Crystal structure of rac-3,9-bis­(2,6-di­fluoro­phen­yl)-2,4,8,10-tetra­oxa­spiro[5.5]undeca­ne

Abstract

The title compound, C₁₉H₁₆F₄O₄, was prepared by the condensation reaction of 2,6-di­fluoro­benzaldehyde and penta­erythritol. The whole mol­ecule is generated by twofold rotational symmetry. The two six-membered O-heterocycles adopt chair conformations through a shared spiro-carbon atom that is located on the crystallographic twofold rotation axis. In this conformation, the two aromatic rings are located at the equatorial positions of the O-heterocycles. The conformation of this doubly substituted tetra­oxa­spiro system is chiral. In the crystal, mol­ecules are linked by C—H⋯O hydrogen bonds, forming layers parallel to (100). These layers are linked by C—H⋯F hydrogen bonds into a three-dimensional structure.

Related literature  

For the use of tetra­oxa­spiro­[5.5]undeca­nes, see: Cismaş et al. (2005 ▸); Sondhi et al. (2009 ▸); Sauriat-Dorizon et al. (2003 ▸). For chiral conformations of tetra­oxa­spiro­[5.5]undeca­nes, see: Mihiş et al. (2008 ▸). For opposite enanti­omers of tetra­oxa­spiro­[5.5]undeca­nes, see: Sun et al. (2010 ▸).

Experimental  

Crystal data  

• C₁₉H₁₆F₄O₄

• M _r = 384.32

• Monoclinic,

• a = 28.960 (5) Å

• b = 5.5627 (11) Å

• c = 11.205 (2) Å

• β = 95.442 (4)°

• V = 1797.0 (6) ų

• Z = 4

• Mo Kα radiation

• μ = 0.13 mm⁻¹

• T = 296 K

• 0.20 × 0.18 × 0.15 mm

Data collection  

• Bruker APEXII CCD area-detector diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2009 ▸) T _min = 0.975, T _max = 0.981

• 4856 measured reflections

• 1671 independent reflections

• 1444 reflections with I > 2σ(I)

• R _int = 0.031

Refinement  

• R[F ² > 2σ(F ²)] = 0.050

• wR(F ²) = 0.148

• S = 1.01

• 1671 reflections

• 124 parameters

• H-atom parameters constrained

• Δρ_max = 0.26 e Å⁻³

• Δρ_min = −0.34 e Å⁻³

Data collection: APEX2 (Bruker, 2009 ▸); cell refinement: SAINT (Bruker, 2009 ▸); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▸); program(s) used to refine structure: SHELXL97 (Sheldrick, 2015 ▸); molecular graphics: SHELXTL (Sheldrick, 2008 ▸); software used to prepare material for publication: SHELXTL.

Supplementary Material

CCDC reference: 859906

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

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
C8H8AO2i	0.97	2.57	3.334(2)	136
C10H10BO1ii	0.97	2.56	3.410(2)	146
C2H2F1iii	0.93	2.56	3.351(3)	143

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

supplementary crystallographic information

S1. Comment

Tetra­oxa­spiro­[5.5]undecanes derived from penta­erythritol are a class of the oxo-spiro­cyclic compounds. 3,9-disubstituted spiro­cyclic compounds have inter­esting stereochemical properties like axial chirality, and play important roles in the fields like, pesticide chemistry (Cismaş et al., 2005), medicinal chemistry (Sondhi et al., 2009), and materials chemistry (Sauriat-Dorizon et al., 2003). Due to their stereochemical properties (Mihiş et al., 2008), these compounds in the solid state always adopt chiral conformations, and are built from opposite enanti­omers (Sun et al., 2010), as shown below.

In the title compound, (I), the molecule is consisted of the identical two components though a shared spiro-C9 atom with a crystallographic two-fold symmetry axis (Fig. 1). The two six-membered heterocycles both adopt chair conformation. And the two aromatic residues both are located in the equatorial positions (atom C7) of the tetra-oxa­spiro skeleton, through the staggered structure with the six-membered heterocycles, with the torsion angle O1—C7—C6—C1 of -112.5 (2) °.

The phenyl rings, as groups are much larger than hydrogen atoms, are located at the equatorial positions (atom C7) of six-membered O-heterocycles, while the H7 atoms are placed at the axial positions. In the oxo-spiro­cyclic skeleton, the distance between atoms O1 and O1A is longer than the distance between atoms O2 and O2A, with difference in value of ca. 1.115 Å. The molecule looks like a two-bladed propeller with the dihedral angle between the mean planes of (C1–C6) and (C1A–C6A) equal to 82.9 (5) °. Two opposite enanti­omers, with equal numbers, are present in the crystal (Fig. 2) with a centrosymmetric space group (C2/c).

The packing of molecules of (I), is determined by the presence of numerous weak inter­molecular inter­actions (Table 1). The C10—H10B···O1 inter­actions link the same molecules with the identical configurations R or S, respectively, into parallel chains along the b axis, furthermore, the C8—H8A···O2 inter­actions link the R and S chains alternatively along the c axis into a two-dimensional layered reticulate structure (Fig. 3) in bc plane. The donors and acceptors of the C—H···O inter­actions are barely constituted by the C and O atoms from the oxo-spiro­cyclic skeleton.

In crystalline states, those achiral layered structures are stacked into a three-dimensional structure by weak C—H···F inter­molecular inter­actions between the same enanti­omers (Fig. 4 and Table 1). It is worth mentioning that the C—H···F inter­actions constitute left/right-handed homochiral helical chains along the b axis (Fig. 4), with left-handed helical chains of the molecules of R configuration (Fig. 4a), and right-handed helical chains of S conformation molecules (Fig. 4c). And, we can clearly see that each helix in the homochiral chains consists of two molecules, with a pitch of 5.5627 (11) A (Fig. 4a). The two kinds of helical chains are arranged parallel to each other in the vertical direction of bc plan, with the same-handed chains along the a axis, and the different-handed chains along the c axis alternatively (Fig. 4b).

S2. Experimental

A catalytic qu­antity (0.04, 0.2 mmol) of p-toluene­sulfonic acid was added to a solution of 2,6-di­fluoro­benzaldehyde (1.14 g, 8 mmol) and penta­erythritol (0.52 mg, 3.8 mmol) in toluene (40 ml), and this mixture was then heated under reflux for 4 h in a flask equipped with a condenser and a water trap. The solution was washed with the sodium carbonate solution (10 %). Then, the organic layer was separated and the solvent was evaporated under the vacuum conditions and the residue was dried. The resulting solid product, (yield: 80%; m.p.: 509.5 - 510.2 K), was recrystallized from ethanol. The colourless crystals suitable for single-crystal X-ray diffraction, were also grown from ethanol. ¹H NMR (300 MHz, DMSO-D6): δ 3.68–3.81(m, 4H), 3.94–3.98 (d, 2H), 4.66–4.69 (d, 2H), 5.89 (s, 2H), 7.11–7.17 (t, 4H), 7.46–7.53 (m, 2H).

S3. Refinement

All the H atoms were placed in calculated positions and allowed to ride on their parent atoms: C—H = 0.93 - 0.98 Å with U_iso(H) = 1.2U_eq(C).

Figures

Fig. 1.

The molecular structure of the title compound, with atom labelling. Displacement ellipsoids are drawn at the 30% probability level.

Fig. 2.

The crystal structure of enantiomers of the title compound, showing the two opposite enantiomers.

Fig. 3.

Part of the layered crystal structure of the title compound, showing the weak C—H···O interactions between the molecules. The same enantiomers are linked along the b axis, and the different enantiomers are linked alternatively along the c axis.

Fig. 4.

A view of a part of the crystal structure of the title compound: (a) Left-handed helical chains of molecules with R configuration connected via the weak C—H···F interactions (represented with the orange dashed lines) along the b axis; (b) the weak C—H···F interactions of the left-handed helical chains (indicated as the orange dashed line in the orange oval rings), the weak C—H···F interactions of the right-handed helical chains (represented as the green dashed line in the green oval rings); and the weak C—H···O interactions (represented as the red dashed lines); (c) Right-handed helical chains of the molecules with S configuration connected via the weak C—H···F interactions (represented with the green dashed lines) along the b axis.

Crystal data

C19H16F4O4	F(000) = 792
Mr = 384.32	Dx = 1.421 Mg m−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 2905 reflections
a = 28.960 (5) Å	θ = 2.8–29.7°
b = 5.5627 (11) Å	µ = 0.13 mm−1
c = 11.205 (2) Å	T = 296 K
β = 95.442 (4)°	Block, colourless
V = 1797.0 (6) Å3	0.20 × 0.18 × 0.15 mm
Z = 4

Data collection

Bruker APEXII CCD area-detector diffractometer	1671 independent reflections
Radiation source: fine-focus sealed tube	1444 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.031
phi and ω scans	θmax = 25.5°, θmin = 1.4°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −34→34
Tmin = 0.975, Tmax = 0.981	k = −6→6
4856 measured reflections	l = −13→11

Refinement

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.050	H-atom parameters constrained
wR(F2) = 0.148	w = 1/[σ2(Fo2) + (0.0997P)2 + 0.5847P] where P = (Fo2 + 2Fc2)/3
S = 1.00	(Δ/σ)max = 0.001
1671 reflections	Δρmax = 0.26 e Å−3
124 parameters	Δρmin = −0.34 e Å−3
0 restraints	Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.057 (5)

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.

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C9	0.5000	1.0314 (3)	0.7500	0.0444 (5)
O2	0.56492 (4)	1.05258 (19)	0.62616 (10)	0.0529 (4)
O1	0.56527 (4)	0.75364 (18)	0.77199 (9)	0.0478 (4)
F2	0.57010 (3)	0.5988 (2)	0.51818 (9)	0.0650 (4)
C8	0.53125 (5)	0.8761 (3)	0.83549 (13)	0.0469 (4)
H8A	0.5468	0.9763	0.8978	0.056*
H8B	0.5126	0.7589	0.8734	0.056*
C7	0.59217 (6)	0.9188 (3)	0.71277 (14)	0.0516 (4)
H7	0.6082	1.0281	0.7716	0.062*
C10	0.46902 (7)	1.1913 (3)	0.81939 (15)	0.0569 (5)
H10A	0.4880	1.2783	0.8810	0.068*
H10B	0.4535	1.3082	0.7652	0.068*
C6	0.62720 (6)	0.7791 (3)	0.65080 (16)	0.0587 (5)
C5	0.61516 (6)	0.6237 (3)	0.55644 (18)	0.0614 (5)
C4	0.64657 (9)	0.4916 (5)	0.4995 (3)	0.0962 (8)
H4	0.6369	0.3890	0.4365	0.115*
C1	0.67413 (8)	0.7922 (6)	0.6860 (3)	0.0917 (8)
F1	0.68770 (5)	0.9389 (5)	0.78045 (18)	0.1351 (8)
C2	0.70735 (8)	0.6647 (9)	0.6309 (4)	0.1288 (13)
H2	0.7387	0.6806	0.6563	0.155*
C3	0.69284 (12)	0.5162 (8)	0.5389 (4)	0.1302 (13)
H3	0.7147	0.4287	0.5015	0.156*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
C9	0.0647 (13)	0.0304 (9)	0.0386 (10)	0.000	0.0074 (9)	0.000
O2	0.0676 (8)	0.0444 (6)	0.0482 (7)	−0.0015 (5)	0.0131 (5)	0.0078 (5)
O1	0.0523 (6)	0.0447 (6)	0.0457 (6)	−0.0014 (4)	0.0011 (4)	0.0065 (4)
F2	0.0611 (7)	0.0655 (7)	0.0669 (7)	−0.0013 (4)	−0.0020 (5)	−0.0138 (5)
C8	0.0595 (9)	0.0458 (8)	0.0350 (7)	−0.0063 (6)	0.0023 (6)	0.0012 (6)
C7	0.0543 (9)	0.0527 (9)	0.0464 (8)	−0.0136 (7)	−0.0020 (7)	−0.0004 (6)
C10	0.0834 (12)	0.0336 (8)	0.0560 (10)	0.0014 (7)	0.0177 (8)	−0.0043 (6)
C6	0.0482 (9)	0.0680 (11)	0.0594 (10)	−0.0062 (7)	0.0029 (7)	0.0097 (8)
C5	0.0591 (10)	0.0624 (11)	0.0640 (11)	0.0034 (8)	0.0114 (8)	0.0034 (8)
C4	0.0832 (15)	0.1023 (18)	0.1070 (19)	0.0196 (14)	0.0290 (14)	−0.0103 (16)
C1	0.0510 (11)	0.124 (2)	0.0972 (17)	−0.0138 (12)	−0.0083 (10)	0.0036 (15)
F1	0.0684 (9)	0.195 (2)	0.1355 (14)	−0.0375 (11)	−0.0249 (9)	−0.0258 (13)
C2	0.0455 (12)	0.183 (4)	0.158 (3)	0.0131 (17)	0.0088 (15)	0.019 (3)
C3	0.0830 (19)	0.149 (3)	0.164 (3)	0.038 (2)	0.042 (2)	−0.001 (3)

Geometric parameters (Å, º)

C9—C8i	1.5226 (19)	C10—O2i	1.4309 (19)
C9—C8	1.5227 (18)	C10—H10A	0.9700
C9—C10	1.5277 (19)	C10—H10B	0.9700
C9—C10i	1.5277 (19)	C6—C1	1.381 (3)
O2—C7	1.405 (2)	C6—C5	1.384 (3)
O2—C10i	1.4309 (19)	C5—C4	1.373 (3)
O1—C7	1.4106 (18)	C4—C3	1.377 (5)
O1—C8	1.4400 (18)	C4—H4	0.9300
F2—C5	1.342 (2)	C1—F1	1.364 (3)
C8—H8A	0.9700	C1—C2	1.386 (5)
C8—H8B	0.9700	C2—C3	1.356 (6)
C7—C6	1.500 (2)	C2—H2	0.9300
C7—H7	0.9800	C3—H3	0.9300
C8i—C9—C8	110.87 (16)	C9—C10—H10A	109.4
C8i—C9—C10	107.93 (9)	O2i—C10—H10B	109.4
C8—C9—C10	110.67 (9)	C9—C10—H10B	109.4
C8i—C9—C10i	110.67 (9)	H10A—C10—H10B	108.0
C8—C9—C10i	107.93 (9)	C1—C6—C5	114.9 (2)
C10—C9—C10i	108.76 (16)	C1—C6—C7	122.08 (19)
C7—O2—C10i	110.78 (12)	C5—C6—C7	123.01 (15)
C7—O1—C8	111.00 (11)	F2—C5—C4	117.6 (2)
O1—C8—C9	110.56 (10)	F2—C5—C6	118.38 (15)
O1—C8—H8A	109.5	C4—C5—C6	124.0 (2)
C9—C8—H8A	109.5	C5—C4—C3	117.7 (3)
O1—C8—H8B	109.5	C5—C4—H4	121.1
C9—C8—H8B	109.5	C3—C4—H4	121.1
H8A—C8—H8B	108.1	F1—C1—C6	117.2 (2)
O2—C7—O1	111.78 (12)	F1—C1—C2	119.4 (2)
O2—C7—C6	108.36 (13)	C6—C1—C2	123.5 (3)
O1—C7—C6	107.94 (13)	C3—C2—C1	118.2 (2)
O2—C7—H7	109.6	C3—C2—H2	120.9
O1—C7—H7	109.6	C1—C2—H2	120.9
C6—C7—H7	109.6	C2—C3—C4	121.8 (3)
O2i—C10—C9	111.29 (12)	C2—C3—H3	119.1
O2i—C10—H10A	109.4	C4—C3—H3	119.1
C7—O1—C8—C9	57.50 (15)	C1—C6—C5—F2	179.13 (19)
C8i—C9—C8—O1	69.20 (9)	C7—C6—C5—F2	0.6 (3)
C10—C9—C8—O1	−171.06 (11)	C1—C6—C5—C4	−0.5 (3)
C10i—C9—C8—O1	−52.16 (15)	C7—C6—C5—C4	−179.1 (2)
C10i—O2—C7—O1	61.60 (16)	F2—C5—C4—C3	−179.8 (3)
C10i—O2—C7—C6	−179.58 (12)	C6—C5—C4—C3	−0.1 (4)
C8—O1—C7—O2	−61.92 (15)	C5—C6—C1—F1	−178.6 (2)
C8—O1—C7—C6	179.00 (11)	C7—C6—C1—F1	0.0 (3)
C8i—C9—C10—O2i	52.40 (16)	C5—C6—C1—C2	1.2 (4)
C8—C9—C10—O2i	−69.09 (16)	C7—C6—C1—C2	179.8 (3)
C10i—C9—C10—O2i	172.51 (17)	F1—C1—C2—C3	178.6 (4)
O2—C7—C6—C1	126.2 (2)	C6—C1—C2—C3	−1.2 (5)
O1—C7—C6—C1	−112.5 (2)	C1—C2—C3—C4	0.5 (6)
O2—C7—C6—C5	−55.3 (2)	C5—C4—C3—C2	0.2 (6)
O1—C7—C6—C5	65.9 (2)

Symmetry code: (i) −x+1, y, −z+3/2.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C8—H8A···O2ii	0.97	2.57	3.334 (2)	136
C10—H10B···O1iii	0.97	2.56	3.410 (2)	146
C2—H2···F1iv	0.93	2.56	3.351 (3)	143

Symmetry codes: (ii) x, −y+2, z+1/2; (iii) −x+1, y+1, −z+3/2; (iv) −x+3/2, y−1/2, −z+3/2.