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

Marcel Sonneck; Tim Peppel; Anke Spannenberg; Sebastian Wohlrab

doi:10.1107/S2056989015011937

. 2015 Jun 30;71(Pt 7):o528–o529. doi: 10.1107/S2056989015011937

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

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

PMCID: PMC4518913 PMID: 26279945

Abstract

The crystal structure of (E)-dodec-2-enoic acid, C₁₂H₂₂O₂, an α,β-unsaturated carboxylic acid with a melting point (295 K) near room temperature, is characterized by carboxylic acid inversion dimers linked by pairs of O—H⋯O hydrogen bonds. The carboxylic acid group and the following three carbon atoms of the chain of the (E)-dodec-2-enoic acid molecule lie almost in one plane (r.m.s. deviation for the four C atoms and two O atoms = 0.012 Å), whereas the remaining carbon atoms of the hydrocarbon chain adopt a nearly fully staggered conformation [moduli of torsion angles vary from 174.01 (13) to 179.97 (13)°].

Keywords: crystal structure, hydrogen bonding, dimer, unsaturated carboxylic acid, fatty acid

Related literature

For the synthesis of unsaturated α,β-carboxylic acids including the title compound by adapted routes established by Knoevenagel (1898 ▸) and Doebner (1902 ▸), see: Shabtai et al. (1981 ▸). For crystal structure determinations of related α,β-unsaturated carboxylic acids, see, for acrylic acid: Higgs et al. (1963 ▸), Chatani et al. (1963 ▸), Boese et al. (1999 ▸), or Oswald et al. (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 ▸); see, for (E)-undecen-2-enoic acid: Sonneck et al. (2015 ▸). For structures of co-crystals containing (E)-hex-2-enoic acid, see: Aakeröy et al. (2003 ▸), or Stanton & Bak (2008 ▸). graphic file with name e-71-0o528-scheme1.jpg

Experimental

Crystal data

C₁₂H₂₂O₂
M _r = 198.29
Triclinic,
a = 4.6475 (2) Å
b = 5.4169 (2) Å
c = 24.7041 (10) Å
α = 91.547 (2)°
β = 91.788 (2)°
γ = 102.3158 (19)°
V = 606.96 (4) Å³
Z = 2
Cu Kα radiation
μ = 0.56 mm⁻¹
T = 150 K
0.44 × 0.30 × 0.12 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2014 ▸) T _min = 0.80, T _max = 0.94
12048 measured reflections
2117 independent reflections
1964 reflections with I > 2σ(I)
R _int = 0.026

Refinement

R[F ² > 2σ(F ²)] = 0.046
wR(F ²) = 0.131
S = 1.13
2117 reflections
129 parameters
H-atom parameters constrained
Δρ_max = 0.29 e Å⁻³
Δρ_min = −0.23 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: SHELXL2014/7 (Sheldrick, 2015 ▸); molecular graphics: SHELXL2014/7; software used to prepare material for publication: SHELXL2014/7.

Supplementary Material

Crystal structure: contains datablock(s) I, New_Global_Publ_Block. DOI: 10.1107/S2056989015011937/hb7452sup1.cif

e-71-0o528-sup1.cif^{(365.2KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015011937/hb7452Isup2.hkl

e-71-0o528-Isup2.hkl^{(169.8KB, hkl)}

Click here for additional data file.^{(4.7KB, cml)}

Supporting information file. DOI: 10.1107/S2056989015011937/hb7452Isup3.cml

Click here for additional data file.^{(920.3KB, tif)}

. DOI: 10.1107/S2056989015011937/hb7452fig1.tif

Molecular structure of the title compound with atom labelling and displacement ellipsoids drawn at 50% probability level.

Click here for additional data file.^{(1.8MB, tif)}

. DOI: 10.1107/S2056989015011937/hb7452fig2.tif

Packing diagram showing intermolecular hydrogen bonding.

CCDC reference: 1407997

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

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
O1H1O2ⁱ	0.84	1.80	2.6319(15)	170

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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 (25.0 g, 240.2 mmol, 1.0 eq) is dissolved in dry pyridine (38.0 g, 480.5 mmol, 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. Decanal (37.5 g, 240.2 mmol, 1.0 eq) is then added in one portion and the resulting clear solution is further stirred for 72 h 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, 600.6 mmol, 2.5 eq). The resulting two layers are extracted three times with 150 mL 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 150 mL 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. 22 °C. ¹H NMR (400 MHz, CDCl₃): δ = 12.15 (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-); 1.50-1.42 (m, 2H, -CH₂-); 1.32-1.24 (m, 12H, 6x -CH₂-); 0.90-0.86 (m, 3H, -CH₃-). ¹³C NMR (100 MHz, CDCl₃): δ = 172.53 (CO); 152.68 (CH); 120.76 (CH); 32.47 (CH₂); 32.02 (CH₂); 29.61 (CH₂), 29.52 (CH₂), 29.43 (CH₂); 29.29 (CH₂); 28.02 (CH₂); 22.81 (CH₂); 14.23 (CH₃). MS (EI, 70eV): m/z = 198 (M⁺, 0), 99 (16), 98 (12), 97 (17), 96 (14), 95 (11), 86 (17), 84 (18), 83 (16), 82 (12), 81 (20), 73 (34), 71 (13), 70 (15), 69 (21), 68 (18), 67 (20), 57 (29), 56 (22), 55 (47), 54 (11), 53 (20), 45 (14), 43 (70), 42 (19), 41 (100), 40 (14), 39 (52), 29 (58). HRMS (ESI-TOF/MS): calculated for C₁₂H₂₂O₂ ([M—H]^-) 197.1547, found 197.15481. Elemental analysis for C₁₂H₂₂O₂ % (calc.): C 72.53 (72.68); H 11.24 (11.18). Suitable single crystals were grown by slow evaporation of an ethanolic solution at -30 °C over one week.

S2. Refinement

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. The carboxylic acid group was assigned by examining the C—O distances and H1 was placed using the AFIX 147 instruction (d(O—H) = 0.84 Å, U_iso(H) fixed at 1.5 U_eq(O)).