9ClN4V = 2117.5 (9) Å3
Mr = 232.67Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 10.065 (2) ŵ = 0.34 mm1
b = 23.178 (4) ÅT = 293 K
c = 9.077 (3) Å0.3 × 0.2 × 0.15 mm
Data collection top
Siemens P3 automatic four circle
diffractometer
Rint = 0.063
5213 measured reflections3 standard reflections every 97 reflections
4669 independent reflections intensity decay: none
1194 reflections with F > 3σ(F)
Refinement top
R[F2 > 2σ(F2)] = 0.042145 parameters
wR(F2) = 0.070H-atom parameters constrained
S = 0.97Δρmax = 0.26 e Å3
1194 reflectionsΔρmin = 0.24 e Å3
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl10.8484 (1)0.2755 (1)0.2733 (2)0.0703 (5)
N10.6985 (3)0.0643 (1)0.1606 (3)0.036 (1)
N20.7708 (3)0.0462 (2)0.0358 (3)0.045 (1)
N30.5533 (3)0.0591 (1)0.3468 (4)0.041 (1)
N40.6142 (4)0.0547 (2)0.0682 (4)0.048 (1)
C10.6053 (4)0.0316 (2)0.2325 (4)0.036 (1)
C20.7060 (4)0.1169 (2)0.2311 (4)0.036 (1)
C30.6153 (4)0.1128 (2)0.3482 (4)0.039 (1)
C40.7788 (4)0.1668 (2)0.2034 (4)0.044 (1)
C50.7592 (4)0.2115 (2)0.3006 (5)0.047 (1)
C60.6718 (4)0.2087 (2)0.4191 (5)0.048 (1)
C70.5993 (4)0.1592 (2)0.4451 (4)0.044 (1)
C80.5653 (4)0.0262 (2)0.1893 (4)0.039 (1)
C90.4711 (4)0.0606 (2)0.2537 (5)0.046 (1)
C100.4638 (5)0.1115 (2)0.1688 (5)0.053 (1)
C110.5529 (5)0.1064 (2)0.0557 (5)0.055 (2)
H1a0.86410.04770.05740.046*
H1b0.75140.07160.04490.046*
H4n0.68150.04020.00300.048*
H4c0.83870.16990.12160.044*
H60.66200.24140.48310.048*
H70.53940.15660.52710.045*
H90.42000.05170.34010.047*
H100.40670.14380.18750.052*
H110.56810.13460.01990.057*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0788 (9)0.0509 (6)0.0812 (9)0.0224 (6)0.0011 (7)0.0001 (6)
N10.032 (1)0.041 (2)0.036 (2)0.004 (1)0.004 (1)0.001 (1)
N20.041 (2)0.057 (2)0.036 (2)0.001 (2)0.009 (1)0.002 (2)
N30.038 (2)0.042 (2)0.041 (2)0.000 (1)0.004 (2)0.000 (1)
N40.047 (2)0.051 (2)0.047 (2)0.004 (2)0.005 (2)0.005 (2)
C10.032 (2)0.038 (2)0.036 (2)0.000 (1)0.003 (2)0.003 (2)
C20.034 (2)0.040 (2)0.034 (2)0.003 (1)0.000 (2)0.003 (2)
C30.035 (2)0.042 (2)0.038 (2)0.002 (2)0.001 (2)0.001 (2)
C40.037 (2)0.050 (2)0.043 (2)0.002 (2)0.001 (2)0.005 (2)
C50.045 (2)0.041 (2)0.056 (2)0.008 (2)0.011 (2)0.002 (2)
C60.054 (3)0.042 (2)0.049 (2)0.001 (2)0.008 (2)0.004 (2)
C70.042 (2)0.051 (2)0.040 (2)0.005 (2)0.002 (2)0.006 (2)
C80.041 (2)0.037 (2)0.039 (2)0.004 (1)0.004 (2)0.001 (2)
C90.048 (2)0.041 (2)0.049 (2)0.003 (2)0.000 (2)0.003 (2)
C100.058 (3)0.038 (2)0.062 (3)0.003 (2)0.013 (2)0.005 (2)
C110.064 (3)0.044 (2)0.058 (3)0.006 (2)0.005 (2)0.007 (2)
Geometric parameters (Å, º) top
Cl1—C51.751 (4)C3—C71.399 (6)
N1—N21.411 (4)C4—C51.376 (6)
N1—C11.372 (5)C4—H4c0.96
N1—C21.380 (5)C5—C61.391 (6)
N2—H1a0.96C6—C71.380 (6)
N2—H1b0.96C6—H60.96
N3—C11.326 (5)C7—H70.96
N3—C31.391 (5)C8—C91.370 (6)
N4—C81.374 (5)C9—C101.411 (6)
N4—C111.354 (6)C9—H90.96
N4—H4n0.96C10—C111.367 (7)
C1—C81.452 (5)C10—H100.96
C2—C31.405 (5)C11—H110.96
C2—C41.390 (5)
N2—N1—C1124.8 (3)Cl1—C5—C6118.2 (3)
C2—N1—C1107.8 (3)C4—C5—C6123.5 (4)
C2—N1—N2127.4 (3)C4—C5—Cl1118.3 (3)
H1a—N2—H1b109.5H6—C6—C5119.7
N1—N2—H1b109.0C7—C6—C5120.3 (4)
N1—N2—H1a109.3C7—C6—H6119.9
C1—N3—C3105.1 (3)H7—C7—C3120.7
H4n—N4—C11125.4C6—C7—C3118.1 (4)
C8—N4—C11109.2 (4)C6—C7—H7121.1
C8—N4—H4n125.3C1—C8—N4124.1 (3)
N1—C1—C8124.8 (3)C9—C8—N4108.1 (3)
N3—C1—C8123.1 (3)C9—C8—C1127.8 (4)
N3—C1—N1112.1 (3)C10—C9—H9126.7
N1—C2—C3104.7 (3)C8—C9—H9126.5
C4—C2—C3122.4 (3)C8—C9—C10106.8 (4)
C4—C2—N1132.8 (3)H10—C10—C9126.0
C2—C3—N3110.2 (3)C11—C10—C9107.8 (4)
C7—C3—N3129.9 (3)C11—C10—H10126.3
C7—C3—C2119.8 (4)C10—C11—N4108.2 (4)
H4c—C4—C2122.3H11—C11—N4126.1
C5—C4—C2115.8 (4)H11—C11—C10125.7
C5—C4—H4c121.9

