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Acta Crystallogr Sect E Struct Rep Online. 2009 August 1; 65(Pt 8): o1843.
Published online 2009 July 11. doi:  10.1107/S1600536809025598
PMCID: PMC2977126

3-Hydr­oxy-3-(methoxy­carbon­yl)penta­nedioic acid

Abstract

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 R 2 2(9) and R 2 2(8) ring motifs.

Related literature

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

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Object name is e-65-o1843-scheme1.jpg

Experimental

Crystal data

  • C7H10O7
  • M r = 206.15
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1843-efi1.jpg
  • 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 [triangle]) 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[F 2 > 2σ(F 2)] = 0.041
  • wR(F 2) = 0.107
  • S = 1.12
  • 4404 reflections
  • 167 parameters
  • All H-atom parameters refined
  • Δρmax = 0.56 e Å−3
  • Δρmin = −0.25 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

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

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

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

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.

supplementary crystallographic information

Comment

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).

Experimental

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.

Refinement

All H atoms were located in a difference Fourier map and refined freely.

Figures

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.

Crystal data

C7H10O7F(000) = 864
Mr = 206.15Dx = 1.547 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 9850 reflections
a = 12.7110 (4) Åθ = 3.2–36.7°
b = 5.8323 (2) ŵ = 0.14 mm1
c = 23.8844 (7) ÅT = 100 K
V = 1770.65 (10) Å3Plate, colourless
Z = 80.54 × 0.18 × 0.11 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer4404 independent reflections
Radiation source: fine-focus sealed tube4059 reflections with I > 2σ(I)
graphiteRint = 0.030
[var phi] and ω scansθmax = 36.7°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −21→21
Tmin = 0.927, Tmax = 0.985k = −8→9
54585 measured reflectionsl = −39→39

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.041Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.107All H-atom parameters refined
S = 1.12w = 1/[σ2(Fo2) + (0.0517P)2 + 0.4849P] where P = (Fo2 + 2Fc2)/3
4404 reflections(Δ/σ)max = 0.001
167 parametersΔρmax = 0.56 e Å3
0 restraintsΔρmin = −0.24 e Å3

Special details

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)

xyzUiso*/Ueq
O10.02576 (5)0.61486 (11)0.25826 (2)0.01728 (11)
O20.17885 (5)0.80419 (12)0.24936 (3)0.01938 (12)
O30.08405 (4)0.23143 (9)0.34206 (2)0.01268 (10)
O40.12975 (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)
C10.10969 (5)0.67852 (13)0.27732 (3)0.01260 (11)
C20.14594 (5)0.62879 (13)0.33592 (3)0.01235 (11)
C30.07801 (5)0.45077 (12)0.36661 (3)0.01026 (11)
C40.12280 (5)0.42501 (12)0.42612 (3)0.01211 (11)
C50.06767 (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)
H2A0.1457 (11)0.771 (2)0.3557 (6)0.020 (3)*
H2B0.2200 (10)0.580 (2)0.3349 (6)0.021 (3)*
H4A0.1116 (10)0.567 (2)0.4477 (6)0.016 (3)*
H4B0.1959 (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)*
H1O20.1539 (13)0.834 (3)0.2177 (7)0.038 (4)*
H1O30.0466 (12)0.225 (3)0.3117 (7)0.032 (4)*
H1O40.0934 (14)−0.032 (4)0.4959 (8)0.046 (5)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0175 (2)0.0178 (3)0.0166 (2)−0.00488 (19)−0.00472 (18)0.00421 (19)
O20.0153 (2)0.0256 (3)0.0172 (3)−0.0040 (2)−0.00089 (18)0.0107 (2)
O30.0149 (2)0.0102 (2)0.0130 (2)0.00161 (16)−0.00136 (16)−0.00159 (16)
O40.0142 (2)0.0180 (3)0.0229 (3)0.00341 (19)0.00330 (19)0.0089 (2)
O50.0123 (2)0.0159 (2)0.0164 (2)0.00103 (17)0.00198 (16)0.00301 (18)
O60.0111 (2)0.0156 (2)0.0145 (2)−0.00290 (17)−0.00018 (16)−0.00210 (17)
O70.0116 (2)0.0115 (2)0.0245 (3)0.00166 (17)−0.00251 (18)−0.00385 (19)
C10.0128 (2)0.0115 (3)0.0135 (3)0.0001 (2)0.00038 (19)0.0027 (2)
C20.0111 (2)0.0132 (3)0.0128 (3)−0.0015 (2)−0.00051 (19)0.0029 (2)
C30.0101 (2)0.0097 (2)0.0110 (2)−0.00015 (19)−0.00016 (18)0.00032 (19)
C40.0120 (2)0.0133 (3)0.0110 (3)−0.0015 (2)−0.00097 (19)0.0013 (2)
C50.0129 (2)0.0136 (3)0.0100 (2)0.0004 (2)0.00019 (18)0.0006 (2)
C60.0110 (2)0.0106 (3)0.0118 (3)−0.00047 (19)−0.00006 (18)0.0002 (2)
C70.0146 (3)0.0169 (3)0.0319 (4)0.0051 (3)−0.0034 (3)−0.0041 (3)

