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Acta Crystallogr Sect E Struct Rep Online. 2008 August 1; 64(Pt 8): o1422.
Published online 2008 July 5. doi:  10.1107/S1600536808019521
PMCID: PMC2962056

N-(2-Hydroxy­ethyl)-3,5-dinitro­benzamide

Abstract

The title compound, C9H9N3O6, was synthesized by the condensation of methyl 3,5-dinitro­benzoate and 2-amino­ethanol. The non-centrosymmetric space group results in the formation of pseudo-chiral helices in the crystal structure, which exhibits a layer packing structure involving intra­molecular N—H(...)O and O—H(...)O inter­actions.

Related literature

For related literature, see: Lin & Smith (1981 [triangle]); Morehouse & McGuire (1959 [triangle]); Percec (1981 [triangle], 1982 [triangle]); Walde (1962 [triangle]).

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Object name is e-64-o1422-scheme1.jpg

Experimental

Crystal data

  • C9H9N3O6
  • M r = 255.19
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1422-efi3.jpg
  • a = 6.514 (4) Å
  • b = 9.097 (3) Å
  • c = 18.177 (3) Å
  • V = 1077.1 (8) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.14 mm−1
  • T = 294 (2) K
  • 0.46 × 0.45 × 0.33 mm

Data collection

  • Enraf–Nonius CAD-4 diffractometer
  • Absorption correction: none
  • 1124 measured reflections
  • 1118 independent reflections
  • 945 reflections with I > 2σ(I)
  • R int = 0.015
  • 3 standard reflections every 100 reflections intensity decay: 3.4%

Refinement

  • R[F 2 > 2σ(F 2)] = 0.035
  • wR(F 2) = 0.092
  • S = 1.10
  • 1118 reflections
  • 164 parameters
  • H-atom parameters constrained
  • Δρmax = 0.14 e Å−3
  • Δρmin = −0.18 e Å−3

Data collection: DIFRAC (Gabe et al., 1993 [triangle]); cell refinement: DIFRAC; data reduction: NRCVAX (Gabe et al., 1989 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]) and DIAMOND (Brandenburg, 1998 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808019521/lx2057sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808019521/lx2057Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors thank the National Natural Science Foundation of China (NSFC, contract No. 20675054) and the Promotion Program Foundation of Sichuan University of China (No. 0082204127090) for financial support of this study.

supplementary crystallographic information

Comment

Non-ionic contrast agents, which are used in the field of intravascular and central nervous system visualization, are mostly complex molecules. However, the iodine in the molecule provides opacification to the x-rays and the remainder of the molecule provides the framework for transport of the iodine atoms. As a result, the structural arrangement of the molecule is very important in providing stability, solubility and biological safety in various organs (Lin & Smith, 1981). The title compound is an important intermediate in the synthesis of a variety of these molecules. It also can be used against coccidiosis and salmonella infection in poultry (Walde, 1962; Morehouse & McGuire, 1959).In addition, it plays an important role in the synthesis of copolymers (Percec, 1982; Percec, 1981). In this paper, we report the crystal structure of the title compound, N-(2-hydroxyethyl)-3,5-dinitrobenzamide (Fig. 1).

The title compound was crystallized in the non-centrosymmetric space group P212121 in spite of having no asymmetric carbon atom in the molecule. In the packing structure, an intermolecular O—H···O hydrogen bond leads to form pseudo-chiral helix about the 21 screw axis, propagating in the [100] direction. Non-centrosymmetric space group P212121 results in the formation of pseudo-chiral helix in the packing structure (Fig. 2). The crystal structure exhibits a layer packing structure with the intramolecular N—H···O and O—H···O hydrogen bonds (Fig. 2 and Table 1; symmetry code as in Fig. 2). On the other hand, adjacent molecules are linked into chains through van der Waals force to stabilize the crystal structure.

Experimental

A mixture of methyl 3,5-dinitrobenzoate (5.65 g, 0.025 mol) and 50% aqueous 2-aminoethanol (30.5 g, 0.5 mol) was stirred for 10 h at room temperture. Then 30 ml water was added and the crystalline product was collected. Recrystallization of the crude product from ethanol gave N-(2-hydroxyethyl)-3,5-dinitrobenzamide (m.p. 416-417 K) (Lin & Smith, 1981). Single crystals of the title compound were obtained and used for X-ray diffraction studies at room temperature.

Refinement

All H atoms were placed in idealized positions {C—H = 0.93 Å% (aromatic); C—H = 0.97 Å% (methylene); N—H = 0.86 Å%; O—H = 0.82 Å%} and refined as riding, with Uiso(H) = 1.2Ueq(C, N) or 1.5Ueq(O). Friedel pairs were merged at final refinement.

Figures

Fig. 1.
Molecular structure of title compound. Displacement ellipsoids are drawn at the 30% probability level.
Fig. 2.
View of the structure projected on the ac plane. Hydrogen bonding shown as dashed lines. [Symmetry code: (i) x+1/2, -y+3/2, -z+1; (ii) x+1, y, z.]

