6-Methyl citrate from Dioscorea opposita Thunb.

The title compound (systematic name: methyl 3-carb­oxy-2-carboxy­methyl-2-hydroxy­propanoate), C₇H₁₀O₇, was isolated from the Chinese yam Dioscorea opposita Thunb. In the crystal structure, the mol­ecules present a two-dimensional structure arising from inter­molecular O—H...O hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 296 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.028
• wR factor = 0.072
• Data-to-parameter ratio = 8.1

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT222_ALERT_3_C Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       3.03 Ratio

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           26.00
           From the CIF: _reflns_number_total               1047
           Count of symmetry unique reflns         1051
           Completeness (_total/calc)             99.62%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         0
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present         no

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

---

S1. Comment

Some medicinal components have been successfully isolated and indentified from the Dioscorea opposite Thumb for the treatment of anorexia and chronic diarrhoea (Sautour et al., 2004). Herein we report the title compound, (I), isolated from the same plant.

Compound (I) consists of a citric acid skeleton, upon which one of the carboxyl units is methylated (Fig. 1). In the crystal, the molecules are connected with each other by intermolecular O—H···O hydrogen bonds and thus construct a two-dimensional network (Fig. 2 and Table 1).

Related literature

For related literature, see: Sautour et al. (2004).

S2. Experimental

Dried Dioscorea opposite Thumb (3 kg) was extracted three times with EtOH, 3 h every time. The solvent was removed under reduced pressure to give a crude extract (80 g) which was then further fractionated by liquid-liquid partition between water and light petroleum, EtOAc and n-BuOH, sequentially. The n-BuOH soluble fraction was separated and purified on silica gel column eluted with CHCl₃—MeOH (90:10, 85:15, 80:20, 75:25, 60:40, 50:50) to yield twelve fractions. After a week, colorless crystals of (I) was crystallized from the ninth fraction.

S3. Refinement

All H atoms were positioned geometrically, with O—H = 0.82 Å, C—H = 0.96 and 0.97 Å for methyl and methylene, respectively, and were refined as riding with U_iso(H)=1.2U_eq(C_methylene) and U_iso(H)=1.5U_eq(O or C_methyl).

Computing details

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: PLATON (Spek, 2003).

Figures

	Fig. 1. The molecular structure of (I), with displacement ellipsoids for the non-hydrogen atoms drawn at the 50% probability level.
	Fig. 2. Two-dimensional structure of (I), For clarity, H atoms not involved in hydrogen bonds are omitted.

methyl 3-carboxy-2-carboxymethyl-2-hydroxypropanoate

Crystal data

C7H10O7	F(000) = 432
Mr = 206.15	Dx = 1.531 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 4374 reflections
a = 5.8826 (14) Å	θ = 3.2–28.3°
b = 11.927 (3) Å	µ = 0.14 mm^−1
c = 12.752 (3) Å	T = 296 K
V = 894.7 (4) Å^3	Block, colourless
Z = 4	0.16 × 0.14 × 0.11 mm

Data collection

Bruker SMART APEX CCD diffractometer	1047 independent reflections
Radiation source: fine-focus sealed tube	1019 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.021
ω scans	θmax = 26.0°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Sheldrick, 2001)	h = −7→7
Tmin = 0.978, Tmax = 0.985	k = −14→14
4979 measured reflections	l = −15→12

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.028	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.072	H-atom parameters constrained
S = 1.14	w = 1/[σ^2(Fo^2) + (0.0397P)^2 + 0.1459P] where P = (Fo^2 + 2Fc^2)/3
1047 reflections	(Δ/σ)max < 0.001
129 parameters	Δρmax = 0.17 e Å^−3
0 restraints	Δρmin = −0.18 e Å^−3

Special details

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.

