Crystal structure of (E)-undec-2-enoic acid

Marcel Sonneck; Tim Peppel; Anke Spannenberg; Sebastian Wohlrab

doi:10.1107/S2056989015009469

. 2015 May 28;71(Pt 6):o426–o427. doi: 10.1107/S2056989015009469

Crystal structure of (E)-undec-2-enoic acid

Marcel Sonneck ^a, Tim Peppel ^a,^*, Anke Spannenberg ^a, Sebastian Wohlrab ^a

PMCID: PMC4459382 PMID: 26090206

Abstract

In the molecule of the title low-melting α,β-unsaturated carboxylic acid, C₁₁H₂₀O₂, the least-squares mean line through the octyl chain forms an angle of 60.10 (13)° with the normal to plane of the acrylic acid fragment (r.m.s. deviation = 0.008 Å). In the crystal, centrosymmetrically related molecules are linked by pairs of O—H⋯O hydrogen bonds into dimers, forming layers parallel to the (041) plane.

Keywords: crystal structure, hydrogen bond, dimer, unsaturated carboxylic acid

Related literature

For an adapted direct synthesis of the title compound following the procedure established by Knoevenagel (1898 ▸) and Doebner (1902 ▸), see: Bikulova et al. (1988 ▸); Kemme et al. (2010 ▸). For crystal structure determinations of related unsaturated α,β-carboxylic acids, see, for acrylic acid: Higgs & Sass (1963 ▸); Chatani et al. (1963 ▸); Boese et al. (1999 ▸); Oswald & Urquhart (2011 ▸); see, for crotonic acid: Shimizu et al. (1974 ▸); see, for (E)-pent-2-enoic acid: Peppel et al. (2015a ▸); see, for (E)-hex-2-enoic acid: Peppel et al. (2015b ▸). For structures of co-crystals containing (E)-hex-2-enoic acid, see: Aakeröy et al. (2003 ▸); Stanton & Bak (2008 ▸).

Experimental

Crystal data

C₁₁H₂₀O₂
M _r = 184.27
Triclinic,
a = 4.6346 (4) Å
b = 5.4200 (5) Å
c = 22.7564 (19) Å
α = 88.386 (2)°
β = 88.357 (2)°
γ = 78.340 (2)°
V = 559.46 (8) Å³
Z = 2
Mo Kα radiation
μ = 0.07 mm⁻¹
T = 150 K
0.50 × 0.41 × 0.12 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2014 ▸) T _min = 0.87, T _max = 0.99
13660 measured reflections
2687 independent reflections
2317 reflections with I > 2σ(I)
R _int = 0.022

Refinement

R[F ² > 2σ(F ²)] = 0.047
wR(F ²) = 0.134
S = 1.10
2687 reflections
122 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.33 e Å⁻³
Δρ_min = −0.24 e Å⁻³

Data collection: APEX2 (Bruker, 2014 ▸); cell refinement: SAINT (Bruker, 2013 ▸); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▸); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015 ▸); molecular graphics: SHELXL2014; software used to prepare material for publication: SHELXL2014.

Supplementary Material

Crystal structure: contains datablock(s) I, New_Global_Publ_Block. DOI: 10.1107/S2056989015009469/rz5160sup1.cif

e-71-0o426-sup1.cif^{(430.1KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015009469/rz5160Isup2.hkl

e-71-0o426-Isup2.hkl^{(214.9KB, hkl)}

Click here for additional data file.^{(4.4KB, cml)}

Supporting information file. DOI: 10.1107/S2056989015009469/rz5160Isup3.cml

Click here for additional data file.^{(917.2KB, tif)}

. DOI: 10.1107/S2056989015009469/rz5160fig1.tif

Molecular structure of the title compound with displacement ellipsoids drawn at 30% probability level.

Click here for additional data file.^{(957.6KB, tif)}

. DOI: 10.1107/S2056989015009469/rz5160fig2.tif

Side view of the molecular structure of the title compound (displacement ellipsoids drawn at 30% probability level).

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

. DOI: 10.1107/S2056989015009469/rz5160fig3.tif

Packing diagram showing intermolecular O—H⋯O hydrogen bonds. Hydrogen atoms not involved in hydrogen bonding are omitted for clarity.

CCDC reference: 1401589

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

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
O1H1O2ⁱ	0.90(2)	1.73(2)	2.6244(14)	172.2(19)

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Symmetry code: (i) Inline graphic .

Acknowledgments

The authors thank P. Thiele (University of Rostock) for the DSC measurements and Professor Dr J. G. de Vries (LIKAT) for helpful support.

supplementary crystallographic information

S1. Synthesis and crystallization

Malonic acid (25.0g, 240.2 mmol, 1.0 eq) is dissolved in dry pyridine (38.0g, 480.5mmol, 2.0 eq) at room temperature in a three-necked flask equipped with a magnetic stir bar and a reflux condenser under a mild flow of argon. Nonanal (34.2g, 240.2mmol, 1.0 eq) is then added in one portion and the resulting clear solution is further stirred for 72h at room temperature under argon. Afterwards, the resulting light yellow to orange solution is brought to an acidic pH value by adding phosphoric acid at 0 °C (42.5wt. %, 138.5 g, 600.6mmol, 2.5 eq). The resulting two layers are extracted three times with 150mL portions of ethyl acetate and reduced to a volume of ca. 150 mL in vacuo. To remove impurities from aldol condensation the raw acid is converted into the corresponding sodium salt by addition of an aqueous solution of sodium carbonate (20.4 g, 192.2 mmol, 0.8 eq in 200 mL). After stirring for 30 minutes the water phase is separated and extracted three times with 150 mL portions of ethyl acetate. The water phase is then acidified with concentrated hydrochloric acid (37.0wt. %, 35.5 g, 360.4 mmol, 1.5 eq), the organic phase is separated and the water phase is again extracted three times with 150mL portions of ethyl acetate. The combined organic phases are dried over Na₂SO₄ and evaporated to dryness under diminished pressure. The resulting raw product is further purified by distillation in vacuo yielding the product in purity >99% (GC). m.p. 18°C. ¹H NMR (400MHz, CDCl₃): δ = 12.24 (br s, 1H, OH); 7.09 (dt, ³J = 15.6 Hz, ³J = 7.0 Hz, 1H, -CH-); 5.82 (dt, ³J = 15.6 Hz, ⁴J = 1.6 Hz, 1H, -CH-); 2.26-2.19 (m, 2H, -CH₂-); 1.50-1.43 (m, 2H, -CH₂-); 1.33-1.24 (m, 10H, 5x -CH₂-); 0.91-0.85 (m, 3H, -CH₃-). ¹³C NMR (100MHz, CDCl₃): δ = 172.50 (CO); 152.69 (CH); 120.76 (CH); 32.47 (CH₂); 31.98 (CH₂); 29.48 (CH₂), 29.32 (CH₂), 29.29 (CH₂); 28.02 (CH₂); 22.79 (CH₂); 14.22 (CH₃). MS (EI, 70eV): m/z = 184 (M⁺, 0), 99 (15), 97 (12), 96 (11), 95 (11), 86 (17), 84 (17), 83 (17), 82 (17), 81 (16), 73 (36), 70 (17), 69 (25), 68 (20), 67 (19), 57 (37), 56 (20), 55 (46), 54 (12), 53 (23), 45 (22), 43 (60), 42 (20), 41 (100), 40 (14), 39 (57), 29 (62). HRMS (ESI-TOF/MS): calculated for C₁₁H₂₀O₂ ([M—H]^-) 183.13905, found 183.13912. Elemental analysis for C₁₁H₂₀O₂ % (calc.): C 71.67 (71.70); H 10.83 (10.94). Suitable single crystals were grown by slow evaporation of an ethanolic solution at -30 °C over one week.

S2. Refinement

H1 could be found from the difference Fourier map and was refined with U_iso(H) fixed at 1.5 U_eq(O) . All other H atoms were placed in idealized positions with d(C—H) = 0.95 Å (CH), 0.99 Å (CH₂), 0.98 Å (CH₃) and refined using a riding model with U_iso(H) fixed at 1.2 U_eq(C) for CH and CH₂ and 1.5 U_eq(C) for CH₃.

S3. Comment

The crystal structure of (E)-undec-2-enoic acid, C₁₁H₂₀O₂, an α,β-unsaturated carboxylic acid with a melting point near room temperature (m. p. 18°C), is characterized by acid dimers. The corresponding dimers are connected via intermolecular hydrogen bonds of the carboxylic groups C=O···H–O. The crystal packing of (E)-undec-2-enoic acid is described by layers of acid dimers parallel to the (0 4 1) plane which are featured by layers of polar headgroups and hydrophobic hydrocarbon chains. The carboxylic group and the following three carbon atoms (C2, C3, C4) of the (E)-undec-2-enoic acid molecule lie in one plane (r.m.s. deviation = 0.008 Å), whereas the atoms of the hydrocarbon chain starting from C4 until C11 adopt a nearly fully staggered conformation.