Crystal data

C9H9N3O6Dx = 1.574 Mg m3
Mr = 255.19Melting point = 416–417 K
Orthorhombic, P212121Mo Kα radiation λ = 0.71073 Å
Hall symbol: p 2ac 2abCell parameters from 24 reflections
a = 6.514 (4) Åθ = 4.5–7.8º
b = 9.097 (3) ŵ = 0.14 mm1
c = 18.177 (3) ÅT = 294 (2) K
V = 1077.1 (8) Å3Block, colourless
Z = 40.46 × 0.45 × 0.33 mm
F000 = 528

Data collection

Enraf–Nonius CAD-4 diffractometerRint = 0.015
Radiation source: fine-focus sealed tubeθmax = 25.0º
Monochromator: graphiteθmin = 2.2º
T = 294(2) Kh = −3→7
ω/2θ scansk = −4→10
Absorption correction: nonel = −10→21
1124 measured reflections3 standard reflections
1118 independent reflections every 100 reflections
945 reflections with I > 2σ(I) intensity decay: 3.4%

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.035  w = 1/[σ2(Fo2) + (0.0522P)2 + 0.1396P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.092(Δ/σ)max < 0.001
S = 1.10Δρmax = 0.14 e Å3
1118 reflectionsΔρmin = −0.18 e Å3
164 parametersExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.219 (12)
Secondary atom site location: difference Fourier map

Special details

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.
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 > 2sigma(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)

xyzUiso*/Ueq
O10.2873 (3)0.5989 (2)0.34735 (10)0.0471 (6)
O20.5044 (3)0.7755 (2)0.56083 (10)0.0476 (6)
H2W0.55350.81060.59850.071*
O30.5495 (4)0.6710 (3)0.02304 (11)0.0717 (8)
O40.3233 (5)0.5573 (4)0.08631 (13)0.1040 (12)
O51.0931 (4)0.9372 (3)0.26737 (12)0.0799 (9)
O61.1272 (4)0.8922 (3)0.15286 (11)0.0696 (8)
N10.5752 (4)0.6420 (2)0.41241 (11)0.0370 (6)
H1N0.69160.68650.41320.044*
N20.4757 (5)0.6333 (3)0.08103 (13)0.0535 (7)
N31.0356 (4)0.8822 (3)0.21046 (13)0.0464 (6)
C10.5713 (4)0.6903 (3)0.28124 (14)0.0316 (6)
C20.7552 (4)0.7679 (3)0.27890 (13)0.0332 (6)
H2A0.81860.79820.32220.040*
C30.8421 (4)0.7994 (3)0.21153 (14)0.0355 (6)
C40.7576 (4)0.7570 (3)0.14550 (13)0.0366 (7)
H40.82020.77790.10070.044*
C50.5739 (5)0.6816 (3)0.14983 (14)0.0386 (7)
C60.4801 (4)0.6487 (3)0.21553 (14)0.0358 (6)
H60.35560.59870.21590.043*
C70.4681 (4)0.6420 (3)0.35076 (14)0.0350 (7)
C80.5042 (5)0.5698 (3)0.47915 (13)0.0437 (7)
H8A0.54030.46640.47680.052*
H8B0.35570.57650.48150.052*
C90.5928 (4)0.6344 (3)0.54759 (14)0.0426 (7)
H9A0.56520.57000.58900.051*
H9B0.74040.64380.54240.051*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0326 (11)0.0647 (13)0.0441 (10)−0.0133 (11)0.0046 (9)−0.0125 (10)
O20.0324 (10)0.0700 (13)0.0405 (10)0.0039 (11)−0.0015 (9)−0.0121 (9)
O30.089 (2)0.0951 (17)0.0311 (11)−0.0176 (17)−0.0042 (13)0.0000 (11)
O40.103 (2)0.156 (3)0.0536 (14)−0.079 (2)−0.0175 (15)−0.0111 (17)
O50.0793 (19)0.113 (2)0.0478 (13)−0.0607 (17)−0.0059 (12)0.0036 (13)
O60.0530 (14)0.104 (2)0.0523 (13)−0.0241 (16)0.0145 (12)0.0089 (13)
N10.0305 (12)0.0486 (13)0.0319 (11)−0.0083 (12)0.0060 (10)0.0000 (10)
N20.0617 (19)0.0631 (16)0.0356 (13)−0.0109 (18)−0.0113 (14)−0.0048 (12)
N30.0415 (14)0.0577 (14)0.0400 (13)−0.0152 (13)0.0011 (13)0.0105 (13)
C10.0287 (13)0.0319 (12)0.0341 (13)0.0022 (12)0.0013 (12)−0.0024 (11)
C20.0334 (14)0.0363 (13)0.0300 (12)−0.0038 (12)−0.0027 (12)−0.0013 (11)
C30.0320 (13)0.0378 (13)0.0367 (13)−0.0040 (12)0.0003 (13)0.0023 (12)
C40.0415 (17)0.0383 (14)0.0300 (12)0.0006 (14)0.0033 (13)0.0031 (11)
C50.0442 (17)0.0414 (14)0.0303 (13)0.0005 (15)−0.0081 (12)−0.0026 (11)
C60.0281 (13)0.0400 (13)0.0391 (14)−0.0011 (12)−0.0031 (13)−0.0039 (12)
C70.0310 (16)0.0392 (15)0.0346 (14)−0.0051 (14)0.0027 (12)−0.0081 (11)
C80.0455 (16)0.0502 (15)0.0354 (13)−0.0075 (15)0.0068 (14)0.0031 (12)
C90.0345 (15)0.0576 (17)0.0356 (13)0.0019 (16)0.0030 (12)0.0081 (13)

Geometric parameters (Å, °)

O1—C71.243 (4)C1—C71.498 (4)
O2—C91.428 (3)C2—C31.379 (3)
O2—H2W0.8200C2—H2A0.9300
O3—N21.208 (3)C3—C41.376 (4)
O4—N21.213 (4)C4—C51.382 (4)
O5—N31.209 (3)C4—H40.9300
O6—N31.209 (3)C5—C61.374 (4)
N1—C71.320 (3)C6—H60.9300
N1—C81.455 (3)C8—C91.492 (4)
N1—H1N0.8600C8—H8A0.9700
N2—C51.472 (4)C8—H8B0.9700
N3—C31.468 (3)C9—H9A0.9700
C1—C61.387 (3)C9—H9B0.9700
C1—C21.391 (4)
C9—O2—H2W109.5C6—C5—C4122.9 (2)
C7—N1—C8122.7 (2)C6—C5—N2118.7 (3)
C7—N1—H1N118.7C4—C5—N2118.4 (3)
C8—N1—H1N118.7C5—C6—C1119.9 (2)
O3—N2—O4123.8 (3)C5—C6—H6120.0
O3—N2—C5119.0 (3)C1—C6—H6120.0
O4—N2—C5117.3 (3)O1—C7—N1122.9 (3)
O6—N3—O5123.9 (2)O1—C7—C1118.4 (2)
O6—N3—C3118.3 (2)N1—C7—C1118.6 (2)
O5—N3—C3117.8 (2)N1—C8—C9113.2 (2)
C6—C1—C2118.8 (2)N1—C8—H8A108.9
C6—C1—C7117.0 (2)C9—C8—H8A108.9
C2—C1—C7124.2 (2)N1—C8—H8B108.9
C3—C2—C1119.1 (2)C9—C8—H8B108.9
C3—C2—H2A120.5H8A—C8—H8B107.7
C1—C2—H2A120.5O2—C9—C8109.8 (2)
C4—C3—C2123.5 (2)O2—C9—H9A109.7
C4—C3—N3118.4 (2)C8—C9—H9A109.7
C2—C3—N3118.1 (2)O2—C9—H9B109.7
C3—C4—C5115.9 (2)C8—C9—H9B109.7
C3—C4—H4122.1H9A—C9—H9B108.2
C5—C4—H4122.1
C6—C1—C2—C3−0.8 (3)O3—N2—C5—C4−5.8 (4)
C7—C1—C2—C3176.3 (2)O4—N2—C5—C4174.3 (3)
C1—C2—C3—C4−0.6 (4)C4—C5—C6—C1−0.8 (4)
C1—C2—C3—N3179.6 (2)N2—C5—C6—C1178.7 (2)
O6—N3—C3—C4−10.1 (4)C2—C1—C6—C51.4 (4)
O5—N3—C3—C4169.5 (3)C7—C1—C6—C5−175.9 (3)
O6—N3—C3—C2169.7 (3)C8—N1—C7—O110.3 (4)
O5—N3—C3—C2−10.7 (4)C8—N1—C7—C1−167.1 (2)
C2—C3—C4—C51.2 (4)C6—C1—C7—O1−16.4 (4)
N3—C3—C4—C5−179.0 (2)C2—C1—C7—O1166.4 (2)
C3—C4—C5—C6−0.6 (4)C6—C1—C7—N1161.2 (2)
C3—C4—C5—N2180.0 (3)C2—C1—C7—N1−16.0 (4)
O3—N2—C5—C6174.7 (3)C7—N1—C8—C9−154.7 (3)
O4—N2—C5—C6−5.2 (4)N1—C8—C9—O271.7 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O2—H2W···O1i0.821.992.737 (3)151
N1—H1N···O2i0.862.122.935 (3)158

Symmetry codes: (i) x+1/2, −y+3/2, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LX2057).

References

  • Brandenburg, K. (1998). DIAMOND Crystal Impact GbR, Bonn, Germany.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Gabe, E. J., Le Page, Y., Charland, J.-P., Lee, F. L. & White, P. S. (1989). J. Appl. Cryst.22, 384–387.
  • Gabe, E. J., White, P. S. & Enright, G. D. (1993). DIFRAC American Crystallographic Association, Pittsburgh meeting. Abstract PA104.
  • Lin, Y. L. & Smith, K. R. (1981). US Patent 4 284 620.
  • Morehouse, N. F. & McGuire, W. C. (1959). Poult. Sci.38, 410–423.
  • Percec, V. (1981). Polym. Bull.5, 651–657.
  • Percec, V. (1982). Polym. Prep.23, 301–302.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Walde, A. W. (1962). US Patent 3 015 606.

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