Literature DB >> 21580671

Ethyl 4-(2-hydroxy-ethyl-amino)-3-nitro-benzoate.

Aisyah Saad Abdul Rahim, Shafida Abd Hamid, Shivanagere Nagojappa Narendra Babu, Wan-Sin Loh, Hoong-Kun Fun.   

Abstract

In the title compound, C(11)H(14)N(2)O(5), the mol-ecular structure is stabilized by an intra-molecular 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, inter-molecular O-H⋯O and C-H⋯O hydrogen bonds link the mol-ecules 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).

Entities:  

Year:  2010        PMID: 21580671      PMCID: PMC2983846          DOI: 10.1107/S1600536810008147

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


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

C11H14N2O5 M = 254.24 Monoclinic, a = 10.6422 (6) Å b = 14.9954 (9) Å c = 7.1975 (4) Å β = 99.607 (2)° V = 1132.50 (11) Å3 Z = 4 Mo Kα radiation μ = 0.12 mm−1 T = 100 K 0.43 × 0.13 × 0.03 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 209 ▶0) T min = 0.951, T max = 0.997 8457 measured reflections 2587 independent reflections 2026 reflections with I > 2σ(I) R int = 0.050

Refinement

R[F 2 > 2σ(F 2)] = 0.051 wR(F 2) = 0.129 S = 1.04 2587 reflections 173 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.50 e Å−3 Δρmin = −0.31 e Å−3 Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: 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 ▶). Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810008147/wn2377sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536810008147/wn2377Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C11H14N2O5F(000) = 536
Mr = 254.24Dx = 1.491 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 1880 reflections
a = 10.6422 (6) Åθ = 2.4–28.1°
b = 14.9954 (9) ŵ = 0.12 mm1
c = 7.1975 (4) ÅT = 100 K
β = 99.607 (2)°Needle, yellow
V = 1132.50 (11) Å30.43 × 0.13 × 0.03 mm
Z = 4
Bruker SMART APEXII CCD area-detector diffractometer2587 independent reflections
Radiation source: fine-focus sealed tube2026 reflections with I > 2σ(I)
graphiteRint = 0.050
φ and ω scansθmax = 27.5°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2090)h = −13→13
Tmin = 0.951, Tmax = 0.997k = −19→19
8457 measured reflectionsl = −8→9
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.051Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.129H atoms treated by a mixture of independent and constrained refinement
S = 1.04w = 1/[σ2(Fo2) + (0.0602P)2 + 0.3204P] where P = (Fo2 + 2Fc2)/3
2587 reflections(Δ/σ)max < 0.001
173 parametersΔρmax = 0.50 e Å3
0 restraintsΔρmin = −0.31 e Å3
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.
xyzUiso*/Ueq
O10.38669 (15)0.04338 (11)1.1300 (3)0.0285 (4)
O20.57298 (13)0.09227 (10)1.2508 (2)0.0193 (4)
O30.04479 (14)0.22764 (10)0.8325 (2)0.0194 (4)
O40.07343 (13)0.37665 (10)0.8413 (2)0.0170 (4)
O50.82105 (15)0.33071 (11)1.0883 (2)0.0192 (4)
N10.46108 (17)0.10564 (12)1.1729 (3)0.0157 (4)
N20.61527 (17)0.26565 (12)1.2825 (3)0.0147 (4)
C10.29266 (19)0.20462 (14)1.0362 (3)0.0141 (5)
H1A0.24450.15390.99980.017*
C20.4166 (2)0.19539 (14)1.1327 (3)0.0135 (4)
C30.49466 (19)0.27115 (14)1.1919 (3)0.0135 (4)
C40.43542 (19)0.35571 (14)1.1508 (3)0.0148 (5)
H4A0.48110.40711.19010.018*
C50.3135 (2)0.36374 (14)1.0555 (3)0.0148 (5)
H5A0.27840.42021.03080.018*
C60.2402 (2)0.28743 (14)0.9938 (3)0.0150 (5)
C70.11002 (19)0.29283 (14)0.8828 (3)0.0148 (5)
C8−0.05110 (19)0.38757 (14)0.7226 (3)0.0168 (5)
H8A−0.11430.35170.77090.020*
H8B−0.04730.36850.59490.020*
C9−0.0866 (2)0.48440 (16)0.7242 (4)0.0254 (6)
H9A−0.16950.49290.65010.038*
H9B−0.02510.51920.67220.038*
H9C−0.08790.50310.85150.038*
C100.69687 (19)0.34151 (14)1.3465 (3)0.0142 (4)
H10A0.76730.32101.44000.017*
H10B0.64840.38411.40730.017*
C110.75012 (19)0.38863 (14)1.1886 (3)0.0157 (5)
H11A0.68010.41411.10110.019*
H11B0.80470.43721.24190.019*
H2A0.642 (2)0.2141 (18)1.310 (4)0.021 (7)*
H5B0.888 (3)0.3148 (18)1.156 (4)0.028 (8)*
U11U22U33U12U13U23
O10.0224 (8)0.0119 (8)0.0480 (12)−0.0046 (7)−0.0035 (8)0.0003 (8)
O20.0169 (8)0.0143 (8)0.0252 (9)0.0027 (6)−0.0004 (7)0.0010 (7)
O30.0145 (7)0.0177 (8)0.0243 (9)−0.0040 (6)−0.0011 (7)0.0005 (7)
O40.0118 (7)0.0168 (8)0.0207 (9)0.0003 (6)−0.0024 (6)0.0005 (7)
O50.0149 (8)0.0216 (9)0.0204 (9)0.0025 (6)0.0012 (7)−0.0020 (7)
N10.0146 (9)0.0129 (9)0.0192 (10)−0.0015 (7)0.0018 (7)−0.0009 (8)
N20.0116 (8)0.0115 (9)0.0201 (10)0.0007 (7)0.0002 (8)0.0017 (8)
C10.0153 (11)0.0145 (10)0.0130 (11)−0.0038 (8)0.0036 (8)−0.0026 (9)
C20.0151 (10)0.0119 (10)0.0144 (11)−0.0002 (8)0.0051 (8)0.0017 (8)
C30.0145 (10)0.0142 (11)0.0118 (11)−0.0018 (8)0.0029 (8)−0.0001 (8)
C40.0135 (10)0.0123 (10)0.0188 (12)−0.0012 (8)0.0030 (8)−0.0016 (9)
C50.0169 (10)0.0128 (10)0.0147 (11)0.0014 (8)0.0027 (8)0.0010 (9)
C60.0132 (10)0.0165 (11)0.0156 (11)0.0003 (8)0.0030 (9)0.0013 (9)
C70.0148 (10)0.0159 (11)0.0144 (11)−0.0004 (8)0.0045 (9)0.0007 (9)
C80.0116 (10)0.0203 (11)0.0161 (11)0.0004 (8)−0.0045 (9)0.0015 (9)
C90.0198 (11)0.0226 (13)0.0301 (14)0.0053 (9)−0.0069 (10)−0.0019 (11)
C100.0116 (9)0.0147 (10)0.0148 (11)−0.0009 (8)−0.0017 (8)−0.0004 (9)
C110.0127 (10)0.0128 (10)0.0208 (11)−0.0013 (8)0.0005 (9)−0.0004 (9)
O1—N11.230 (2)C4—C51.368 (3)
O2—N11.245 (2)C4—H4A0.9300
O3—C71.218 (3)C5—C61.414 (3)
O4—C71.335 (3)C5—H5A0.9300
O4—C81.461 (2)C6—C71.482 (3)
O5—C111.424 (3)C8—C91.501 (3)
O5—H5B0.83 (3)C8—H8A0.9700
N1—C21.440 (3)C8—H8B0.9700
N2—C31.342 (3)C9—H9A0.9600
N2—C101.459 (3)C9—H9B0.9600
N2—H2A0.84 (3)C9—H9C0.9600
C1—C61.375 (3)C10—C111.526 (3)
C1—C21.391 (3)C10—H10A0.9700
C1—H1A0.9300C10—H10B0.9700
C2—C31.430 (3)C11—H11A0.9700
C3—C41.425 (3)C11—H11B0.9700
C7—O4—C8116.01 (16)O3—C7—C6123.46 (19)
C11—O5—H5B110 (2)O4—C7—C6112.56 (18)
O1—N1—O2121.21 (17)O4—C8—C9107.99 (17)
O1—N1—C2118.86 (17)O4—C8—H8A110.1
O2—N1—C2119.92 (17)C9—C8—H8A110.1
C3—N2—C10125.21 (19)O4—C8—H8B110.1
C3—N2—H2A115.5 (18)C9—C8—H8B110.1
C10—N2—H2A119.1 (18)H8A—C8—H8B108.4
C6—C1—C2121.12 (19)C8—C9—H9A109.5
C6—C1—H1A119.4C8—C9—H9B109.5
C2—C1—H1A119.4H9A—C9—H9B109.5
C1—C2—C3121.68 (19)C8—C9—H9C109.5
C1—C2—N1116.49 (18)H9A—C9—H9C109.5
C3—C2—N1121.82 (19)H9B—C9—H9C109.5
N2—C3—C4120.65 (19)N2—C10—C11113.65 (18)
N2—C3—C2123.9 (2)N2—C10—H10A108.8
C4—C3—C2115.47 (18)C11—C10—H10A108.8
C5—C4—C3122.1 (2)N2—C10—H10B108.8
C5—C4—H4A118.9C11—C10—H10B108.8
C3—C4—H4A118.9H10A—C10—H10B107.7
C4—C5—C6120.9 (2)O5—C11—C10112.94 (18)
C4—C5—H5A119.5O5—C11—H11A109.0
C6—C5—H5A119.5C10—C11—H11A109.0
C1—C6—C5118.61 (19)O5—C11—H11B109.0
C1—C6—C7118.53 (19)C10—C11—H11B109.0
C5—C6—C7122.85 (19)H11A—C11—H11B107.8
O3—C7—O4123.96 (19)
C6—C1—C2—C30.0 (3)C3—C4—C5—C60.3 (3)
C6—C1—C2—N1178.9 (2)C2—C1—C6—C5−1.9 (3)
O1—N1—C2—C1−3.9 (3)C2—C1—C6—C7177.1 (2)
O2—N1—C2—C1176.5 (2)C4—C5—C6—C11.8 (3)
O1—N1—C2—C3175.0 (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—C6176.60 (18)
C10—N2—C3—C2−179.3 (2)C1—C6—C7—O32.8 (3)
C1—C2—C3—N2−178.8 (2)C5—C6—C7—O3−178.3 (2)
N1—C2—C3—N22.4 (3)C1—C6—C7—O4−176.1 (2)
C1—C2—C3—C42.0 (3)C5—C6—C7—O42.9 (3)
N1—C2—C3—C4−176.81 (19)C7—O4—C8—C9168.7 (2)
N2—C3—C4—C5178.7 (2)C3—N2—C10—C11−76.3 (3)
C2—C3—C4—C5−2.1 (3)N2—C10—C11—O5−57.4 (2)
D—H···AD—HH···AD···AD—H···A
N2—H2A···O20.84 (3)1.99 (3)2.642 (2)134 (2)
O5—H5B···O3i0.83 (3)2.02 (3)2.851 (2)177 (3)
C8—H8A···O5ii0.972.513.271 (3)135
C10—H10A···O5iii0.972.543.267 (3)132
C10—H10B···O1iv0.972.433.168 (3)133
C11—H11A···O2v0.972.593.403 (3)142
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N2—H2A⋯O20.84 (3)1.99 (3)2.642 (2)134 (2)
O5—H5B⋯O3i0.83 (3)2.02 (3)2.851 (2)177 (3)
C8—H8A⋯O5ii0.972.513.271 (3)135
C10—H10A⋯O5iii0.972.543.267 (3)132
C10—H10B⋯O1iv0.972.433.168 (3)133
C11—H11A⋯O2v0.972.593.403 (3)142

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .

  6 in total

1.  The chemistry of the benzimidazoles.

Authors:  J B WRIGHT
Journal:  Chem Rev       Date:  1951-06       Impact factor: 60.622

2.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

3.  Design of benzoic acid inhibitors of influenza neuraminidase containing a cyclic substitution for the N-acetyl grouping.

Authors:  W J Brouillette; V R Atigadda; M Luo; G M Air; Y S Babu; S Bantia
Journal:  Bioorg Med Chem Lett       Date:  1999-07-19       Impact factor: 2.823

4.  4-Ethyl-amino-3-nitro-benzoic acid.

Authors:  Shivanagere Nagojappa Narendra Babu; Aisyah Saad Abdul Rahim; Shafida Abd Hamid; Ching Kheng Quah; Hoong-Kun Fun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-04-22

5.  4-Cyclo-butyl-amino-3-nitro-benzoic acid.

Authors:  Shivanagere Nagojappa Narendra Babu; Aisyah Saad Abdul Rahim; Hasnah Osman; Ching Kheng Quah; Hoong-Kun Fun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-06-13

6.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  6 in total
  2 in total

1.  Ethyl 3-amino-4-[(2-hy-droxy-ethyl)-amino]benzoate.

Authors:  Natarajan Arumugam; Aisyah Saad Abdul Rahim; Shafida Abd Hamid; Mohd Mustaqim Rosli; Hoong-Kun Fun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-07-31

2.  Isolation of 3-amino-4-nitro-benzyl acetate: evidence of an undisclosed impurity in 5-amino-2-nitro-benzoic acid.

Authors:  Brandon Quillian; Jordan Hendricks; Matthew Trivitayakhun; Clifford W Padgett
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2015-05-13
  2 in total

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