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

Peppel, T.; Sonneck, M.; Spannenberg, A.; Wohlrab, S.

doi:10.1107/S2056989015007380

organic compounds

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

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

^aLeibniz-Institut für Katalyse e. V. an der Universität Rostock, Albert-Einstein-Strasse 29a, 18059 Rostock, Germany
^*Correspondence e-mail: tim.peppel@catalysis.de

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 10 April 2015; accepted 14 April 2015; online 18 April 2015)

The crystal structure of the title compound, C₆H₁₀O₂, an α,β-unsaturated carboxylic acid, displays carboxylic acid inversion dimers linked by pairs of O—H⋯O hydrogen bonds. The packing is characterized by layers of acid dimers. All the non-H atoms of the (E)-hex-2-enoic acid molecule lie almost in the same plane (r.m.s. deviation for the non-H atoms = 0.018 Å).

Keywords: crystal structure; hydrogen bond; dimer; unsaturated carboxylic acid.

CCDC reference: 1059596

1. Related literature

For the synthesis of unsaturated α,β-carboxylic acids including the title compound, see: Shabtai et al. (1981 ); Lee et al. (1990 ); Zhang et al. (2010 ). For crystal structure determinations of related unsaturated carboxylic acids, see, for acrylic acid: Higgs et al. (1963 ); Chatani et al. (1963 ); Boese et al. (1999 ); Oswald et al. (2011 ); see, for crotonic acid: Shimizu et al. (1974 ). For the structures of co-crystals containing the title compound, see: Aakeröy et al. (2003 ); Stanton & Bak (2008 ).

2. Experimental

2.1. Crystal data

C₆H₁₀O₂
M_r = 114.14
Triclinic, $[P \overline 1]$
a = 6.8556 (3) Å
b = 6.9894 (3) Å
c = 7.4967 (3) Å
α = 79.477 (1)°
β = 80.620 (1)°
γ = 63.654 (1)°
V = 315.12 (2) Å³
Z = 2
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 150 K
0.45 × 0.41 × 0.31 mm

2.2. Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2014 ) T_min = 0.91, T_max = 0.97
5046 measured reflections
1518 independent reflections
1399 reflections with I > 2σ(I)
R_int = 0.013

2.3. Refinement

R[F² > 2σ(F²)] = 0.034
wR(F²) = 0.092
S = 1.09
1518 reflections
78 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.34 e Å⁻³
Δρ_min = −0.16 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯O2ⁱ	0.918 (19)	1.721 (19)	2.6343 (9)	173.3 (17)
Symmetry code: (i) -x, -y+1, -z+1.

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.

Supporting information

CCDC reference: 1059596

Crystal structure: contains datablocks I, New_Global_Publ_Block. DOI: https://doi.org/10.1107/S2056989015007380/hb7405sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989015007380/hb7405Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989015007380/hb7405Isup3.cml

checkCIF report

Synthesis and crystallization top

Malonic acid (24.8 g, 237.8 mmol, 1 eq) was dissolved in dry pyridine (37.6 g, 475.7 mmol, 2 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. Butyraldehyde (17.2 g, 237.8 mmol, 1 eq) was then added in one portion and the resulting clear solution was further stirred for 72 h at room temperature under argon. Afterwards, the resulting light yellow to orange solution was brought to an acidic pH value by adding phosphoric acid at 0°C (42.5 wt.-%, 582.7 mmol, 2.45 eq). The resulting two layers were extracted three times with 150 ml portions of ethyl acetate and reduced to a volume of ca. 150 ml. To remove impurities from the aldol condensation the raw acid was converted into the corresponding sodium salt by addition of an aqueous solution of sodium carbonate (18.9 g, 178.4 mmol, 0.75 eq in 200 ml). After stirring for 30 minutes the water phase was separated und extracted three times with 150 ml portions of ethyl acetate. The water phase was then acidified with concentrated hydrochloric acid (35.2 g, 356.7 mmol, 1.5 eq), the organic phase was separated and the water phase was again extracted three times with 150 ml portions of ethyl acetate. The combined organic phases were dried over Na₂SO₄ and evaporated to dryness under diminished pressure. The resulting raw product was further purified by distillation in vacuo yielding the product in purity >99% (GC). mp. 32°C. ¹H NMR (400MHz, CDCl₃): δ = 12.13 (br s, 1H, OH); 7.08 (dt, ³J = 15.6 Hz, ³J = 7.0 Hz, 1H, -CH-); 5.82 (dt, ³J = 15.6 Hz, ⁴J = 1.6 Hz, 1H, -CH-); 2.23-2.17 (m, 2H, -CH₂-); 1.49 (ps-sext, J = 7.4 Hz, 2H, -CH₂-); 0.93 (t, ³J = 7.6 Hz; 3H, -CH₃-). ¹³C NMR (100MHz, CDCl₃): δ = 172.59 (CO); 152.33 (CH); 120.95 (CH); 34.40 (CH₂); 21.25 (CH₂); 13.72 (CH₃). MS (EI, 70eV): m/z = 114 (M⁺, 10), 99 (27), 81 (11), 73 (70), 71 (12), 69 (16), 68 (52), 67 (14), 57 (11), 55 (43), 53 (28), 51 (13), 50 (11), 45 (53), 43 (24), 42 (47), 41 (64), 40 (24), 39 (100), 38 (20), 29 (44). HRMS (ESI-TOF/MS): calculated for C₆H₁₀O₂ (M⁺) 114.06753, found 114.06768. Elemental analysis for C₆H₁₀O₂ % (calc.): C 63.13 (63.14); H 8.84 (8.83). Colourless prisms were grown by slow evaporation of an ethanolic solution at -30 °C over one week.

