organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890
Volume 71| Part 3| March 2015| Pages o165-o166

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

CROSSMARK_Color_square_no_text.svg

aDepartment of Chemistry, College of Education for Pure Science, University of Basrah, Iraq, bSchool of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, England, and cDepartment of Chemistry, College of Education (Ibn Al-Haitham) for Pure Science, University of Baghdad, Iraq
*Correspondence e-mail: mohamadaljeboori@yahoo.com

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 6 February 2015; accepted 8 February 2015; online 13 February 2015)

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 R22(10) ring motifs with inversion symmetry, propagating parallel to the (101) plane.

1. Related literature

For general background on the applications of Schiff bases and the use of pyrrole compounds, see: Köse et al. (2015[Köse, M., Ceyhan, G., Tümer, M., Demirtaş, İ., Gönül, İ. & McKee, V. (2015). Spectrochim. Acta Part A, 137, 477-485.]); Trofimov et al. (2015[Trofimov, B. A., Mikhaleva, A., Schmidt, E. Y. & Sobenina, L. N. (2015). In Chemistry of Pyrroles. Boca Raton: CRC Press.]). For the synthesis of di­pyrrole Schiff bases ligands, see: Meghdadi et al. (2010[Meghdadi, S., Amirnasr, M., Mereiter, K. & Karimi Abdolmaleki, M. (2010). Acta Cryst. E66, m332-m333.]); Munro et al. (2004[Munro, O., Strydom, S. & Grimmer, C. (2004). New J. Chem. 28, 34-42.]). For the synthesis of pyrrole ester precursors, see: Koriatopoulou et al. (2008[Koriatopoulou, K., Karousis, N. & Varvounis, G. (2008). Tetrahedron, 64, 10009-10013.]); Singh & Pal (2010[Singh, K. & Pal, D. (2010). J. Serb. Chem. Soc. 75, 917-927.]). For the preparation of Schiff bases, see: Yang et al. (2004[Yang, L., Shan, X., Chen, Q., Wang, Z. & Ma, J. S. (2004). Eur. J. Inorg. Chem. 2004, 1474-1477.]); Ourari et al. (2013[Ourari, A., Aggoun, D. & Ouahab, L. (2013). Inorg. Chem. Commun. 33, 118-124.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • C24H32N4O4

  • Mr = 440.54

  • Triclinic, [P \overline 1]

  • 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

2.2. Data collection

  • Agilent SuperNova (single source at offset, Atlas) diffractometer

  • Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2013[Agilent (2013). CrysAlis PRO. Agilent Technologies, Yarnton, England.]) Tmin = 0.933, Tmax = 1.000

  • 4657 measured reflections

  • 2734 independent reflections

  • 1827 reflections with I > 2σ(I)

  • Rint = 0.028

2.3. Refinement

  • R[F2 > 2σ(F2)] = 0.055

  • wR(F2) = 0.124

  • S = 1.07

  • 2734 reflections

  • 146 parameters

  • H-atom parameters constrained

  • Δρmax = 0.18 e Å−3

  • Δρmin = −0.25 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C14—H14A⋯O16i 0.97 2.50 3.317 (3) 142
Symmetry code: (i) -x+1, -y+1, -z+1.

Data collection: CrysAlis PRO (Agilent, 2013[Agilent (2013). CrysAlis PRO. Agilent Technologies, Yarnton, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS2014 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]); molecular graphics: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]); software used to prepare material for publication: SHELXL2014 and PLATON.

Supporting information


Synthesis top

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).

Refinement top

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 Uiso(H) = 1.5Ueq(C) for methyl H atoms and = 1.2Ueq(C) for other H atoms.

Comment top

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 CN 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 –CO 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 N7C6 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.

Related literature top

For general background on the applications of Schiff bases and the use of pyrrole compounds, see: Kösea 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).