Experimental details

Crystal data
Chemical formulaC11H9ClN4
Mr232.67
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)293
a, b, c (Å)10.065 (2), 23.178 (4), 9.077 (3)
V3)2117.5 (9)
Z8
Radiation typeMo Kα
µ (mm1)0.34
Crystal size (mm)0.3 × 0.2 × 0.15
Data collection
DiffractometerSiemens P3 automatic four circle
diffractometer
Absorption correction
No. of measured, independent and
observed [F > 3σ(F)] reflections
5213, 4669, 1194
Rint0.063
(sin θ/λ)max1)0.808
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.070, 0.97
No. of reflections1194
No. of parameters145
No. of restraints?
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.26, 0.24

Computer programs: R3m/V (Siemens, 1989), R3m/V, XDISK (Siemens, 1989), SIR97 (Altomare et al., 1999), CAOS (Camalli & Spagna, 1994), CAOS.

 

Subscribe to Acta Crystallographica Section E: Crystallographic Communications

The full text of this article is available to subscribers to the journal.

If you have already registered and are using a computer listed in your registration details, please email support@iucr.org for assistance.

Buy online

You may purchase this article in PDF and/or HTML formats. For purchasers in the European Community who do not have a VAT number, VAT will be added at the local rate. Payments to the IUCr are handled by WorldPay, who will accept payment by credit card in several currencies. To purchase the article, please complete the form below (fields marked * are required), and then click on `Continue'.
E-mail address* 
Repeat e-mail address* 
(for error checking) 

Format*   PDF (US $40)
   HTML (US $40)
   PDF+HTML (US $50)
In order for VAT to be shown for your country javascript needs to be enabled.

VAT number 
(non-UK EC countries only) 
Country* 
 

Terms and conditions of use
Contact us

Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds