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Acta Crystallogr Sect E Struct Rep Online. 2009 August 1; 65(Pt 8): o1842.
Published online 2009 July 11. doi:  10.1107/S1600536809026191
PMCID: PMC2977119

2-[(E)-(2-Morpholinoeth­yl)iminiometh­yl]-4-nitro-1-oxocyclo­hexa­dienide

Abstract

The mol­ecule of the title compound, C13H17N3O4, exists as a zwitterion, with the H atom of the phenol group being transferred to the imine N atom. The C=O, CAr—CAr and C—N bond lengths are in agreement with the oxocyclo­hexa­dienide–iminium zwitterionic form. A strong intra­molecular N+—H(...)O hydrogen bond generates an S(6) ring motif. The morpholine ring adopts a chair conformation. In the crystal, mol­ecules are linked into centrosymmetric dimers by inter­molecular N—H(...)O hydrogen bonds. In addition, C—H(...)O hydrogen bonds and very weak C—H(...)π inter­actions are observed.

Related literature

For general background, photochromic and thermochromic characteristics of Schiff base compounds, see: Calligaris et al. (1972 [triangle]); Cohen et al. (1964 [triangle]); Hadjoudis et al. (1987 [triangle]); Karabıyık et al. (2008 [triangle]). For related structures, see: Butt et al. (1987 [triangle]); Petek et al. (2006 [triangle]); Krygowski & Stepien (2005 [triangle]); Santos-Contreras et al. (2009 [triangle]). For graph-set analysis of hydrogen bonds, see: Bernstein et al. (1995 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1842-scheme1.jpg

Experimental

Crystal data

  • C13H17N3O4
  • M r = 279.30
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1842-efi1.jpg
  • a = 5.3520 (4) Å
  • b = 10.8972 (9) Å
  • c = 12.4537 (9) Å
  • α = 102.329 (7)°
  • β = 97.143 (6)°
  • γ = 104.173 (9)°
  • V = 675.91 (10) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 296 K
  • 0.75 × 0.70 × 0.40 mm

Data collection

  • Stoe IPDSII diffractometer
  • Absorption correction: none
  • 11340 measured reflections
  • 3094 independent reflections
  • 2664 reflections with I > 2σ(I)
  • R int = 0.039

Refinement

  • R[F 2 > 2σ(F 2)] = 0.040
  • wR(F 2) = 0.110
  • S = 1.06
  • 3094 reflections
  • 186 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.26 e Å−3
  • Δρmin = −0.17 e Å−3

Data collection: X-AREA (Stoe & Cie, 2002 [triangle]); cell refinement: X-AREA; data reduction: X-RED32 (Stoe & Cie, 2002 [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 for Windows (Farrugia, 1997 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809026191/ci2842sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809026191/ci2842Isup2.hkl

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

Acknowledgments

The authors acknowledge the Faculty of Arts and Sciences of Ondokuz Mayıs University, Turkey, for the use of the Stoe IPDSII diffractometer (purchased under grant No. F279 of the University Research Fund).

supplementary crystallographic information

Comment

Schiff bases have been extensively used as ligands in the field of coordination chemistry (Calligaris et al., 1972). Schiff base compounds can be classified by their photochromic and thermochromic characteristics (Cohen et al. 1964). These properties result from proton transfer from the hydroxyl O atom to the imine N atom (Hadjoudis et al., 1987). Schiff bases exhibit two well-known tautomeric forms viz. OH and NH tautomers, and they also exist in zwitterionic form (Karabıyık et al., 2008). Our investigations show that compund (I) exists in a zwitterionic form.

The molecular structure of (I) is shown in Fig.1. The C1—C7 [1.4241 (15) Å], C7═N2 [1.2894 (15) Å] and N2—C8 [1.4615 (14) Å] bond lengths agree with the corresponding distances in (E)-2-methoxy-6-[(2- morpholinoethylimino)methyl]phenolate [1.425 (2), 1.287 (2) and 1.464 (2) Å; Petek et al., 2006]. The bonds lengths in the C1-C6 benzene ring show clear alternation in the delocalized C2-C5 portion. The nitro group is tilted out of the mean plane of adjacent ring by 7.02 (3)°, whereas the C3—N1 distance of 1.4398 (15) Å is in the characteristic range suggesting limited conjugation with the ring. Thus, the whole geometry is in the agreement with the predominace of the oxocyclohexadienide-iminum zwitterion bonding scheme (see scheme) (Krygowski & Stepien, 2005; Santos-Contreras et al., 2009), in close agreement with the reported configurations of p-nitrophenolates of alkali metal cations (Butt et al., 1987). The morpholine ring adopts a chair conformation. An intramolecular N—H···O hydrogen bond generates an S(6) ring motif (Bernstein et al., 1995).

