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

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.

Key indicators

• Single-crystal X-ray study
• T = 150 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.055
• wR factor = 0.124
• Data-to-parameter ratio = 18.7

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Alert level C
PLAT761_ALERT_1_C CIF Contains no X-H Bonds ......................     Please Check
PLAT762_ALERT_1_C CIF Contains no X-Y-H or H-Y-H Angles ..........     Please Check
PLAT906_ALERT_3_C Large K value in the Analysis of Variance ......      3.581 Check

Alert level G
PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Th(Min) ...          3 Report
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600        523 Note

   0 ALERT level A = Most likely a serious problem - resolve or explain
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   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
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PUBL024_ALERT_1_A The number of authors is greater than 5.
              Please specify the role of each of the co-authors
              for your paper.

Author Response: Jasim Alshawi is the PhD student; Prof. Muoayed Yousif is the PhD's supervisor in IRAQ; Karzan Zankna and Inigo J. Vitorica Yrezabal have solved the crystal structure; Prof. Richard Winpenny is the PhD's supervisor in UK; Prof. Mohamed J. Al-Jeboori is the PhD's supervisor in IRAQ.

   1 ALERT level A = Data missing that is essential or data in wrong format
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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.

Related literature

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

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

	Fig. 1. A view of the molecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level.
	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

Crystal data

C24H32N4O4	Z = 1
Mr = 440.54	F(000) = 236
Triclinic, P1	Dx = 1.245 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 8.5531 (6) Å	Cell parameters from 1515 reflections
b = 8.8379 (7) Å	θ = 3.3–26.7°
c = 9.6492 (9) Å	µ = 0.09 mm^−1
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) Å^3

Data collection

Agilent SuperNova (single source at offset, Atlas) diffractometer	2734 independent reflections
Radiation source: SuperNova (Mo) X-ray Source	1827 reflections with I > 2σ(I)
Mirror monochromator	Rint = 0.028
Detector resolution: 10.37 pixels mm^-1	θmax = 29.4°, θmin = 2.9°
ω scans	h = −11→11
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2013)	k = −10→12
Tmin = 0.933, Tmax = 1.000	l = −13→8
4657 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.055	H-atom parameters constrained
wR(F^2) = 0.124	w = 1/[σ^2(Fo^2) + (0.0363P)^2 + 0.1039P] where P = (Fo^2 + 2Fc^2)/3
S = 1.07	(Δ/σ)max < 0.001
2734 reflections	Δρmax = 0.18 e Å^−3
146 parameters	Δρmin = −0.25 e Å^−3
0 restraints

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
O13	0.46898 (16)	0.46998 (17)	0.19574 (15)	0.0317 (3)
O16	0.63475 (17)	0.71083 (17)	0.43494 (15)	0.0338 (4)
N1	0.67517 (19)	0.9650 (2)	0.32094 (18)	0.0274 (4)
N7	0.87176 (19)	0.7539 (2)	0.17968 (18)	0.0313 (4)
C12	0.5599 (2)	0.6517 (3)	0.3013 (2)	0.0270 (4)
C6	0.9477 (2)	0.9265 (3)	0.2821 (2)	0.0297 (5)
H6	1.0695	0.9854	0.3163	0.036*
C5	0.8559 (2)	1.0361 (2)	0.3483 (2)	0.0275 (4)
C10	0.9066 (2)	0.4733 (2)	0.1181 (2)	0.0311 (5)
H10A	0.7851	0.3992	0.0575	0.037*
H10B	0.9087	0.4935	0.2252	0.037*
C11	0.5474 (2)	0.7689 (2)	0.2290 (2)	0.0279 (4)
H11A	0.5653	0.7192	0.1233	0.033*
H11B	0.4302	0.7597	0.2201	0.033*
C2	0.6355 (3)	1.1083 (3)	0.4039 (2)	0.0317 (5)
H2	0.5229	1.0970	0.4061	0.038*
C9	1.0097 (2)	0.3654 (3)	0.0461 (2)	0.0307 (5)
H9A	0.9545	0.2438	0.0420	0.037*
H9B	1.1280	0.4334	0.1127	0.037*
C8	0.9819 (2)	0.6620 (2)	0.1201 (2)	0.0304 (5)
H8	1.1007	0.7412	0.1897	0.036*
C4	0.9269 (3)	1.2260 (3)	0.4484 (2)	0.0340 (5)
H4	1.0459	1.3098	0.4864	0.041*
C3	0.7880 (3)	1.2712 (3)	0.4833 (2)	0.0377 (5)
H3	0.7980	1.3898	0.5483	0.045*
C14	0.4577 (3)	0.3383 (3)	0.2513 (2)	0.0400 (5)
H14A	0.4025	0.3576	0.3392	0.048*
H14B	0.5743	0.3562	0.2869	0.048*
C15	0.3512 (3)	0.1451 (3)	0.1175 (3)	0.0544 (7)
H15A	0.4111	0.1242	0.0342	0.082*
H15B	0.2388	0.1314	0.0787	0.082*
H15C	0.3349	0.0551	0.1534	0.082*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O13	0.0352 (8)	0.0259 (7)	0.0293 (8)	0.0091 (6)	0.0017 (6)	0.0141 (6)
O16	0.0378 (8)	0.0349 (7)	0.0245 (8)	0.0133 (6)	0.0036 (6)	0.0140 (6)
N1	0.0295 (8)	0.0254 (8)	0.0269 (9)	0.0133 (7)	0.0060 (6)	0.0114 (7)
N7	0.0275 (8)	0.0302 (8)	0.0281 (9)	0.0150 (7)	0.0050 (7)	0.0054 (7)
C12	0.0238 (10)	0.0303 (10)	0.0253 (10)	0.0116 (8)	0.0079 (8)	0.0124 (8)
C6	0.0255 (10)	0.0337 (10)	0.0262 (10)	0.0119 (9)	0.0061 (8)	0.0126 (9)
C5	0.0291 (10)	0.0282 (10)	0.0231 (10)	0.0120 (8)	0.0062 (8)	0.0115 (8)
C10	0.0250 (10)	0.0340 (10)	0.0249 (10)	0.0115 (9)	0.0054 (8)	0.0083 (8)
C11	0.0250 (10)	0.0305 (10)	0.0265 (10)	0.0120 (8)	0.0052 (8)	0.0129 (8)
C2	0.0412 (11)	0.0355 (10)	0.0299 (11)	0.0252 (10)	0.0127 (9)	0.0178 (9)
C9	0.0259 (10)	0.0280 (10)	0.0300 (11)	0.0104 (8)	0.0039 (8)	0.0089 (8)
C8	0.0204 (9)	0.0302 (10)	0.0293 (11)	0.0116 (8)	0.0034 (7)	0.0050 (8)
C4	0.0361 (11)	0.0269 (10)	0.0308 (11)	0.0105 (9)	0.0062 (9)	0.0106 (9)
C3	0.0519 (13)	0.0269 (10)	0.0341 (12)	0.0207 (10)	0.0109 (10)	0.0118 (9)
C14	0.0480 (13)	0.0336 (11)	0.0396 (13)	0.0130 (10)	0.0065 (10)	0.0240 (10)
C15	0.0690 (16)	0.0316 (11)	0.0498 (15)	0.0101 (12)	−0.0021 (12)	0.0217 (11)

