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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 64| Part 3| March 2008| Page o634
doi:10.1107/S1600536808005023

Benznidazole

José Lamartine Soares-Sobrinho,a Marcílio S. S. Cunha-Filho,b Pedro José Rolim Neto,a Juan J. Torres-Labandeirab and Bruno Dacunha-Marinhoc*

aPrograma de Pós-graduação em Ciências Farmacêuticas, Universidade Federal de Pernambuco, 50740-521 Recife, Brazil, bDepartamento de Farmacia y Tecnología Farmacéutica, Facultad de Farmacia, Universidad de Santiago de Compostela, 15872, Spain, and cEd. CACTUS, Campus Sur, Unidade de Raios X, Universidad de Santiago de Compostela, 15782, Spain
*Correspondence e-mail: raiosxp@usc.es

(Received 6 February 2008; accepted 22 February 2008; online 27 February 2008)

The conformation of the title compound [systematic name: N-benzyl-2-(2-nitro­imidazol-1-yl)acetamide], C12H12N4O3, can be described in terms of the relative orientation of three planar fragments, the imidazol group (A), benzyl group (B), and the acetamide fragment (C), with corresponding dihedral angles: A/C = 88.17 (4), B/C = 67.12 (5) and A/B = 21.11 (4)°. The crystal packing is enhanced by a network of strong inter­molecular N—H⋯O hydrogen bonds.

Related literature

For related literature, see: Coura & Castro (2002[Coura, J. R. & Castro, S. L. (2002). Mem. Inst. Oswaldo Cruz, 97, 2-24.]); Lamas et al. (2006[Lamas, M. C., Villaggi, L., Nocito, I., Bassani, G., Leonardi, D., Pascutti, F., Serra, E. & Salomón, C. J. (2006). Int. J. Pharm. 307, 239-243.]); Morilla et al. (2004[Morilla, M. J., Montanari, J. A., Prieto, M. J., Lopez, M. O., Petray, P. B. & Romero, E. L. (2004). Int. J. Pharm. 278, 311-318.]); Silva et al. (2007[Silva, A. L. M., Soares-Sobrinho, J. L., Rolim-Neto, P. J., Silva, R. M. F., Medeiros, F. P. M. & Lima, L. G. (2007). Quím. Nova, 30, 1163-1166.]).

[Scheme 1]

Experimental

Crystal data

  • C12H12N4O3

  • Mr = 260.26

  • Monoclinic, P 21

  • a = 4.65560 (10) Å

  • b = 10.9113 (2) Å

  • c = 11.7681 (3) Å

  • β = 90.6680 (10)°

  • V = 597.76 (2) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.11 mm−1

  • T = 100 (2) K

  • 0.34 × 0.16 × 0.12 mm
Data collection

  • Bruker APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2001[Bruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.861, Tmax = 0.987

  • 11597 measured reflections

  • 1287 independent reflections

  • 1216 reflections with I > 2σ(I)

  • Rint = 0.012
Refinement

  • R[F2 > 2σ(F2)] = 0.025

  • wR(F2) = 0.066

  • S = 1.08

  • 1287 reflections

  • 176 parameters

  • 1 restraint

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.14 e Å−3

  • Δρmin = −0.22 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N8—H8⋯O10i 0.835 (19) 2.037 (18) 2.837 (2) 160.2 (17)
Symmetry code: (i) x-1, y, z.

Data collection: APEX2 (Bruker, 2007[Bruker (2007). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: APEX2; data reduction: APEX2; program(s) used to solve structure: SIR97 (Altomare et al., 1999[Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115-119.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: Mercury (Macrae et al., 2006[Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.]) and ORTEP-3 for Windows (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]) and PLATON (Spek, 2003[Spek, A. L. (2003). J. Appl. Cryst. 36, 7-13.]).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808005023/om2213sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536808005023/om2213Isup2.hkl

checkCIF report


Comment top

The title compound, Benznidazole, is the drug of choice in the treatment of Chagas disease, a protozoan infection caused by the parasite Trypanosoma cruzi. This illness constitutes a major public health problem for developing nations, affecting sundries Latin America countries, being considered a neglected disease according to World Health Organization (Coura & Castro, 2002; Lamas et al., 2006). In spite of the epidemiological importance of this disease, currently the only available therapeutic agent is Benznidazole, especially effective in the acute phase of infection (Morilla et al., 2004).

The conformation of the title compound (Fig. 1) can be described by the mutual orientation of three approximately planar fragments, A, B and C: one imidazole group (fragment A: N12, C13, N14, C15, C16, N17, O18 and O19 atoms) for which the maximum deviation from the least-squares plane is -0.067 (1) Å, the benzene group (fragment B: C1, C2, C3, C4, C5, C6 and C7 atoms) whose maximum deviation from the mentioned planarity is -0.013 (2), and the central acetamide (fragment C: N8, C9, O10 and C11 atoms), with a deviation of 0.024 (1) Å. The corresponding dihedral angles are: A/C = 88.17 (4)°, B/C = 67.12 (5)° and A/B = 21.11 (4)°.

The strategy of self-assembly through weak interactions is of central importance for efficient and specific biological reactions. In our case we can find one strong intermolecular O···HN hydrogen bond between N(8)–H(8) and O(10) that almost lies along the "a" axis (Fig. 2).

Related literature top

For related literature, see: Macrae et al. (2006); Coura & Castro (2002); Lamas et al. (2006); Morilla et al. (2004); Silva et al. (2007); Spek (2003).

Experimental top

Benznidazole was supplied by Laboratório Farmacêutico do Estado de Pernambuco/LAFEPE batch 13871(Recife, Brazil). Purity was estimated by differential scanning calorimetry (DSC-50 Shimadzu) and high-performance liquid chromatography (HPLC Shimadzu) and found to be 99.9% (Silva et al., 2007). Yellow crystals suitable for X-ray analysis were grown from a solution of methanol and acetonitrile (1:1 v/v) at 298 K over a period of a few days in air.

Data collection: APEX2 (Bruker, 2007); cell refinement: APEX2 (Bruker, 2007); data reduction: APEX2 (Bruker, 2007); Absorption correction: SADABS (Bruker, 2001); program used to solve structure: SIR97 (Altomare et al., 1999); program used to refinement structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2006); software used to prepare material for publication: WinGX (Farrugia, 1999); geometric calculations: PLATON (Spek, 2003).

Refinement top

The H8 atom was located in a difference map and refined. The rest of the H atoms were positioned geometrically and refined with use of a riding model with C—H = 0.95 - 0.99Å and Uiso = 1.2 times Ueq of the bonded C. Friedel pairs were merged for the final refinement.

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: APEX2 (Bruker, 2007); data reduction: APEX2 (Bruker, 2007); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top
[Figure 1] Fig. 1. The molecule of Benznidazole showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. Hydrogen bond network along the a direction.
[Figure 3] Fig. 3. An interactive view of Benznidazole.
N-benzyl-2-(2-nitroimidazol-1-yl)acetamide top
Crystal data top
C12H12N4O3F(000) = 272
Mr = 260.26Dx = 1.446 Mg m−3
Monoclinic, P21Mo Kα radiation, λ = 0.7107 Å
Hall symbol: P 2ybCell parameters from 1992 reflections
a = 4.6556 (1) Åθ = 3.0–28.3°
b = 10.9113 (2) ŵ = 0.11 mm−1
c = 11.7681 (3) ÅT = 100 K
β = 90.668 (1)°Prism, colourless
V = 597.76 (2) Å30.34 × 0.16 × 0.12 mm
Z = 2
Data collection top
Bruker APEXII CCD
diffractometer		1287 independent reflections
Radiation source: fine-focus sealed tube1216 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.012
ω and ϕ scansθmax = 26.4°, θmin = 1.7°
Absorption correction: multi-scan
(SADABS; Bruker, 2001)		h = −5→5
Tmin = 0.861, Tmax = 0.987k = −13→13
11597 measured reflectionsl = −14→14
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.025Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.066H atoms treated by a mixture of independent and constrained refinement
S = 1.08 w = 1/[σ2(Fo2) + (0.0385P)2 + 0.0782P]
where P = (Fo2 + 2Fc2)/3
1287 reflections(Δ/σ)max = 0.001
176 parametersΔρmax = 0.14 e Å−3
1 restraintΔρmin = −0.22 e Å−3
Crystal data top
C12H12N4O3V = 597.76 (2) Å3
Mr = 260.26Z = 2
Monoclinic, P21Mo Kα radiation
a = 4.6556 (1) ŵ = 0.11 mm−1
b = 10.9113 (2) ÅT = 100 K
c = 11.7681 (3) Å0.34 × 0.16 × 0.12 mm
β = 90.668 (1)°
Data collection top
Bruker APEXII CCD
diffractometer		1287 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2001)		1216 reflections with I > 2σ(I)
Tmin = 0.861, Tmax = 0.987Rint = 0.012
11597 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0251 restraint
wR(F2) = 0.066H atoms treated by a mixture of independent and constrained refinement
S = 1.08Δρmax = 0.14 e Å−3
1287 reflectionsΔρmin = −0.22 e Å−3
176 parameters
Special details top

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 (Å2) top
xyzUiso*/Ueq
C10.4003 (3)0.40584 (12)0.08674 (11)0.0161 (3)
C20.2787 (3)0.42354 (13)−0.02020 (12)0.0185 (3)
H20.33680.4915−0.06490.022*
C30.0725 (3)0.34290 (15)−0.06277 (12)0.0228 (3)
H3−0.00960.3558−0.13610.027*
C4−0.0126 (3)0.24393 (15)0.00205 (14)0.0249 (3)
H4−0.15590.1896−0.02630.03*
C50.1101 (3)0.22366 (13)0.10809 (13)0.0245 (3)
H50.05360.15480.15180.029*
C60.3162 (3)0.30441 (13)0.15048 (12)0.0199 (3)
H60.40030.29040.22330.024*
C70.6208 (3)0.49433 (14)0.13271 (12)0.0183 (3)
H7A0.79960.44940.15210.022*
H7B0.66640.55580.07370.022*
N80.5145 (3)0.55688 (11)0.23428 (10)0.0162 (3)
H80.338 (4)0.5619 (16)0.2452 (14)0.019 (4)*
C90.6898 (3)0.62199 (12)0.30060 (11)0.0136 (3)
O100.94844 (19)0.63427 (9)0.28473 (8)0.0174 (2)
C110.5490 (3)0.67480 (13)0.40651 (12)0.0169 (3)
H11A0.35790.70850.38590.02*
H11B0.52110.60870.46290.02*
N120.7269 (2)0.77163 (10)0.45668 (9)0.0155 (2)
C130.7665 (3)0.89028 (13)0.42442 (11)0.0173 (3)
N140.9577 (3)0.94933 (12)0.48657 (10)0.0212 (3)
C151.0495 (3)0.86385 (13)0.56313 (12)0.0202 (3)
H151.19010.87810.62080.024*
C160.9113 (3)0.75456 (13)0.54557 (11)0.0178 (3)
H160.9390.6810.58750.021*
N170.6082 (3)0.94740 (12)0.33348 (10)0.0239 (3)
O180.4426 (2)0.88404 (11)0.27695 (9)0.0306 (3)
O190.6452 (3)1.05789 (11)0.31808 (11)0.0419 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0137 (6)0.0156 (7)0.0191 (6)0.0026 (6)0.0028 (5)−0.0051 (5)
C20.0202 (7)0.0166 (7)0.0187 (7)0.0025 (6)0.0021 (5)−0.0016 (5)
C30.0208 (7)0.0276 (8)0.0199 (7)0.0040 (7)−0.0040 (6)−0.0089 (6)
C40.0191 (7)0.0216 (8)0.0340 (8)−0.0045 (6)0.0008 (6)−0.0137 (6)
C50.0251 (8)0.0152 (8)0.0333 (8)−0.0025 (6)0.0055 (6)−0.0029 (6)
C60.0212 (7)0.0192 (8)0.0193 (7)−0.0006 (6)0.0004 (5)−0.0023 (6)
C70.0161 (7)0.0196 (7)0.0193 (7)−0.0006 (6)0.0030 (5)−0.0047 (6)
N80.0106 (6)0.0182 (6)0.0198 (6)−0.0003 (5)0.0016 (4)−0.0057 (5)
C90.0153 (7)0.0096 (6)0.0159 (6)0.0013 (5)0.0000 (5)0.0008 (5)
O100.0134 (5)0.0189 (5)0.0198 (4)−0.0008 (4)0.0010 (4)−0.0031 (4)
C110.0160 (6)0.0155 (7)0.0194 (7)−0.0036 (6)0.0012 (5)−0.0059 (5)
N120.0168 (6)0.0139 (6)0.0159 (5)−0.0011 (5)0.0020 (4)−0.0024 (5)
C130.0221 (7)0.0133 (7)0.0164 (6)0.0005 (6)−0.0001 (5)−0.0013 (5)
N140.0281 (7)0.0169 (6)0.0187 (6)−0.0036 (6)−0.0021 (5)−0.0029 (5)
C150.0236 (8)0.0176 (7)0.0194 (7)0.0005 (6)−0.0037 (6)−0.0044 (5)
C160.0210 (7)0.0153 (7)0.0171 (6)0.0029 (6)−0.0014 (5)−0.0014 (5)
N170.0325 (8)0.0211 (7)0.0179 (6)0.0008 (6)−0.0037 (5)0.0002 (5)
O180.0347 (6)0.0323 (7)0.0244 (5)−0.0023 (5)−0.0114 (5)−0.0012 (5)
O190.0699 (10)0.0196 (6)0.0358 (6)−0.0031 (6)−0.0180 (6)0.0077 (5)
Geometric parameters (Å, º) top
O10—C91.2281 (16)C15—C161.370 (2)
N17—O181.2260 (17)C15—H150.95
N17—O191.2316 (18)C4—C31.383 (2)
N17—C131.4348 (18)C4—C51.384 (2)
N12—C161.3581 (18)C4—H40.95
N12—C131.3622 (19)C5—C61.391 (2)
N12—C111.4628 (17)C5—H50.95
N8—C91.3286 (17)C3—H30.95
N8—C71.4675 (17)C7—C11.505 (2)
N8—H80.836 (18)C7—H7A0.99
C9—C111.5278 (18)C7—H7B0.99
C2—C11.3875 (19)C1—C61.396 (2)
C2—C31.391 (2)C11—H11A0.99
C2—H20.95C11—H11B0.99
N14—C131.3144 (19)C16—H160.95
N14—C151.3620 (19)C6—H60.95
O18—N17—O19124.07 (13)C4—C3—H3120.1
O18—N17—C13118.30 (12)C2—C3—H3120.1
O19—N17—C13117.62 (13)N8—C7—C1110.86 (11)
C16—N12—C13104.99 (12)N8—C7—H7A109.5
C16—N12—C11124.17 (12)C1—C7—H7A109.5
C13—N12—C11130.67 (12)N8—C7—H7B109.5
C9—N8—C7121.09 (12)C1—C7—H7B109.5
C9—N8—H8118.2 (12)H7A—C7—H7B108.1
C7—N8—H8119.9 (11)C2—C1—C6118.93 (13)
O10—C9—N8124.46 (12)C2—C1—C7120.41 (13)
O10—C9—C11120.91 (12)C6—C1—C7120.65 (12)
N8—C9—C11114.48 (11)N12—C11—C9110.81 (11)
C1—C2—C3120.75 (13)N12—C11—H11A109.5
C1—C2—H2119.6C9—C11—H11A109.5
C3—C2—H2119.6N12—C11—H11B109.5
C13—N14—C15103.74 (12)C9—C11—H11B109.5
N14—C15—C16110.69 (12)H11A—C11—H11B108.1
N14—C15—H15124.7N12—C16—C15106.76 (13)
C16—C15—H15124.7N12—C16—H16126.6
C3—C4—C5120.29 (14)C15—C16—H16126.6
C3—C4—H4119.9C5—C6—C1120.41 (13)
C5—C4—H4119.9C5—C6—H6119.8
C4—C5—C6119.86 (14)C1—C6—H6119.8
C4—C5—H5120.1N14—C13—N12113.81 (12)
C6—C5—H5120.1N14—C13—N17122.74 (13)
C4—C3—C2119.74 (13)N12—C13—N17123.42 (12)
C7—N8—C9—O10−1.0 (2)C11—N12—C16—C15176.45 (12)
C7—N8—C9—C11−176.53 (13)N14—C15—C16—N12−0.46 (16)
C13—N14—C15—C160.00 (16)C4—C5—C6—C10.0 (2)
C3—C4—C5—C61.1 (2)C2—C1—C6—C5−1.1 (2)
C5—C4—C3—C2−1.1 (2)C7—C1—C6—C5179.30 (13)
C1—C2—C3—C40.0 (2)C15—N14—C13—N120.48 (16)
C9—N8—C7—C1167.75 (12)C15—N14—C13—N17178.56 (13)
C3—C2—C1—C61.1 (2)C16—N12—C13—N14−0.77 (16)
C3—C2—C1—C7−179.29 (13)C11—N12—C13—N14−176.13 (13)
N8—C7—C1—C2116.20 (14)C16—N12—C13—N17−178.83 (13)
N8—C7—C1—C6−64.20 (17)C11—N12—C13—N175.8 (2)
C16—N12—C11—C9−97.72 (15)O18—N17—C13—N14177.06 (14)
C13—N12—C11—C976.86 (17)O19—N17—C13—N14−3.8 (2)
O10—C9—C11—N1220.40 (18)O18—N17—C13—N12−5.0 (2)
N8—C9—C11—N12−163.87 (11)O19—N17—C13—N12174.08 (14)
C13—N12—C16—C150.70 (14)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N8—H8···O10i0.835 (19)2.037 (18)2.837 (2)160.2 (17)
Symmetry code: (i) x−1, y, z.