Computing details top

Data collection: CrysAlis PRO (Agilent, 2013); cell refinement: CrysAlis PRO (Agilent, 2013); data reduction: CrysAlis PRO (Agilent, 2013); 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 (Sheldrick, 2015) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. A view of the molecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. 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).
Diethyl 2,2'-[((1E,1'E)-{[(1R,4R)-cyclohexane-1,4-diyl]bis(azanylylidene)}bis(methanylylidene))bis(1H-pyrrole-2,1-diyl)]diacetate top
Crystal data top
C24H32N4O4Z = 1
Mr = 440.54F(000) = 236
Triclinic, P1Dx = 1.245 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 8.5531 (6) ÅCell parameters from 1515 reflections
b = 8.8379 (7) Åθ = 3.3–26.7°
c = 9.6492 (9) ŵ = 0.09 mm1
α = 115.166 (9)°T = 150 K
β = 92.105 (7)°Block, colourless
γ = 113.288 (8)°0.4 × 0.3 × 0.3 mm
V = 587.68 (10) Å3
Data collection top
Agilent SuperNova (single source at offset, Atlas)
diffractometer
2734 independent reflections
Radiation source: SuperNova (Mo) X-ray Source1827 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.028
Detector resolution: 10.37 pixels mm-1θmax = 29.4°, θmin = 2.9°
ω scansh = 1111
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2013)
k = 1012
Tmin = 0.933, Tmax = 1.000l = 138
4657 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.055H-atom parameters constrained
wR(F2) = 0.124 w = 1/[σ2(Fo2) + (0.0363P)2 + 0.1039P]
where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max < 0.001
2734 reflectionsΔρmax = 0.18 e Å3
146 parametersΔρmin = 0.25 e Å3
0 restraints
Crystal data top
C24H32N4O4γ = 113.288 (8)°
Mr = 440.54V = 587.68 (10) Å3
Triclinic, P1Z = 1
a = 8.5531 (6) ÅMo Kα radiation
b = 8.8379 (7) ŵ = 0.09 mm1
c = 9.6492 (9) ÅT = 150 K
α = 115.166 (9)°0.4 × 0.3 × 0.3 mm
β = 92.105 (7)°
Data collection top
Agilent SuperNova (single source at offset, Atlas)
diffractometer
2734 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2013)
1827 reflections with I > 2σ(I)
Tmin = 0.933, Tmax = 1.000Rint = 0.028
4657 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0550 restraints
wR(F2) = 0.124H-atom parameters constrained
S = 1.07Δρmax = 0.18 e Å3
2734 reflectionsΔρmin = 0.25 e Å3
146 parameters
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O130.46898 (16)0.46998 (17)0.19574 (15)0.0317 (3)
O160.63475 (17)0.71083 (17)0.43494 (15)0.0338 (4)
N10.67517 (19)0.9650 (2)0.32094 (18)0.0274 (4)
N70.87176 (19)0.7539 (2)0.17968 (18)0.0313 (4)
C120.5599 (2)0.6517 (3)0.3013 (2)0.0270 (4)
C60.9477 (2)0.9265 (3)0.2821 (2)0.0297 (5)
H61.06950.98540.31630.036*
C50.8559 (2)1.0361 (2)0.3483 (2)0.0275 (4)
C100.9066 (2)0.4733 (2)0.1181 (2)0.0311 (5)
H10A0.78510.39920.05750.037*
H10B0.90870.49350.22520.037*
C110.5474 (2)0.7689 (2)0.2290 (2)0.0279 (4)
H11A0.56530.71920.12330.033*
H11B0.43020.75970.22010.033*
C20.6355 (3)1.1083 (3)0.4039 (2)0.0317 (5)
H20.52291.09700.40610.038*
C91.0097 (2)0.3654 (3)0.0461 (2)0.0307 (5)
H9A0.95450.24380.04200.037*
H9B1.12800.43340.11270.037*
C80.9819 (2)0.6620 (2)0.1201 (2)0.0304 (5)
H81.10070.74120.18970.036*
C40.9269 (3)1.2260 (3)0.4484 (2)0.0340 (5)
H41.04591.30980.48640.041*
C30.7880 (3)1.2712 (3)0.4833 (2)0.0377 (5)
H30.79801.38980.54830.045*
C140.4577 (3)0.3383 (3)0.2513 (2)0.0400 (5)
H14A0.40250.35760.33920.048*
H14B0.57430.35620.28690.048*
C150.3512 (3)0.1451 (3)0.1175 (3)0.0544 (7)
H15A0.41110.12420.03420.082*
H15B0.23880.13140.07870.082*
H15C0.33490.05510.15340.082*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O130.0352 (8)0.0259 (7)0.0293 (8)0.0091 (6)0.0017 (6)0.0141 (6)
O160.0378 (8)0.0349 (7)0.0245 (8)0.0133 (6)0.0036 (6)0.0140 (6)
N10.0295 (8)0.0254 (8)0.0269 (9)0.0133 (7)0.0060 (6)0.0114 (7)
N70.0275 (8)0.0302 (8)0.0281 (9)0.0150 (7)0.0050 (7)0.0054 (7)
C120.0238 (10)0.0303 (10)0.0253 (10)0.0116 (8)0.0079 (8)0.0124 (8)
C60.0255 (10)0.0337 (10)0.0262 (10)0.0119 (9)0.0061 (8)0.0126 (9)
C50.0291 (10)0.0282 (10)0.0231 (10)0.0120 (8)0.0062 (8)0.0115 (8)
C100.0250 (10)0.0340 (10)0.0249 (10)0.0115 (9)0.0054 (8)0.0083 (8)
C110.0250 (10)0.0305 (10)0.0265 (10)0.0120 (8)0.0052 (8)0.0129 (8)
C20.0412 (11)0.0355 (10)0.0299 (11)0.0252 (10)0.0127 (9)0.0178 (9)
C90.0259 (10)0.0280 (10)0.0300 (11)0.0104 (8)0.0039 (8)0.0089 (8)
C80.0204 (9)0.0302 (10)0.0293 (11)0.0116 (8)0.0034 (7)0.0050 (8)
C40.0361 (11)0.0269 (10)0.0308 (11)0.0105 (9)0.0062 (9)0.0106 (9)
C30.0519 (13)0.0269 (10)0.0341 (12)0.0207 (10)0.0109 (10)0.0118 (9)
C140.0480 (13)0.0336 (11)0.0396 (13)0.0130 (10)0.0065 (10)0.0240 (10)
C150.0690 (16)0.0316 (11)0.0498 (15)0.0101 (12)0.0021 (12)0.0217 (11)
Geometric parameters (Å, º) top
O13—C121.336 (2)C6—C51.441 (2)
O13—C141.448 (2)C5—C41.375 (2)
O16—C121.203 (2)C10—C91.522 (2)
N1—C51.384 (2)C10—C81.522 (3)
N1—C111.452 (2)C2—C31.365 (3)
N1—C21.363 (2)C9—C8i1.526 (3)
N7—C61.270 (2)C8—C9i1.526 (3)
N7—C81.458 (2)C4—C31.405 (3)
C12—C111.506 (3)C14—C151.490 (3)
C12—O13—C14116.15 (15)C4—C5—C6127.83 (17)
C5—N1—C11126.32 (15)C8—C10—C9111.74 (14)
C2—N1—C5108.70 (15)N1—C11—C12112.58 (15)
C2—N1—C11124.84 (15)N1—C2—C3108.91 (17)
C6—N7—C8117.71 (15)C10—C9—C8i111.47 (17)
O13—C12—C11109.47 (16)N7—C8—C10109.64 (14)
O16—C12—O13124.75 (19)N7—C8—C9i109.49 (17)
O16—C12—C11125.74 (17)C10—C8—C9i110.20 (15)
N7—C6—C5123.74 (17)C5—C4—C3107.99 (18)
N1—C5—C6124.91 (15)C2—C3—C4107.14 (17)
C4—C5—N1107.27 (16)O13—C14—C15107.88 (18)
O13—C12—C11—N1166.07 (14)C11—N1—C5—C63.5 (3)
O16—C12—C11—N116.3 (3)C11—N1—C5—C4176.36 (17)
N1—C5—C4—C30.4 (2)C11—N1—C2—C3176.43 (17)
N1—C2—C3—C40.3 (2)C2—N1—C5—C6179.33 (19)
N7—C6—C5—N16.4 (3)C2—N1—C5—C40.6 (2)
N7—C6—C5—C4173.7 (2)C2—N1—C11—C12110.7 (2)
C12—O13—C14—C15179.68 (16)C9—C10—C8—N7176.06 (15)
C6—N7—C8—C10134.27 (18)C9—C10—C8—C9i55.5 (2)
C6—N7—C8—C9i104.71 (19)C8—N7—C6—C5178.46 (18)
C6—C5—C4—C3179.5 (2)C8—C10—C9—C8i56.2 (2)
C5—N1—C11—C1264.5 (2)C14—O13—C12—O162.0 (3)
C5—N1—C2—C30.6 (2)C14—O13—C12—C11175.70 (15)
C5—C4—C3—C20.0 (2)
Symmetry code: (i) x+2, y+1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C14—H14A···O16ii0.972.503.317 (3)142
Symmetry code: (ii) x+1, y+1, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C14—H14A···O16i0.972.503.317 (3)142
Symmetry code: (i) x+1, y+1, z+1.
 

Acknowledgements

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

References

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Volume 71| Part 3| March 2015| Pages o165-o166
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