Refinement top

H1 could be found from the difference Fourier map and was refined freely. 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.

Related literature top

For the synthesis of unsaturated α,β-carboxylic acids including the title compound, see: Shabtai et al. (1981); Lee et al. (1990); Zhang et al. (2010). For crystal structure determinations of related unsaturated carboxylic acids, see, for acrylic acid: Higgs et al. (1963); Chatani et al. (1963); Boese et al. (1999); Oswald et al. (2011); see, for crotonic acid: Shimizu et al. (1974). For the structures of co-crystals containing the title compound, see: Aakeröy et al. (2003); Stanton & Bak (2008).

Structure description top

For the synthesis of unsaturated α,β-carboxylic acids including the title compound, see: Shabtai et al. (1981); Lee et al. (1990); Zhang et al. (2010). For crystal structure determinations of related unsaturated carboxylic acids, see, for acrylic acid: Higgs et al. (1963); Chatani et al. (1963); Boese et al. (1999); Oswald et al. (2011); see, for crotonic acid: Shimizu et al. (1974). For the structures of co-crystals containing the title compound, see: Aakeröy et al. (2003); Stanton & Bak (2008).

Synthesis and crystallization top

Refinement details top

Computing details top

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

Figures top

	Fig. 1. Molecular structure of the title compound with displacement ellipsoids drawn at 50% probability level.
	Fig. 2. Packing diagram showing O—H···O hydrogen bonding.

(E)-Hex-2-enoic acid top

Crystal data top

C₆H₁₀O₂	Z = 2
M_r = 114.14	F(000) = 124
Triclinic, P1	D_x = 1.203 Mg m⁻³
a = 6.8556 (3) Å	Mo Kα radiation, λ = 0.71073 Å
b = 6.9894 (3) Å	Cell parameters from 3906 reflections
c = 7.4967 (3) Å	θ = 2.8–28.9°
α = 79.477 (1)°	µ = 0.09 mm⁻¹
β = 80.620 (1)°	T = 150 K
γ = 63.654 (1)°	Prism, colourless
V = 315.12 (2) Å³	0.45 × 0.41 × 0.31 mm

Data collection top

Bruker APEXII CCD diffractometer	1518 independent reflections
Radiation source: fine-focus sealed tube	1399 reflections with I > 2σ(I)
Detector resolution: 8.3333 pixels mm^-1	R_int = 0.013
φ and ω scans	θ_max = 28.0°, θ_min = 2.8°
Absorption correction: multi-scan (SADABS; Bruker, 2014)	h = −9→8
T_min = 0.91, T_max = 0.97	k = −9→9
5046 measured reflections	l = −9→9

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.034	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.092	w = 1/[σ²(F_o²) + (0.0441P)² + 0.0656P] where P = (F_o² + 2F_c²)/3
S = 1.09	(Δ/σ)_max < 0.001
1518 reflections	Δρ_max = 0.34 e Å⁻³
78 parameters	Δρ_min = −0.16 e Å⁻³

Crystal data top

C₆H₁₀O₂	γ = 63.654 (1)°
M_r = 114.14	V = 315.12 (2) Å³
Triclinic, P1	Z = 2
a = 6.8556 (3) Å	Mo Kα radiation
b = 6.9894 (3) Å	µ = 0.09 mm⁻¹
c = 7.4967 (3) Å	T = 150 K
α = 79.477 (1)°	0.45 × 0.41 × 0.31 mm
β = 80.620 (1)°