In the crystal structure of (I), the molecules form centrosymmetric dimers connected by intermolecular N—H···O hydrogen bonds (Fig. 2). In addition, C—H···O hydrogen bonds and very weak C—H···π interactions between C13-H13B group and C1-C6 benzene ring are observed (Table 1).

Experimental

2-Hydroxy-5-nitrobenzaldehyde (0.0535 g, 0.32 mmol) in ethanol (20 ml) was added to 2-morpholinoethylamine (0.0417 g, 0.32 mmol) in ethanol (20 ml) and the reaction mixture was stirred for 1 h under reflux. Single crystals of the title compound suitable for X-ray analysis were obtained by slow evaporation of an ethanol solution (yield % 65; m.p. 435-438 K).

Refinement

Atom H1 was located in a difference map and refined freely. All other H atoms were placed in calculated positions and constrained to ride on their parent atoms, with C-H = 0.93–0.97 Å and Uiso(H) = 1.2 Ueq(C).

Figures

Fig. 1.
The molecular structure of (I), showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
Fig. 2.
A packing diagram for (I), showing O—H···O hydrogen-bonded (dashed lines) dimers. H atoms not involved in hydrogen bonding have been omitted for clarity.

Crystal data

C13H17N3O4Z = 2
Mr = 279.30F(000) = 296
Triclinic, P1Dx = 1.372 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 5.3520 (4) ÅCell parameters from 23053 reflections
b = 10.8972 (9) Åθ = 1.7–28.0°
c = 12.4537 (9) ŵ = 0.10 mm1
α = 102.329 (7)°T = 296 K
β = 97.143 (6)°Prism, orange
γ = 104.173 (9)°0.75 × 0.70 × 0.40 mm
V = 675.91 (10) Å3

Data collection

Stoe IPDSII diffractometer2664 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.039
graphiteθmax = 27.6°, θmin = 1.7°
Detector resolution: 6.67 pixels mm-1h = −6→6
ω scansk = −14→14
11340 measured reflectionsl = −16→16
3094 independent reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.040H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.110w = 1/[σ2(Fo2) + (0.0512P)2 + 0.1309P] where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.001
3094 reflectionsΔρmax = 0.26 e Å3
186 parametersΔρmin = −0.17 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.077 (7)

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
C10.4611 (2)0.77887 (11)0.53094 (9)0.0335 (2)
C20.6439 (2)0.90243 (11)0.56526 (9)0.0341 (2)
H20.78960.92040.53150.041*
C30.6067 (2)0.99713 (10)0.64924 (9)0.0348 (3)
C40.3899 (3)0.97257 (12)0.70256 (10)0.0396 (3)
H40.36921.03770.75970.048*
C50.2112 (3)0.85348 (12)0.67033 (11)0.0426 (3)
H50.06980.83820.70690.051*
C60.2318 (2)0.74989 (11)0.58183 (10)0.0363 (3)
C70.5074 (2)0.68324 (11)0.44412 (9)0.0358 (3)
H70.65660.70740.41380.043*
C80.4146 (3)0.46932 (12)0.31724 (10)0.0430 (3)
H8A0.39370.38780.33930.052*
H8B0.59560.50040.30930.052*
C90.2370 (3)0.44450 (12)0.20590 (10)0.0437 (3)
H9A0.05720.40500.21130.052*
H9B0.24530.52680.18650.052*
C100.2038 (3)0.36092 (15)0.00679 (11)0.0513 (3)
H10A0.25270.4500−0.00090.062*
H10B0.01400.3307−0.00470.062*
C110.3025 (3)0.27445 (17)−0.07913 (12)0.0640 (4)
H11A0.23040.2783−0.15340.077*
H11B0.49200.3062−0.06810.077*
C120.3364 (4)0.13651 (16)0.03730 (15)0.0665 (5)
H12A0.52640.16450.04870.080*
H12B0.28340.04670.04290.080*
C130.2450 (3)0.22200 (13)0.12725 (12)0.0504 (3)
H13A0.05610.19040.11940.060*
H13B0.32440.21770.20020.060*
N10.7884 (2)1.12600 (10)0.68031 (9)0.0410 (3)
N20.3567 (2)0.56554 (9)0.40467 (8)0.0378 (2)
N30.3171 (2)0.35764 (10)0.11888 (8)0.0422 (3)
O10.06162 (19)0.64042 (9)0.55030 (9)0.0513 (3)
O20.7384 (2)1.21314 (9)0.74731 (9)0.0600 (3)
O30.9854 (2)1.14568 (9)0.63771 (9)0.0549 (3)
O40.2302 (3)0.14272 (12)−0.07115 (9)0.0727 (4)
H10.214 (4)0.5433 (18)0.4335 (15)0.065 (5)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0382 (6)0.0302 (5)0.0305 (5)0.0089 (4)0.0086 (4)0.0041 (4)
C20.0370 (6)0.0324 (5)0.0316 (5)0.0083 (4)0.0096 (4)0.0055 (4)
C30.0410 (6)0.0286 (5)0.0310 (5)0.0073 (4)0.0048 (4)0.0035 (4)
C40.0493 (7)0.0363 (6)0.0335 (6)0.0162 (5)0.0120 (5)0.0020 (4)
C50.0450 (7)0.0419 (6)0.0422 (6)0.0125 (5)0.0198 (5)0.0065 (5)
C60.0388 (6)0.0319 (5)0.0372 (6)0.0085 (4)0.0102 (5)0.0063 (4)
C70.0398 (6)0.0336 (5)0.0323 (5)0.0088 (5)0.0098 (4)0.0049 (4)
C80.0508 (7)0.0361 (6)0.0374 (6)0.0151 (5)0.0086 (5)−0.0038 (5)
C90.0545 (7)0.0391 (6)0.0375 (6)0.0195 (5)0.0105 (5)0.0008 (5)
C100.0532 (8)0.0582 (8)0.0358 (7)0.0119 (6)0.0063 (6)0.0030 (6)
C110.0646 (10)0.0736 (10)0.0367 (7)0.0046 (8)0.0132 (6)−0.0071 (7)
C120.0776 (11)0.0501 (8)0.0648 (10)0.0231 (8)0.0203 (8)−0.0105 (7)
C130.0625 (9)0.0409 (7)0.0457 (7)0.0180 (6)0.0147 (6)−0.0003 (5)
N10.0491 (6)0.0311 (5)0.0371 (5)0.0070 (4)0.0045 (4)0.0030 (4)
N20.0443 (6)0.0317 (5)0.0331 (5)0.0083 (4)0.0105 (4)−0.0002 (4)
N30.0497 (6)0.0406 (5)0.0324 (5)0.0146 (5)0.0088 (4)−0.0020 (4)
O10.0483 (5)0.0358 (5)0.0617 (6)−0.0002 (4)0.0219 (4)0.0025 (4)
O20.0719 (7)0.0337 (5)0.0622 (6)0.0106 (4)0.0133 (5)−0.0092 (4)
O30.0556 (6)0.0417 (5)0.0564 (6)−0.0031 (4)0.0169 (5)0.0047 (4)
O40.0816 (8)0.0612 (7)0.0526 (6)0.0055 (6)0.0197 (6)−0.0207 (5)

Geometric parameters (Å, °)

C1—C21.3994 (16)C9—H9A0.97
C1—C71.4241 (15)C9—H9B0.97
C1—C61.4478 (16)C10—N31.4625 (17)
C2—C31.3748 (15)C10—C111.505 (2)
C2—H20.93C10—H10A0.97
C3—C41.4051 (17)C10—H10B0.97
C3—N11.4398 (15)C11—O41.421 (2)
C4—C51.3543 (18)C11—H11A0.97
C4—H40.93C11—H11B0.97
C5—C61.4357 (16)C12—O41.421 (2)
C5—H50.93C12—C131.5086 (19)
C6—O11.2594 (14)C12—H12A0.97
C7—N21.2894 (15)C12—H12B0.97
C7—H70.93C13—N31.4632 (18)
C8—N21.4615 (14)C13—H13A0.97
C8—C91.5117 (18)C13—H13B0.97
C8—H8A0.97N1—O21.2293 (14)
C8—H8B0.97N1—O31.2315 (14)
C9—N31.4596 (15)N2—H10.887 (19)
C2—C1—C7117.84 (10)N3—C10—H10A109.8
C2—C1—C6120.88 (10)C11—C10—H10A109.8
C7—C1—C6121.27 (10)N3—C10—H10B109.8
C3—C2—C1119.54 (10)C11—C10—H10B109.8
C3—C2—H2120.2H10A—C10—H10B108.2
C1—C2—H2120.2O4—C11—C10111.17 (13)
C2—C3—C4121.54 (10)O4—C11—H11A109.4
C2—C3—N1119.24 (10)C10—C11—H11A109.4
C4—C3—N1119.18 (10)O4—C11—H11B109.4
C5—C4—C3119.65 (11)C10—C11—H11B109.4
C5—C4—H4120.2H11A—C11—H11B108.0
C3—C4—H4120.2O4—C12—C13111.48 (14)
C4—C5—C6122.50 (11)O4—C12—H12A109.3
C4—C5—H5118.8C13—C12—H12A109.3
C6—C5—H5118.8O4—C12—H12B109.3
O1—C6—C5122.23 (11)C13—C12—H12B109.3
O1—C6—C1121.91 (10)H12A—C12—H12B108.0
C5—C6—C1115.86 (10)N3—C13—C12110.35 (13)
N2—C7—C1124.56 (11)N3—C13—H13A109.6
N2—C7—H7117.7C12—C13—H13A109.6
C1—C7—H7117.7N3—C13—H13B109.6
N2—C8—C9111.99 (10)C12—C13—H13B109.6
N2—C8—H8A109.2H13A—C13—H13B108.1
C9—C8—H8A109.2O2—N1—O3122.35 (11)
N2—C8—H8B109.2O2—N1—C3118.53 (11)
C9—C8—H8B109.2O3—N1—C3119.11 (10)
H8A—C8—H8B107.9C7—N2—C8122.84 (11)
N3—C9—C8110.22 (10)C7—N2—H1117.3 (12)
N3—C9—H9A109.6C8—N2—H1119.8 (12)
C8—C9—H9A109.6C9—N3—C10111.82 (10)
N3—C9—H9B109.6C9—N3—C13112.22 (10)
C8—C9—H9B109.6C10—N3—C13108.56 (11)
H9A—C9—H9B108.1C12—O4—C11109.63 (11)
N3—C10—C11109.46 (13)
C7—C1—C2—C3−179.68 (10)N3—C10—C11—O460.36 (17)
C6—C1—C2—C30.69 (17)O4—C12—C13—N3−57.64 (18)
C1—C2—C3—C40.62 (18)C2—C3—N1—O2172.71 (11)
C1—C2—C3—N1−176.92 (10)C4—C3—N1—O2−4.89 (17)
C2—C3—C4—C5−0.61 (18)C2—C3—N1—O3−6.09 (17)
N1—C3—C4—C5176.93 (11)C4—C3—N1—O3176.31 (11)
C3—C4—C5—C6−0.7 (2)C1—C7—N2—C8−178.52 (11)
C4—C5—C6—O1−178.16 (12)C9—C8—N2—C7−106.90 (14)
C4—C5—C6—C11.93 (19)C8—C9—N3—C10−163.51 (11)
C2—C1—C6—O1178.21 (11)C8—C9—N3—C1374.22 (14)
C7—C1—C6—O1−1.41 (18)C11—C10—N3—C9177.47 (12)
C2—C1—C6—C5−1.89 (17)C11—C10—N3—C13−58.19 (15)
C7—C1—C6—C5178.49 (11)C12—C13—N3—C9−178.84 (12)
C2—C1—C7—N2179.62 (11)C12—C13—N3—C1057.05 (16)
C6—C1—C7—N2−0.75 (18)C13—C12—O4—C1157.82 (18)
N2—C8—C9—N3174.64 (11)C10—C11—O4—C12−59.34 (18)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H1···O10.89 (2)1.99 (2)2.6760 (14)133 (2)
N2—H1···O1i0.89 (2)2.24 (2)2.9587 (14)138 (2)
C4—H4···O4ii0.932.473.3547 (16)160
C7—H7···O3iii0.932.433.3020 (15)157
C13—H13B···Cg2iv0.972.993.9254162

Symmetry codes: (i) −x, −y+1, −z+1; (ii) x, y+1, z+1; (iii) −x+2, −y+2, −z+1; (iv) −x+1, −y+1, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CI2842).

References

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