Geometric parameters (Å, º)

O13—C12	1.336 (2)	C6—C5	1.441 (2)
O13—C14	1.448 (2)	C5—C4	1.375 (2)
O16—C12	1.203 (2)	C10—C9	1.522 (2)
N1—C5	1.384 (2)	C10—C8	1.522 (3)
N1—C11	1.452 (2)	C2—C3	1.365 (3)
N1—C2	1.363 (2)	C9—C8^i	1.526 (3)
N7—C6	1.270 (2)	C8—C9^i	1.526 (3)
N7—C8	1.458 (2)	C4—C3	1.405 (3)
C12—C11	1.506 (3)	C14—C15	1.490 (3)
C12—O13—C14	116.15 (15)	C4—C5—C6	127.83 (17)
C5—N1—C11	126.32 (15)	C8—C10—C9	111.74 (14)
C2—N1—C5	108.70 (15)	N1—C11—C12	112.58 (15)
C2—N1—C11	124.84 (15)	N1—C2—C3	108.91 (17)
C6—N7—C8	117.71 (15)	C10—C9—C8^i	111.47 (17)
O13—C12—C11	109.47 (16)	N7—C8—C10	109.64 (14)
O16—C12—O13	124.75 (19)	N7—C8—C9^i	109.49 (17)
O16—C12—C11	125.74 (17)	C10—C8—C9^i	110.20 (15)
N7—C6—C5	123.74 (17)	C5—C4—C3	107.99 (18)
N1—C5—C6	124.91 (15)	C2—C3—C4	107.14 (17)
C4—C5—N1	107.27 (16)	O13—C14—C15	107.88 (18)
O13—C12—C11—N1	−166.07 (14)	C11—N1—C5—C6	3.5 (3)
O16—C12—C11—N1	16.3 (3)	C11—N1—C5—C4	−176.36 (17)
N1—C5—C4—C3	0.4 (2)	C11—N1—C2—C3	176.43 (17)
N1—C2—C3—C4	−0.3 (2)	C2—N1—C5—C6	179.33 (19)
N7—C6—C5—N1	6.4 (3)	C2—N1—C5—C4	−0.6 (2)
N7—C6—C5—C4	−173.7 (2)	C2—N1—C11—C12	−110.7 (2)
C12—O13—C14—C15	179.68 (16)	C9—C10—C8—N7	176.06 (15)
C6—N7—C8—C10	134.27 (18)	C9—C10—C8—C9^i	55.5 (2)
C6—N7—C8—C9^i	−104.71 (19)	C8—N7—C6—C5	178.46 (18)
C6—C5—C4—C3	−179.5 (2)	C8—C10—C9—C8^i	−56.2 (2)
C5—N1—C11—C12	64.5 (2)	C14—O13—C12—O16	2.0 (3)
C5—N1—C2—C3	0.6 (2)	C14—O13—C12—C11	−175.70 (15)
C5—C4—C3—C2	0.0 (2)

Symmetry code: (i) −x+2, −y+1, −z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C14—H14A···O16^ii	0.97	2.50	3.317 (3)	142

Symmetry code: (ii) −x+1, −y+1, −z+1.