Data collection top

Bruker APEXII CCD diffractometer	1518 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2014)	1399 reflections with I > 2σ(I)
T_min = 0.91, T_max = 0.97	R_int = 0.013
5046 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.034	0 restraints
wR(F²) = 0.092	H atoms treated by a mixture of independent and constrained refinement
S = 1.09	Δρ_max = 0.34 e Å⁻³
1518 reflections	Δρ_min = −0.16 e Å⁻³
78 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

	x	y	z	U_iso*/U_eq
O1	0.25416 (11)	0.27334 (11)	0.55896 (10)	0.03153 (19)
H1	0.105 (3)	0.340 (3)	0.585 (2)	0.065 (5)*
O2	0.16993 (10)	0.55854 (11)	0.34602 (9)	0.02998 (19)
C1	0.30580 (14)	0.39036 (14)	0.41827 (12)	0.0232 (2)
C2	0.54014 (14)	0.29972 (14)	0.35596 (12)	0.0245 (2)
H2	0.6366	0.1656	0.4144	0.029*
C3	0.61808 (14)	0.40324 (14)	0.21920 (12)	0.0246 (2)
H3	0.5155	0.5375	0.1661	0.030*
C4	0.84965 (14)	0.33135 (15)	0.13986 (12)	0.0261 (2)
H4A	0.8960	0.4454	0.1455	0.031*
H4B	0.8554	0.3186	0.0095	0.031*
C5	1.01424 (15)	0.12084 (15)	0.22844 (13)	0.0286 (2)
H5A	0.9700	0.0049	0.2245	0.034*
H5B	1.0148	0.1327	0.3579	0.034*
C6	1.24357 (16)	0.06180 (18)	0.13358 (15)	0.0354 (2)
H6A	1.2465	0.0372	0.0084	0.053*
H6B	1.3469	−0.0695	0.1996	0.053*
H6C	1.2850	0.1796	0.1316	0.053*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0231 (3)	0.0305 (4)	0.0339 (4)	−0.0104 (3)	0.0043 (3)	0.0036 (3)
O2	0.0214 (3)	0.0309 (4)	0.0305 (4)	−0.0086 (3)	0.0022 (3)	0.0022 (3)
C1	0.0228 (4)	0.0254 (4)	0.0228 (4)	−0.0121 (3)	0.0011 (3)	−0.0045 (3)
C2	0.0201 (4)	0.0247 (4)	0.0266 (4)	−0.0086 (3)	0.0007 (3)	−0.0033 (3)
C3	0.0215 (4)	0.0254 (4)	0.0252 (4)	−0.0091 (3)	−0.0004 (3)	−0.0032 (3)
C4	0.0229 (4)	0.0295 (4)	0.0253 (4)	−0.0128 (4)	0.0030 (3)	−0.0021 (3)
C5	0.0229 (4)	0.0294 (5)	0.0310 (5)	−0.0106 (4)	0.0015 (3)	−0.0029 (4)
C6	0.0222 (4)	0.0390 (5)	0.0417 (6)	−0.0102 (4)	0.0029 (4)	−0.0102 (4)

Geometric parameters (Å, º) top

O1—C1	1.3141 (11)	C4—H4A	0.9900
O1—H1	0.918 (19)	C4—H4B	0.9900
O2—C1	1.2259 (11)	C5—C6	1.5214 (13)
C1—C2	1.4699 (12)	C5—H5A	0.9900
C2—C3	1.3243 (13)	C5—H5B	0.9900
C2—H2	0.9500	C6—H6A	0.9800
C3—C4	1.4900 (12)	C6—H6B	0.9800
C3—H3	0.9500	C6—H6C	0.9800
C4—C5	1.5142 (13)

C1—O1—H1	107.1 (11)	C5—C4—H4B	108.2
O2—C1—O1	122.73 (8)	H4A—C4—H4B	107.3
O2—C1—C2	123.58 (8)	C4—C5—C6	111.81 (8)
O1—C1—C2	113.69 (8)	C4—C5—H5A	109.3
C3—C2—C1	120.65 (8)	C6—C5—H5A	109.3
C3—C2—H2	119.7	C4—C5—H5B	109.3
C1—C2—H2	119.7	C6—C5—H5B	109.3
C2—C3—C4	126.86 (8)	H5A—C5—H5B	107.9
C2—C3—H3	116.6	C5—C6—H6A	109.5
C4—C3—H3	116.6	C5—C6—H6B	109.5
C3—C4—C5	116.56 (7)	H6A—C6—H6B	109.5
C3—C4—H4A	108.2	C5—C6—H6C	109.5
C5—C4—H4A	108.2	H6A—C6—H6C	109.5
C3—C4—H4B	108.2	H6B—C6—H6C	109.5

O2—C1—C2—C3	2.65 (14)	C2—C3—C4—C5	−1.89 (14)
O1—C1—C2—C3	−177.75 (8)	C3—C4—C5—C6	178.77 (8)
C1—C2—C3—C4	−179.32 (8)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O2ⁱ	0.918 (19)	1.721 (19)	2.6343 (9)	173.3 (17)

Symmetry code: (i) −x, −y+1, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O2ⁱ	0.918 (19)	1.721 (19)	2.6343 (9)	173.3 (17)

Symmetry code: (i) −x, −y+1, −z+1.

Acknowledgements

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

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 71| Part 5| May 2015| Page o323

https://doi.org/10.1107/S2056989015007380

Open

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