3-Hydr­oxy-3-(methoxy­carbon­yl)penta­nedioic acid

Aliyu, L.; Mohamed, N.; Quah, C.K.; Fun, H.-K.

doi:10.1107/S1600536809025598

organic compounds

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ISSN: 2056-9890

Volume 65| Part 8| August 2009| Page o1843

doi:10.1107/S1600536809025598

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3-Hydroxy-3-(methoxycarbonyl)pentanedioic acid

Lawal Aliyu,^a Nornisah Mohamed,^a ‡ Ching Kheng Quah ^b § and Hoong-Kun Fun ^b ^*¶

^aSchool of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and ^bX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
^*Correspondence e-mail: hkfun@usm.my

(Received 30 June 2009; accepted 1 July 2009; online 11 July 2009)

In the title compound, C₇H₁₀O₇, the aliphatic chain is approximately planar [maximum deviation = 0.013 (1) Å] and makes a dihedral angle of 78.75 (7)° with the methoxycarbonyl group. In the crystal, molecules are linked via intermolecular O—H⋯O and C—H⋯O hydrogen bonds into sheets parallel to (100). In the sheet, O—H⋯O hydrogen bonds generate R₂²(9) and R₂²(8) ring motifs.

Related literature

For hydrogen-bond motifs, see: Bernstein et al. (1995 ). For bond-length data, see: Allen et al. (1987 ). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986 ).

Experimental

Crystal data

C₇H₁₀O₇
M_r = 206.15
Orthorhombic, P b c a
a = 12.7110 (4) Å
b = 5.8323 (2) Å
c = 23.8844 (7) Å
V = 1770.65 (10) Å³
Z = 8
Mo Kα radiation
μ = 0.14 mm⁻¹
T = 100 K
0.54 × 0.18 × 0.11 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2005 ) T_min = 0.927, T_max = 0.985
54585 measured reflections
4404 independent reflections
4059 reflections with I > 2σ(I)
R_int = 0.030

Refinement

R[F² > 2σ(F²)] = 0.041
wR(F²) = 0.107
S = 1.12
4404 reflections
167 parameters
All H-atom parameters refined
Δρ_max = 0.56 e Å⁻³
Δρ_min = −0.25 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H1O2⋯O6ⁱ	0.84 (2)	1.85 (2)	2.6838 (8)	173 (2)
O3—H1O3⋯O1ⁱⁱ	0.87 (2)	2.01 (2)	2.8549 (8)	163 (2)
O4—H1O4⋯O5ⁱⁱⁱ	0.91 (2)	1.73 (2)	2.6391 (9)	176 (2)
C4—H4A⋯O5^iv	0.99 (1)	2.53 (1)	3.4035 (9)	147 (1)
Symmetry codes: (i) $[-x, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[-x, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iii) -x, -y, -z+1; (iv) -x, -y+1, -z+1.

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809025598/ci2844sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809025598/ci2844Isup2.hkl

checkCIF report

Comment top

Research in natural products often results in the discovery of novel and interesting compounds. Chemical constituents from mango have been found to exhibit bioactivities against certain in silico disease models. Herein, we report the crystal structure of the title compound which was isolated from the mango extract.

The bond lengths (Allen et al., 1987) and angles in the molecule (Fig. 1) are within normal ranges. Atoms C1, C2, C3 and C4 is approximately planar, with a maximum deviation of 0.013 (1) Å for atom C2. This plane makes a dihedral angle of 78.75 (4)° with the mean plane of methoxycarbonyl group (C6/C7/O6/O7).

In the solid state (Fig. 2), the molecules are linked via intermolecular O2—H1O2···O6 and O3—H1O3···O1 hydrogen bonds to generate R₂²(9) ring motifs (Bernstein et al., 1995) (Table 1) and pairs of intermolecular O4—H1O4···O5 hydrogen bonds form R₂²(8) ring motifs. The crystal structure is further stabilized by intermolecular C4—H4A···O5 hydrogen bonds. The molecules are linked by these hydrogen bonds to form layers parallel to the (100).

Related literature top

For hydrogen-bond motifs, see: Bernstein et al. (1995). For bond-length data, see: Allen et al. (1987). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986).

Experimental top

The title compound was extracted by Soxhlet extraction method using methanol from oven-dried mangoes. The dried extract was dissolved in water and fractionated using different solvents. The ethyl acetate fraction was evaporated using rotary evaporator and the residue was purified using column chromatography (40% ethyl acetate: 60% n-hexane) to give crystals after washing with ethyl acetate. The crystals were later found to be suitable for X-ray analysis.

Computing details top

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top

	Fig. 1. The molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme.
	Fig. 2. The crystal packing of the title compound, viewed along the a axis. H atoms not involved in hydrogen bonds (dashed lines) have been omitted for clarity.

3-Hydroxy-3-(methoxycarbonyl)pentanedioic acid top

Crystal data top

C₇H₁₀O₇	F(000) = 864
M_r = 206.15	D_x = 1.547 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 9850 reflections
a = 12.7110 (4) Å	θ = 3.2–36.7°
b = 5.8323 (2) Å	µ = 0.14 mm⁻¹
c = 23.8844 (7) Å	T = 100 K
V = 1770.65 (10) Å³	Plate, colourless
Z = 8	0.54 × 0.18 × 0.11 mm

Data collection top

Bruker SMART APEXII CCD area-detector diffractometer	4404 independent reflections
Radiation source: fine-focus sealed tube	4059 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.030
ϕ and ω scans	θ_max = 36.7°, θ_min = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2005)	h = −21→21
T_min = 0.927, T_max = 0.985	k = −8→9
54585 measured reflections	l = −39→39

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.041	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.107	All H-atom parameters refined
S = 1.12	w = 1/[σ²(F_o²) + (0.0517P)² + 0.4849P] where P = (F_o² + 2F_c²)/3
4404 reflections	(Δ/σ)_max = 0.001
167 parameters	Δρ_max = 0.56 e Å⁻³
0 restraints	Δρ_min = −0.25 e Å⁻³

Crystal data top

C₇H₁₀O₇	V = 1770.65 (10) Å³
M_r = 206.15	Z = 8
Orthorhombic, Pbca	Mo Kα radiation
a = 12.7110 (4) Å	µ = 0.14 mm⁻¹
b = 5.8323 (2) Å	T = 100 K
c = 23.8844 (7) Å	0.54 × 0.18 × 0.11 mm

Data collection top

Bruker SMART APEXII CCD area-detector diffractometer	4404 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2005)	4059 reflections with I > 2σ(I)
T_min = 0.927, T_max = 0.985	R_int = 0.030
54585 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.041	0 restraints
wR(F²) = 0.107	All H-atom parameters refined
S = 1.12	Δρ_max = 0.56 e Å⁻³
4404 reflections	Δρ_min = −0.25 e Å⁻³
167 parameters

Special details top

Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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 (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.02576 (5)	0.61486 (11)	0.25826 (2)	0.01728 (11)
O2	0.17885 (5)	0.80419 (12)	0.24936 (3)	0.01938 (12)
O3	0.08405 (4)	0.23143 (9)	0.34206 (2)	0.01268 (10)
O4	0.12975 (5)	0.07178 (11)	0.47512 (3)	0.01837 (12)
O5	−0.02721 (4)	0.24507 (10)	0.46792 (2)	0.01487 (11)
O6	−0.11179 (4)	0.42068 (10)	0.35333 (2)	0.01375 (10)
O7	−0.04401 (4)	0.74583 (10)	0.38809 (3)	0.01586 (11)
C1	0.10969 (5)	0.67852 (13)	0.27732 (3)	0.01260 (11)
C2	0.14594 (5)	0.62879 (13)	0.33592 (3)	0.01235 (11)
C3	0.07801 (5)	0.45077 (12)	0.36661 (3)	0.01026 (11)
C4	0.12280 (5)	0.42501 (12)	0.42612 (3)	0.01211 (11)
C5	0.06767 (5)	0.23834 (12)	0.45814 (3)	0.01218 (11)
C6	−0.03676 (5)	0.53355 (12)	0.36864 (3)	0.01112 (11)
C7	−0.14757 (6)	0.85003 (15)	0.38333 (4)	0.02113 (15)
H2A	0.1457 (11)	0.771 (2)	0.3557 (6)	0.020 (3)*
H2B	0.2200 (10)	0.580 (2)	0.3349 (6)	0.021 (3)*
H4A	0.1116 (10)	0.567 (2)	0.4477 (6)	0.016 (3)*
H4B	0.1959 (10)	0.390 (2)	0.4241 (5)	0.015 (3)*
H7A	−0.1957 (12)	0.773 (3)	0.4079 (7)	0.033 (4)*
H7B	−0.1406 (11)	1.010 (3)	0.3934 (6)	0.023 (3)*
H7C	−0.1741 (14)	0.827 (3)	0.3455 (7)	0.039 (4)*
H1O2	0.1539 (13)	0.834 (3)	0.2177 (7)	0.038 (4)*
H1O3	0.0466 (12)	0.225 (3)	0.3117 (7)	0.032 (4)*
H1O4	0.0934 (14)	−0.032 (4)	0.4959 (8)	0.046 (5)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0175 (2)	0.0178 (3)	0.0166 (2)	−0.00488 (19)	−0.00472 (18)	0.00421 (19)
O2	0.0153 (2)	0.0256 (3)	0.0172 (3)	−0.0040 (2)	−0.00089 (18)	0.0107 (2)
O3	0.0149 (2)	0.0102 (2)	0.0130 (2)	0.00161 (16)	−0.00136 (16)	−0.00159 (16)
O4	0.0142 (2)	0.0180 (3)	0.0229 (3)	0.00341 (19)	0.00330 (19)	0.0089 (2)
O5	0.0123 (2)	0.0159 (2)	0.0164 (2)	0.00103 (17)	0.00198 (16)	0.00301 (18)
O6	0.0111 (2)	0.0156 (2)	0.0145 (2)	−0.00290 (17)	−0.00018 (16)	−0.00210 (17)
O7	0.0116 (2)	0.0115 (2)	0.0245 (3)	0.00166 (17)	−0.00251 (18)	−0.00385 (19)
C1	0.0128 (2)	0.0115 (3)	0.0135 (3)	0.0001 (2)	0.00038 (19)	0.0027 (2)
C2	0.0111 (2)	0.0132 (3)	0.0128 (3)	−0.0015 (2)	−0.00051 (19)	0.0029 (2)
C3	0.0101 (2)	0.0097 (2)	0.0110 (2)	−0.00015 (19)	−0.00016 (18)	0.00032 (19)
C4	0.0120 (2)	0.0133 (3)	0.0110 (3)	−0.0015 (2)	−0.00097 (19)	0.0013 (2)
C5	0.0129 (2)	0.0136 (3)	0.0100 (2)	0.0004 (2)	0.00019 (18)	0.0006 (2)
C6	0.0110 (2)	0.0106 (3)	0.0118 (3)	−0.00047 (19)	−0.00006 (18)	0.0002 (2)
C7	0.0146 (3)	0.0169 (3)	0.0319 (4)	0.0051 (3)	−0.0034 (3)	−0.0041 (3)

Geometric parameters (Å, º) top

O1—C1	1.2179 (9)	C2—C3	1.5365 (9)
O2—C1	1.3251 (9)	C2—H2A	0.956 (14)
O2—H1O2	0.838 (17)	C2—H2B	0.984 (13)
O3—C3	1.4094 (9)	C3—C6	1.5373 (9)
O3—H1O3	0.869 (16)	C3—C4	1.5386 (9)
O4—C5	1.3156 (9)	C4—C5	1.5037 (10)
O4—H1O4	0.91 (2)	C4—H4A	0.984 (13)
O5—C5	1.2290 (9)	C4—H4B	0.953 (13)
O6—C6	1.2152 (8)	C7—H7A	0.960 (16)
O7—C6	1.3256 (9)	C7—H7B	0.966 (15)
O7—C7	1.4543 (10)	C7—H7C	0.973 (17)
C1—C2	1.5020 (10)

C1—O2—H1O2	108.5 (12)	C5—C4—C3	111.60 (6)
C3—O3—H1O3	111.0 (11)	C5—C4—H4A	106.0 (8)
C5—O4—H1O4	110.8 (12)	C3—C4—H4A	110.4 (8)
C6—O7—C7	115.21 (6)	C5—C4—H4B	108.9 (8)
O1—C1—O2	124.15 (7)	C3—C4—H4B	109.6 (8)
O1—C1—C2	123.93 (6)	H4A—C4—H4B	110.4 (11)
O2—C1—C2	111.90 (6)	O5—C5—O4	123.61 (7)
C1—C2—C3	113.75 (6)	O5—C5—C4	122.06 (6)
C1—C2—H2A	107.0 (8)	O4—C5—C4	114.32 (6)
C3—C2—H2A	110.5 (8)	O6—C6—O7	123.84 (6)
C1—C2—H2B	109.1 (8)	O6—C6—C3	124.41 (6)
C3—C2—H2B	110.7 (8)	O7—C6—C3	111.74 (6)
H2A—C2—H2B	105.5 (12)	O7—C7—H7A	109.5 (10)
O3—C3—C2	112.60 (5)	O7—C7—H7B	107.5 (8)
O3—C3—C6	110.48 (5)	H7A—C7—H7B	111.0 (13)
C2—C3—C6	109.64 (5)	O7—C7—H7C	109.2 (10)
O3—C3—C4	106.00 (5)	H7A—C7—H7C	106.4 (14)
C2—C3—C4	107.38 (5)	H7B—C7—H7C	113.3 (13)
C6—C3—C4	110.65 (5)

O1—C1—C2—C3	11.29 (11)	C3—C4—C5—O4	120.28 (7)
O2—C1—C2—C3	−170.15 (6)	C7—O7—C6—O6	−7.76 (11)
C1—C2—C3—O3	65.49 (8)	C7—O7—C6—C3	170.92 (7)
C1—C2—C3—C6	−57.93 (8)	O3—C3—C6—O6	2.90 (9)
C1—C2—C3—C4	−178.20 (6)	C2—C3—C6—O6	127.56 (7)
O3—C3—C4—C5	−54.29 (7)	C4—C3—C6—O6	−114.18 (8)
C2—C3—C4—C5	−174.86 (6)	O3—C3—C6—O7	−175.77 (6)
C6—C3—C4—C5	65.51 (7)	C2—C3—C6—O7	−51.11 (8)
C3—C4—C5—O5	−60.67 (9)	C4—C3—C6—O7	67.15 (7)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H1O2···O6ⁱ	0.84 (2)	1.85 (2)	2.6838 (8)	173 (2)
O3—H1O3···O1ⁱⁱ	0.87 (2)	2.01 (2)	2.8549 (8)	163 (2)
O4—H1O4···O5ⁱⁱⁱ	0.91 (2)	1.73 (2)	2.6391 (9)	176 (2)
C4—H4A···O5^iv	0.99 (1)	2.53 (1)	3.4035 (9)	147 (1)

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

Experimental details

Crystal data
Chemical formula	C₇H₁₀O₇
M_r	206.15
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	100
a, b, c (Å)	12.7110 (4), 5.8323 (2), 23.8844 (7)
V (Å³)	1770.65 (10)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.14
Crystal size (mm)	0.54 × 0.18 × 0.11

Data collection
Diffractometer	Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2005)
T_min, T_max	0.927, 0.985
No. of measured, independent and observed [I > 2σ(I)] reflections	54585, 4404, 4059
R_int	0.030
(sin θ/λ)_max (Å⁻¹)	0.841

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.041, 0.107, 1.12
No. of reflections	4404
No. of parameters	167
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.56, −0.25

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H1O2···O6ⁱ	0.84 (2)	1.85 (2)	2.6838 (8)	173 (2)
O3—H1O3···O1ⁱⁱ	0.87 (2)	2.01 (2)	2.8549 (8)	163 (2)
O4—H1O4···O5ⁱⁱⁱ	0.91 (2)	1.73 (2)	2.6391 (9)	176 (2)
C4—H4A···O5^iv	0.99 (1)	2.53 (1)	3.4035 (9)	147 (1)

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

Footnotes

‡Additional correspondence author, e-mail: nornisah@usm.my.

§Thomson Reuters ResearcherID: A-5525-2009.

¶Thomson Reuters ResearcherID: A-3561-2009.

Acknowledgements

LA and NM gratefully acknowledge funding from Universiti Sains Malaysia (USM) under the University Research Grant (No. 1001/PFARMASI/815025). HKF and CKQ thank USM for the Research University Golden Goose Grant (No. 1001/PFIZIK/811012). CKQ thanks USM for a Research Fellowship.

References

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