organic compounds
Ethyl 4-(2-hydroxyethylamino)-3-nitrobenzoate
aSchool of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, bKulliyyah of Science, International Islamic University Malaysia (IIUM), Jalan Istana, Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia, and cX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hkfun@usm.my
In the title compound, C11H14N2O5, the molecular structure is stabilized by an intramolecular N—H⋯O hydrogen bond, which generates an S(6) ring motif. The nitro group is twisted slightly from the attached benzene ring, forming a dihedral angle of 5.2 (2)°. In the crystal packing, intermolecular O—H⋯O and C—H⋯O hydrogen bonds link the molecules into a three-dimensional network. The crystal studied was a non-merohedral twin, the refined ratio of the twin components being 0.264 (2):0.736 (2).
Related literature
For background to benzimidazoles, see: Mayer et al. (1998); Brouillette et al. (1999); Williams et al. (1995); Wright (1951). For reference bond-length data, see: Allen et al. (1987). For related structures, see: Narendra Babu, Abdul Rahim, Abd Hamid et al. (2009); Narendra Babu, Abdul Rahim, Osman et al. (2009). For hydrogen-bond motifs, see: Bernstein et al. (1995). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986).
Experimental
Crystal data
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Refinement
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Data collection: APEX2 (Bruker, 2009); cell SAINT (Bruker, 2009); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009).
Supporting information
10.1107/S1600536810008147/wn2377sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536810008147/wn2377Isup2.hkl
The synthesis of the title compound was performed by the dropwise addition of N,N-diisopropyl ethylamine (1.1 mmol) to a stirred solution of ethyl 4-fluoro-3-nitrobenzoate (1.0 mmol) in dry dichloromethane (10.0 ml), followed by ethanolamine (1.1 mmol). The reaction mixture was left stirring overnight at room temperature under an inert atmosphere. Upon completion, the reaction mixture was washed with 10% Na2CO3 (3 x 10.0 ml). The combined organic fractions were dried over MgSO4 and evaporated in vacuo. Recrystallisation with hot hexane gave the title compound as bright yellow crystals, which were found to be suitable for characterisation by X-ray crystallography.
H2A and H5B were located in a difference Fourier map and were refined freely [N—H = 0.84 (3) Å; O—H = 0.83 (3) Å]. The remaining H atoms were positioned geometrically [C—H = 0.93 to 0.97 Å] and were refined using a riding model, with Uiso(H) = xUeq(C), where x = 1.5 for methyl H and 1.2 for all other H atoms. A rotating group model was applied to the methyl group. The crystal studied was a non-merohedral twin, the refined ratio of the twin components being 0.264 (2):0.736 (2).
Data collection: APEX2 (Bruker, 2009); cell
SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).Fig. 1. The molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme. Hydrogen atoms are shown as spheres of arbitrary radius. The dashed line indicates an intramolecular hydrogen bond. | |
Fig. 2. The crystal packing of the title compound, viewed along the c axis. H atoms not involved in the intermolecular interactions (dashed lines) have been omitted for clarity. |
C11H14N2O5 | F(000) = 536 |
Mr = 254.24 | Dx = 1.491 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 1880 reflections |
a = 10.6422 (6) Å | θ = 2.4–28.1° |
b = 14.9954 (9) Å | µ = 0.12 mm−1 |
c = 7.1975 (4) Å | T = 100 K |
β = 99.607 (2)° | Needle, yellow |
V = 1132.50 (11) Å3 | 0.43 × 0.13 × 0.03 mm |
Z = 4 |
Bruker SMART APEXII CCD area-detector diffractometer | 2587 independent reflections |
Radiation source: fine-focus sealed tube | 2026 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.050 |
ϕ and ω scans | θmax = 27.5°, θmin = 2.4° |
Absorption correction: multi-scan (SADABS; Bruker, 2090) | h = −13→13 |
Tmin = 0.951, Tmax = 0.997 | k = −19→19 |
8457 measured reflections | l = −8→9 |
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)] = 0.051 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.129 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0602P)2 + 0.3204P] where P = (Fo2 + 2Fc2)/3 |
2587 reflections | (Δ/σ)max < 0.001 |
173 parameters | Δρmax = 0.50 e Å−3 |
0 restraints | Δρmin = −0.31 e Å−3 |
C11H14N2O5 | V = 1132.50 (11) Å3 |
Mr = 254.24 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 10.6422 (6) Å | µ = 0.12 mm−1 |
b = 14.9954 (9) Å | T = 100 K |
c = 7.1975 (4) Å | 0.43 × 0.13 × 0.03 mm |
β = 99.607 (2)° |
Bruker SMART APEXII CCD area-detector diffractometer | 2587 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2090) | 2026 reflections with I > 2σ(I) |
Tmin = 0.951, Tmax = 0.997 | Rint = 0.050 |
8457 measured reflections |
R[F2 > 2σ(F2)] = 0.051 | 0 restraints |
wR(F2) = 0.129 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | Δρmax = 0.50 e Å−3 |
2587 reflections | Δρmin = −0.31 e Å−3 |
173 parameters |
Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K. |
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 > 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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.38669 (15) | 0.04338 (11) | 1.1300 (3) | 0.0285 (4) | |
O2 | 0.57298 (13) | 0.09227 (10) | 1.2508 (2) | 0.0193 (4) | |
O3 | 0.04479 (14) | 0.22764 (10) | 0.8325 (2) | 0.0194 (4) | |
O4 | 0.07343 (13) | 0.37665 (10) | 0.8413 (2) | 0.0170 (4) | |
O5 | 0.82105 (15) | 0.33071 (11) | 1.0883 (2) | 0.0192 (4) | |
N1 | 0.46108 (17) | 0.10564 (12) | 1.1729 (3) | 0.0157 (4) | |
N2 | 0.61527 (17) | 0.26565 (12) | 1.2825 (3) | 0.0147 (4) | |
C1 | 0.29266 (19) | 0.20462 (14) | 1.0362 (3) | 0.0141 (5) | |
H1A | 0.2445 | 0.1539 | 0.9998 | 0.017* | |
C2 | 0.4166 (2) | 0.19539 (14) | 1.1327 (3) | 0.0135 (4) | |
C3 | 0.49466 (19) | 0.27115 (14) | 1.1919 (3) | 0.0135 (4) | |
C4 | 0.43542 (19) | 0.35571 (14) | 1.1508 (3) | 0.0148 (5) | |
H4A | 0.4811 | 0.4071 | 1.1901 | 0.018* | |
C5 | 0.3135 (2) | 0.36374 (14) | 1.0555 (3) | 0.0148 (5) | |
H5A | 0.2784 | 0.4202 | 1.0308 | 0.018* | |
C6 | 0.2402 (2) | 0.28743 (14) | 0.9938 (3) | 0.0150 (5) | |
C7 | 0.11002 (19) | 0.29283 (14) | 0.8828 (3) | 0.0148 (5) | |
C8 | −0.05110 (19) | 0.38757 (14) | 0.7226 (3) | 0.0168 (5) | |
H8A | −0.1143 | 0.3517 | 0.7709 | 0.020* | |
H8B | −0.0473 | 0.3685 | 0.5949 | 0.020* | |
C9 | −0.0866 (2) | 0.48440 (16) | 0.7242 (4) | 0.0254 (6) | |
H9A | −0.1695 | 0.4929 | 0.6501 | 0.038* | |
H9B | −0.0251 | 0.5192 | 0.6722 | 0.038* | |
H9C | −0.0879 | 0.5031 | 0.8515 | 0.038* | |
C10 | 0.69687 (19) | 0.34151 (14) | 1.3465 (3) | 0.0142 (4) | |
H10A | 0.7673 | 0.3210 | 1.4400 | 0.017* | |
H10B | 0.6484 | 0.3841 | 1.4073 | 0.017* | |
C11 | 0.75012 (19) | 0.38863 (14) | 1.1886 (3) | 0.0157 (5) | |
H11A | 0.6801 | 0.4141 | 1.1011 | 0.019* | |
H11B | 0.8047 | 0.4372 | 1.2419 | 0.019* | |
H2A | 0.642 (2) | 0.2141 (18) | 1.310 (4) | 0.021 (7)* | |
H5B | 0.888 (3) | 0.3148 (18) | 1.156 (4) | 0.028 (8)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0224 (8) | 0.0119 (8) | 0.0480 (12) | −0.0046 (7) | −0.0035 (8) | 0.0003 (8) |
O2 | 0.0169 (8) | 0.0143 (8) | 0.0252 (9) | 0.0027 (6) | −0.0004 (7) | 0.0010 (7) |
O3 | 0.0145 (7) | 0.0177 (8) | 0.0243 (9) | −0.0040 (6) | −0.0011 (7) | 0.0005 (7) |
O4 | 0.0118 (7) | 0.0168 (8) | 0.0207 (9) | 0.0003 (6) | −0.0024 (6) | 0.0005 (7) |
O5 | 0.0149 (8) | 0.0216 (9) | 0.0204 (9) | 0.0025 (6) | 0.0012 (7) | −0.0020 (7) |
N1 | 0.0146 (9) | 0.0129 (9) | 0.0192 (10) | −0.0015 (7) | 0.0018 (7) | −0.0009 (8) |
N2 | 0.0116 (8) | 0.0115 (9) | 0.0201 (10) | 0.0007 (7) | 0.0002 (8) | 0.0017 (8) |
C1 | 0.0153 (11) | 0.0145 (10) | 0.0130 (11) | −0.0038 (8) | 0.0036 (8) | −0.0026 (9) |
C2 | 0.0151 (10) | 0.0119 (10) | 0.0144 (11) | −0.0002 (8) | 0.0051 (8) | 0.0017 (8) |
C3 | 0.0145 (10) | 0.0142 (11) | 0.0118 (11) | −0.0018 (8) | 0.0029 (8) | −0.0001 (8) |
C4 | 0.0135 (10) | 0.0123 (10) | 0.0188 (12) | −0.0012 (8) | 0.0030 (8) | −0.0016 (9) |
C5 | 0.0169 (10) | 0.0128 (10) | 0.0147 (11) | 0.0014 (8) | 0.0027 (8) | 0.0010 (9) |
C6 | 0.0132 (10) | 0.0165 (11) | 0.0156 (11) | 0.0003 (8) | 0.0030 (9) | 0.0013 (9) |
C7 | 0.0148 (10) | 0.0159 (11) | 0.0144 (11) | −0.0004 (8) | 0.0045 (9) | 0.0007 (9) |
C8 | 0.0116 (10) | 0.0203 (11) | 0.0161 (11) | 0.0004 (8) | −0.0045 (9) | 0.0015 (9) |
C9 | 0.0198 (11) | 0.0226 (13) | 0.0301 (14) | 0.0053 (9) | −0.0069 (10) | −0.0019 (11) |
C10 | 0.0116 (9) | 0.0147 (10) | 0.0148 (11) | −0.0009 (8) | −0.0017 (8) | −0.0004 (9) |
C11 | 0.0127 (10) | 0.0128 (10) | 0.0208 (11) | −0.0013 (8) | 0.0005 (9) | −0.0004 (9) |
O1—N1 | 1.230 (2) | C4—C5 | 1.368 (3) |
O2—N1 | 1.245 (2) | C4—H4A | 0.9300 |
O3—C7 | 1.218 (3) | C5—C6 | 1.414 (3) |
O4—C7 | 1.335 (3) | C5—H5A | 0.9300 |
O4—C8 | 1.461 (2) | C6—C7 | 1.482 (3) |
O5—C11 | 1.424 (3) | C8—C9 | 1.501 (3) |
O5—H5B | 0.83 (3) | C8—H8A | 0.9700 |
N1—C2 | 1.440 (3) | C8—H8B | 0.9700 |
N2—C3 | 1.342 (3) | C9—H9A | 0.9600 |
N2—C10 | 1.459 (3) | C9—H9B | 0.9600 |
N2—H2A | 0.84 (3) | C9—H9C | 0.9600 |
C1—C6 | 1.375 (3) | C10—C11 | 1.526 (3) |
C1—C2 | 1.391 (3) | C10—H10A | 0.9700 |
C1—H1A | 0.9300 | C10—H10B | 0.9700 |
C2—C3 | 1.430 (3) | C11—H11A | 0.9700 |
C3—C4 | 1.425 (3) | C11—H11B | 0.9700 |
C7—O4—C8 | 116.01 (16) | O3—C7—C6 | 123.46 (19) |
C11—O5—H5B | 110 (2) | O4—C7—C6 | 112.56 (18) |
O1—N1—O2 | 121.21 (17) | O4—C8—C9 | 107.99 (17) |
O1—N1—C2 | 118.86 (17) | O4—C8—H8A | 110.1 |
O2—N1—C2 | 119.92 (17) | C9—C8—H8A | 110.1 |
C3—N2—C10 | 125.21 (19) | O4—C8—H8B | 110.1 |
C3—N2—H2A | 115.5 (18) | C9—C8—H8B | 110.1 |
C10—N2—H2A | 119.1 (18) | H8A—C8—H8B | 108.4 |
C6—C1—C2 | 121.12 (19) | C8—C9—H9A | 109.5 |
C6—C1—H1A | 119.4 | C8—C9—H9B | 109.5 |
C2—C1—H1A | 119.4 | H9A—C9—H9B | 109.5 |
C1—C2—C3 | 121.68 (19) | C8—C9—H9C | 109.5 |
C1—C2—N1 | 116.49 (18) | H9A—C9—H9C | 109.5 |
C3—C2—N1 | 121.82 (19) | H9B—C9—H9C | 109.5 |
N2—C3—C4 | 120.65 (19) | N2—C10—C11 | 113.65 (18) |
N2—C3—C2 | 123.9 (2) | N2—C10—H10A | 108.8 |
C4—C3—C2 | 115.47 (18) | C11—C10—H10A | 108.8 |
C5—C4—C3 | 122.1 (2) | N2—C10—H10B | 108.8 |
C5—C4—H4A | 118.9 | C11—C10—H10B | 108.8 |
C3—C4—H4A | 118.9 | H10A—C10—H10B | 107.7 |
C4—C5—C6 | 120.9 (2) | O5—C11—C10 | 112.94 (18) |
C4—C5—H5A | 119.5 | O5—C11—H11A | 109.0 |
C6—C5—H5A | 119.5 | C10—C11—H11A | 109.0 |
C1—C6—C5 | 118.61 (19) | O5—C11—H11B | 109.0 |
C1—C6—C7 | 118.53 (19) | C10—C11—H11B | 109.0 |
C5—C6—C7 | 122.85 (19) | H11A—C11—H11B | 107.8 |
O3—C7—O4 | 123.96 (19) | ||
C6—C1—C2—C3 | 0.0 (3) | C3—C4—C5—C6 | 0.3 (3) |
C6—C1—C2—N1 | 178.9 (2) | C2—C1—C6—C5 | −1.9 (3) |
O1—N1—C2—C1 | −3.9 (3) | C2—C1—C6—C7 | 177.1 (2) |
O2—N1—C2—C1 | 176.5 (2) | C4—C5—C6—C1 | 1.8 (3) |
O1—N1—C2—C3 | 175.0 (2) | C4—C5—C6—C7 | −177.2 (2) |
O2—N1—C2—C3 | −4.6 (3) | C8—O4—C7—O3 | −2.2 (3) |
C10—N2—C3—C4 | −0.1 (3) | C8—O4—C7—C6 | 176.60 (18) |
C10—N2—C3—C2 | −179.3 (2) | C1—C6—C7—O3 | 2.8 (3) |
C1—C2—C3—N2 | −178.8 (2) | C5—C6—C7—O3 | −178.3 (2) |
N1—C2—C3—N2 | 2.4 (3) | C1—C6—C7—O4 | −176.1 (2) |
C1—C2—C3—C4 | 2.0 (3) | C5—C6—C7—O4 | 2.9 (3) |
N1—C2—C3—C4 | −176.81 (19) | C7—O4—C8—C9 | 168.7 (2) |
N2—C3—C4—C5 | 178.7 (2) | C3—N2—C10—C11 | −76.3 (3) |
C2—C3—C4—C5 | −2.1 (3) | N2—C10—C11—O5 | −57.4 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···O2 | 0.84 (3) | 1.99 (3) | 2.642 (2) | 134 (2) |
O5—H5B···O3i | 0.83 (3) | 2.02 (3) | 2.851 (2) | 177 (3) |
C8—H8A···O5ii | 0.97 | 2.51 | 3.271 (3) | 135 |
C10—H10A···O5iii | 0.97 | 2.54 | 3.267 (3) | 132 |
C10—H10B···O1iv | 0.97 | 2.43 | 3.168 (3) | 133 |
C11—H11A···O2v | 0.97 | 2.59 | 3.403 (3) | 142 |
Symmetry codes: (i) x+1, −y+1/2, z+1/2; (ii) x−1, y, z; (iii) x, −y+1/2, z+1/2; (iv) −x+1, y+1/2, −z+5/2; (v) x, −y+1/2, z−1/2. |
Experimental details
Crystal data | |
Chemical formula | C11H14N2O5 |
Mr | 254.24 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 100 |
a, b, c (Å) | 10.6422 (6), 14.9954 (9), 7.1975 (4) |
β (°) | 99.607 (2) |
V (Å3) | 1132.50 (11) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.43 × 0.13 × 0.03 |
Data collection | |
Diffractometer | Bruker SMART APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2090) |
Tmin, Tmax | 0.951, 0.997 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8457, 2587, 2026 |
Rint | 0.050 |
(sin θ/λ)max (Å−1) | 0.650 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.051, 0.129, 1.04 |
No. of reflections | 2587 |
No. of parameters | 173 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.50, −0.31 |
Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···O2 | 0.84 (3) | 1.99 (3) | 2.642 (2) | 134 (2) |
O5—H5B···O3i | 0.83 (3) | 2.02 (3) | 2.851 (2) | 177 (3) |
C8—H8A···O5ii | 0.9700 | 2.5100 | 3.271 (3) | 135.00 |
C10—H10A···O5iii | 0.97 | 2.54 | 3.267 (3) | 132.0 |
C10—H10B···O1iv | 0.9700 | 2.4300 | 3.168 (3) | 133.00 |
C11—H11A···O2v | 0.97 | 2.59 | 3.403 (3) | 141.6 |
Symmetry codes: (i) x+1, −y+1/2, z+1/2; (ii) x−1, y, z; (iii) x, −y+1/2, z+1/2; (iv) −x+1, y+1/2, −z+5/2; (v) x, −y+1/2, z−1/2. |
Acknowledgements
HKF and WSL thank Universiti Sains Malaysia (USM) for the Research University Golden Goose Grant (1001/PFIZIK/811012). WSL thanks the Malaysian Government and USM for the award of a Research Fellowship. ASAR, SAH and SNNB thank USM for funding the synthetic chemistry work under the University Research Grant (1001/PFARMASI/815026). SNNB acknowledges USM for a post-doctoral research fellowship.
References
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Benzimidazoles serve as a common scaffold used worldwide for various successful drugs (Mayer et al., 1998). Construction of pharmacologically important benzimidazoles could be accessed via nitrobenzoic acid precursors (Brouillette et al., 1999; Williams et al., 1995; Wright, 1951). The title compound was obtained as an intermediate in the synthesis of benzimidazole derivatives; we present here its crystal structure.
In the title compound (Fig. 1), the molecular structure is stabilized by an intramolecular N2—H2A···O2 hydrogen bond which generates an S(6) ring motif (Bernstein et al., 1995). The nitro group is slightly twisted away from the benzene ring, the dihedral angle between N1/O1/O2/C2 and C1–C6 being 5.2 (2)°. The bond lengths (Allen et al., 1987) and angles in the molecule are within normal ranges and are similiar to those in other related structures (Narendra Babu, Abdul Rahim, Abd Hamid et al., 2009; Narendra Babu, Abdul Rahim, Osman et al., 2009).
In the crystal packing (Fig. 2), intermolecular O5—H5B···O3, C8—H8A···O5, C10—H10A···O5, C10—H10B···O1 and C11—H11A···O2 hydrogen bonds (Table 1) link the molecules into a three-dimensional network.