Geometric parameters (Å, °)

O1—C11.2179 (9)C2—C31.5365 (9)
O2—C11.3251 (9)C2—H2A0.956 (14)
O2—H1O20.838 (17)C2—H2B0.984 (13)
O3—C31.4094 (9)C3—C61.5373 (9)
O3—H1O30.869 (16)C3—C41.5386 (9)
O4—C51.3156 (9)C4—C51.5037 (10)
O4—H1O40.91 (2)C4—H4A0.984 (13)
O5—C51.2290 (9)C4—H4B0.953 (13)
O6—C61.2152 (8)C7—H7A0.960 (16)
O7—C61.3256 (9)C7—H7B0.966 (15)
O7—C71.4543 (10)C7—H7C0.973 (17)
C1—C21.5020 (10)
C1—O2—H1O2108.5 (12)C5—C4—C3111.60 (6)
C3—O3—H1O3111.0 (11)C5—C4—H4A106.0 (8)
C5—O4—H1O4110.8 (12)C3—C4—H4A110.4 (8)
C6—O7—C7115.21 (6)C5—C4—H4B108.9 (8)
O1—C1—O2124.15 (7)C3—C4—H4B109.6 (8)
O1—C1—C2123.93 (6)H4A—C4—H4B110.4 (11)
O2—C1—C2111.90 (6)O5—C5—O4123.61 (7)
C1—C2—C3113.75 (6)O5—C5—C4122.06 (6)
C1—C2—H2A107.0 (8)O4—C5—C4114.32 (6)
C3—C2—H2A110.5 (8)O6—C6—O7123.84 (6)
C1—C2—H2B109.1 (8)O6—C6—C3124.41 (6)
C3—C2—H2B110.7 (8)O7—C6—C3111.74 (6)
H2A—C2—H2B105.5 (12)O7—C7—H7A109.5 (10)
O3—C3—C2112.60 (5)O7—C7—H7B107.5 (8)
O3—C3—C6110.48 (5)H7A—C7—H7B111.0 (13)
C2—C3—C6109.64 (5)O7—C7—H7C109.2 (10)
O3—C3—C4106.00 (5)H7A—C7—H7C106.4 (14)
C2—C3—C4107.38 (5)H7B—C7—H7C113.3 (13)
C6—C3—C4110.65 (5)
O1—C1—C2—C311.29 (11)C3—C4—C5—O4120.28 (7)
O2—C1—C2—C3−170.15 (6)C7—O7—C6—O6−7.76 (11)
C1—C2—C3—O365.49 (8)C7—O7—C6—C3170.92 (7)
C1—C2—C3—C6−57.93 (8)O3—C3—C6—O62.90 (9)
C1—C2—C3—C4−178.20 (6)C2—C3—C6—O6127.56 (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—C565.51 (7)C2—C3—C6—O7−51.11 (8)
C3—C4—C5—O5−60.67 (9)C4—C3—C6—O767.15 (7)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O2—H1O2···O6i0.84 (2)1.85 (2)2.6838 (8)173 (2)
O3—H1O3···O1ii0.87 (2)2.01 (2)2.8549 (8)163 (2)
O4—H1O4···O5iii0.91 (2)1.73 (2)2.6391 (9)176 (2)
C4—H4A···O5iv0.99 (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

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CI2844).

References

  • Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.
  • Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl.34, 1555–1573.
  • Bruker (2005). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst.19, 105–107.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography