Crystal structure of diethyl 2,2′-[((1E,1′E)-{[(1R,4R)-cyclo­hexane-1,4-di­yl]bis­(aza­nylyl­idene)}bis­(methanylyl­idene))bis­(1H-pyrrole-2,1-di­yl)]di­acetate

Jasim Alshawi; Muoayed Yousif; Karzan H Zangana; Inigo J Vitorica Yrezabal; Richard Winpenny; Mohamad J Al-Jeboori

doi:10.1107/S2056989015002674

. 2015 Feb 13;71(Pt 3):o165–o166. doi: 10.1107/S2056989015002674

Crystal structure of diethyl 2,2′-[((1E,1′E)-{[(1R,4R)-cyclohexane-1,4-diyl]bis(azanylylidene)}bis(methanylylidene))bis(1H-pyrrole-2,1-diyl)]diacetate

Jasim Alshawi ^a, Muoayed Yousif ^a, Karzan H Zangana ^b, Inigo J Vitorica Yrezabal ^b, Richard Winpenny ^b, Mohamad J Al-Jeboori ^c,^*

PMCID: PMC4350751 PMID: 25844229

Abstract

The whole molecule of the title compound, C₂₄H₃₂N₄O₄, is generated by inversion symmetry. The cyclohexane ring adopts a chair conformation and the conformation about the C=N bonds is E. The pyrrole rings have an anti confirmation with respect to the cyclohexane moiety and the ethyl acetate groups have extended conformations. In the crystal, molecules are linked by pairs of C—H⋯O hydrogen bonds forming chains, enclosing R ₂ ²(10) ring motifs with inversion symmetry, propagating parallel to the (101) plane.

Keywords: crystal structure, Schiff base, bispyrrole, C—H⋯O hydrogen bonding

Related literature

For general background on the applications of Schiff bases and the use of pyrrole compounds, see: Köse et al. (2015 ▸); Trofimov et al. (2015 ▸). For the synthesis of dipyrrole Schiff bases ligands, see: Meghdadi et al. (2010 ▸); Munro et al. (2004 ▸). For the synthesis of pyrrole ester precursors, see: Koriatopoulou et al. (2008 ▸); Singh & Pal (2010 ▸). For the preparation of Schiff bases, see: Yang et al. (2004 ▸); Ourari et al. (2013 ▸). graphic file with name e-71-0o165-scheme1.jpg

Experimental

Crystal data

C₂₄H₃₂N₄O₄
M _r = 440.54
Triclinic,
a = 8.5531 (6) Å
b = 8.8379 (7) Å
c = 9.6492 (9) Å
α = 115.166 (9)°
β = 92.105 (7)°
γ = 113.288 (8)°
V = 587.68 (10) Å³
Z = 1
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 150 K
0.4 × 0.3 × 0.3 mm

Data collection

Agilent SuperNova (single source at offset, Atlas) diffractometer
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2013 ▸) T _min = 0.933, T _max = 1.000
4657 measured reflections
2734 independent reflections
1827 reflections with I > 2σ(I)
R _int = 0.028

Refinement

R[F ² > 2σ(F ²)] = 0.055
wR(F ²) = 0.124
S = 1.07
2734 reflections
146 parameters
H-atom parameters constrained
Δρ_max = 0.18 e Å⁻³
Δρ_min = −0.25 e Å⁻³

Data collection: CrysAlis PRO (Agilent, 2013 ▸); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS2014 (Sheldrick, 2008 ▸); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015 ▸); molecular graphics: PLATON (Spek, 2009 ▸); software used to prepare material for publication: SHELXL2014 and PLATON.

Supplementary Material

Crystal structure: contains datablock(s) Gobal, I. DOI: 10.1107/S2056989015002674/su5080sup1.cif

e-71-0o165-sup1.cif^{(170.9KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015002674/su5080Isup2.hkl

e-71-0o165-Isup2.hkl^{(134.2KB, hkl)}

Click here for additional data file.^{(1.1MB, tif)}

. DOI: 10.1107/S2056989015002674/su5080fig1.tif

A view of the molecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level.

Click here for additional data file.^{(1.2MB, tif)}

b . DOI: 10.1107/S2056989015002674/su5080fig2.tif

A view along the b axis of the crystal packing of the title compound. The C—H⋯O hydrogen bonds are drawn as dashed lines (see Table 1 for details; H atom not involved in hydrogen bonding have been omitted for clarity).

CCDC reference: 1048163

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
C14H14AO16ⁱ	0.97	2.50	3.317(3)	142

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Symmetry code: (i) Inline graphic .

Acknowledgments

The authors are grateful to the Iraqi Ministry for Higher Education for providing six months funding for JA’s PhD scholarship.

supplementary crystallographic information

S1. Synthesis

The title compound was prepared in a two step procedure:

Synthesis of ethyl (2-formyl-1H-pyrrole-1-yl)-acetate (L): prepared by reported procedures (Koriatopoulou et al., 2008; Singh & Pal, 2010) as follows: To a mixture of 1H-pyrrole-2-carbaldehyde (1.00 g, 10.51 mmol), K₂CO₃ (2.90g, 21.02 mmol) and (2.64 g, 10.51 mmol) of 18-crown-6 in dry 1,4-dioxane (20ml), was added drop wise a solution of ethyl bromoacetate (2.00 g, 12 mmol) in dry 1,4-dioxane (20 ml), over a period of 30 min. The reaction mixture was allowed to reflux under a nitrogen atmosphere for 6 h, and then the solvent was removed under reduced pressure. Water (50ml) was added to the residue, and the mixture was extracted with ethyl acetate (3 × 15ml). The combined organic layers were washed with brine (15 ml), and then dried over Na₂SO₄. The solvent was removed under reduced pressure, and the oily residue was purified by flash chromatography with an eluent mixture (33% ethyl acetate / hexane), giving compound (L) as a yellow oil product (yield: 0.75 g, 75%). NMR data (p.p.m), δH: (500 MHz, CDCl₃): 1.20 (3H, t, C12—H), 4.15 (2H, q, C11—H), 4.97 (2H, s, C8—H), 6.21 (1H, t, C3—H), 6.84 (1H, d, C4—H), 6.90 (1H, d, C2—H) and 9.45 (1H, s, C6—H); δC (125.75 MHz, CDCl3), 14.13 C12, 50.25 C8, 61.63 C11, 110.20 C3, 124.61 C4, 131.71 C5 and 132.10 C2. C=O for the carboxylate moiety at 168.37 (C12) and at 179.74 for C6. The positive ES mass spectrum at m/z = 182.4 (M+H)⁺ (62%) for C₉H₁₁NO₃, requires = 181.1. The other peaks detected at m/z =153.4 (100%), 109.3 (6%), 95 (9%) and 67 (4%) correspond to [M—CH₂CH₃]⁺, [M-(CH₂CH₃+CO₂)]⁺, [M-(CH₂CH₃+CO₂+CH₂)]⁺ and [M-(CH₂CH₃+CO₂+CH₂+CO)]+, respectively. IR (ATR cm^-1): 1650 ν(C=O) aldehyde moiety. 1710 ν(C=O) ester group.

Synthesis of the title Schiff-base: performed using conventional procedures (Yang et al., 2004; Ourari et al., 2013). To a mixture of L (1.81 g, 10 mmol) in ethanol (20 ml) with 3 drops of glacial acetic acid, a solution of 1,4-diaminocyclohexan (0.57 g, 5 mmol) in ethanol (20ml) was added drop wise over a period of 20 min. The reaction mixture was allowed to reflux for 3h, and then cooled to room temperature. A white precipitate was collected by filtration and recrystallised from ethanol (yield: 1.09g, 60%). Crystals were obtained by slow evaporation of a solution in methanol/acetone. NMR data (p.p.m), δH (500 MHz, CDCl₃): 1.19 (6H, t,C15, 15–H), 1.47 (C10, 10- ,4H, q), δH = 1.67 (C9, 9-, 4H, q), 2.94 (2H, p, C8, 8–H), 4.10 (4H, q,C14, 14–H), 5.03 (C11, 11–H, 4H, s), 6.11 (2H, t, C3, 3–H), 6.38 (2H, d, C4, 4–H), 6.61 (2H, d, C2, 2–H) and 8.07 (2H, s, C6, 6–H); δC (125.75 MHz, CDCl3), 14.28 (C15, 15-). 32.61 (C10, 10- and C19, 9- ), 51.13 (C11, 11-), 61.07 (C14, 14- ), 68.8 (C8, 8-), 108.53 (C2, 2-), 116.58 (C5, 5-), 127.69 (C3, 3-), 129.93 (C4, 4-), 150.04 (C6, 6-), C=O 169.37 (C12, 12-). The positive ES mass spectrum at m/z = 441.52 (M+H)⁺ (100%) for C₂₄H₃₂N₄O₄, requires = 440.24. The other peaks detected at m/z = 412.42 (5%), 383 (3%), 295.19 (9%) and 267.1 (4%) correspond to [M—CH₂CH₃]⁺, [M-(2CH₂CH₃)]⁺, [M-(2CH₂CH₃+2CO₂)]⁺ and [M(2CH₂CH₃+2CO₂+2CH₂)]⁺, respectively. IR (ATR, cm^-1): 1580 (C=N), 1630 (C=O).

S2. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. All H atoms were placed in calculated positions and treated as riding atoms: C—H = 0.95 - 0.99 Å with U_iso(H) = 1.5U_eq(C) for methyl H atoms and = 1.2U_eq(C) for other H atoms.

S3. Comment

The whole molecule of the title compound, Fig.1, is generated by inversion symmetry. The cyclohexane ring adopts a chair conformation and the conformation about the C═N bonds is E. The pyrrole rings crystallize in the anti-confirmation with respect to the cyclohexane moiety and the ethyl acetate moieties have extended conformations.

In the crystal, molecules are linked by pairs of C—H···O hydrogen bonds forming chains, enclosing R²₂(10) ring motifs with inversion symmetry, propagating parallel to plane (101); see Table 1 and Fig. 2.

Infrared spectrum indicated typical absorbance bands of the functional –C═ N and carbonyl –C═O at 1580 and 1630 cm^-1, respectively. The positive ES mass spectrum of the bis Schiff-base showed a parent ion peak at m/z = 441.52 (M+H)⁺, corresponding to C₂₆H₃₂N₄O₄, for which the required value is 440.24. The N7═C6 bond distance [1.270 (2) Å] is shorter than the N2—C8 bond distance [1.458 (2) Å], indicating a double bond order. However, the N1—C5 bond distance [1.384 (2) Å] indicates resonance has occurred in the pyrrole system between the lone pair electron of the nitrogen atom and the pyrrole ring.