Experimental details

Crystal data
Chemical formulaC12H12N4O3
Mr260.26
Crystal system, space groupMonoclinic, P21
Temperature (K)100
a, b, c (Å)4.6556 (1), 10.9113 (2), 11.7681 (3)
β (°) 90.668 (1)
V (Å3)597.76 (2)
Z2
Radiation typeMo Kα
µ (mm−1)0.11
Crystal size (mm)0.34 × 0.16 × 0.12
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2001)
Tmin, Tmax0.861, 0.987
No. of measured, independent and
observed [I > 2σ(I)] reflections		11597, 1287, 1216
Rint0.012
(sin θ/λ)max (Å−1)0.626
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.025, 0.066, 1.08
No. of reflections1287
No. of parameters176
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.14, −0.22

Computer programs: APEX2 (Bruker, 2007), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).

Selected geometric parameters (Å, º) top
O10—C91.2281 (16)N12—C111.4628 (17)
N17—O181.2260 (17)N8—C91.3286 (17)
N17—O191.2316 (18)N8—C71.4675 (17)
N17—C131.4348 (18)C9—C111.5278 (18)
C9—N8—C7121.09 (12)N12—C11—C9110.81 (11)
N8—C7—C1110.86 (11)N12—C13—N17123.42 (12)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N8—H8···O10i0.835 (19)2.037 (18)2.837 (2)160.2 (17)
Symmetry code: (i) x−1, y, z.
 

Acknowledgements

The authors thank LAFEPE/Brazil, CNPq/Brazil and Xunta de Galicia (project No. PGIDT01BIO20302PR) for supporting this work.

References

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ISSN: 2056-9890
Volume 64| Part 3| March 2008| Page o634
doi:10.1107/S1600536808005023
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