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 > σ(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 (Ų)

	x	y	z	Uiso*/Ueq
C1	0.4925 (3)	0.69161 (15)	0.39585 (14)	0.0343 (4)
C2	0.4378 (4)	0.57648 (14)	0.35749 (13)	0.0322 (4)
H2A	0.5755	0.5318	0.3576	0.039*
H2B	0.3842	0.5813	0.2857	0.039*
C3	0.2577 (3)	0.51732 (12)	0.42384 (12)	0.0248 (3)
C4	0.2234 (3)	0.40041 (13)	0.37674 (12)	0.0273 (4)
H4A	0.1832	0.4077	0.3033	0.033*
H4B	0.3651	0.3590	0.3809	0.033*
C5	0.0418 (3)	0.33632 (12)	0.43216 (13)	0.0276 (4)
C6	0.3374 (3)	0.50941 (12)	0.53815 (12)	0.0257 (3)
C7	0.6422 (4)	0.4600 (2)	0.64713 (16)	0.0538 (6)
H7A	0.7871	0.4232	0.6430	0.081*
H7B	0.5460	0.4203	0.6953	0.081*
H7C	0.6630	0.5356	0.6713	0.081*
O1	0.5924 (4)	0.75236 (12)	0.32416 (11)	0.0669 (6)
H1	0.6223	0.8143	0.3483	0.100*
O2	0.4556 (3)	0.72368 (11)	0.48306 (11)	0.0486 (4)
O3	0.0456 (2)	0.57004 (10)	0.41776 (10)	0.0326 (3)
H2	0.0493	0.6290	0.4508	0.049*
O4	−0.1301 (3)	0.30863 (13)	0.37240 (11)	0.0473 (4)
H4	−0.2223	0.2724	0.4067	0.071*
O5	0.0531 (2)	0.30970 (10)	0.52392 (9)	0.0346 (3)
O6	0.2305 (2)	0.54263 (10)	0.61229 (8)	0.0323 (3)
O7	0.5378 (2)	0.46140 (12)	0.54464 (9)	0.0378 (3)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0390 (10)	0.0313 (9)	0.0326 (8)	−0.0110 (9)	−0.0006 (8)	0.0030 (7)
C2	0.0421 (10)	0.0301 (8)	0.0245 (7)	−0.0086 (8)	0.0040 (8)	−0.0009 (7)
C3	0.0285 (8)	0.0221 (7)	0.0237 (7)	−0.0004 (7)	0.0000 (7)	−0.0014 (6)
C4	0.0334 (9)	0.0226 (7)	0.0259 (7)	−0.0017 (7)	0.0023 (7)	−0.0026 (6)
C5	0.0310 (9)	0.0199 (6)	0.0319 (8)	0.0013 (7)	0.0014 (8)	−0.0019 (6)
C6	0.0287 (8)	0.0228 (7)	0.0256 (7)	−0.0008 (7)	0.0012 (7)	−0.0006 (6)
C7	0.0449 (12)	0.0809 (15)	0.0358 (10)	0.0199 (13)	−0.0125 (9)	−0.0083 (11)
O1	0.1153 (16)	0.0492 (8)	0.0362 (7)	−0.0478 (11)	0.0083 (10)	0.0014 (6)
O2	0.0634 (10)	0.0381 (7)	0.0442 (8)	−0.0201 (8)	0.0179 (8)	−0.0127 (6)
O3	0.0347 (7)	0.0272 (6)	0.0360 (6)	0.0057 (5)	−0.0054 (6)	−0.0053 (5)
O4	0.0419 (8)	0.0582 (9)	0.0418 (8)	−0.0217 (8)	−0.0052 (6)	0.0073 (6)
O5	0.0352 (7)	0.0349 (6)	0.0337 (6)	0.0011 (6)	0.0025 (6)	0.0075 (5)
O6	0.0400 (7)	0.0321 (6)	0.0247 (5)	0.0070 (6)	0.0048 (5)	−0.0010 (5)
O7	0.0319 (7)	0.0532 (8)	0.0282 (6)	0.0120 (7)	−0.0024 (5)	−0.0060 (6)

Geometric parameters (Å, º)

C1—O2	1.196 (2)	C5—O5	1.214 (2)
C1—O1	1.306 (2)	C5—O4	1.309 (2)
C1—C2	1.493 (2)	C6—O6	1.203 (2)
C2—C3	1.528 (2)	C6—O7	1.313 (2)
C2—H2A	0.9700	C7—O7	1.444 (2)
C2—H2B	0.9700	C7—H7A	0.9600
C3—O3	1.399 (2)	C7—H7B	0.9600
C3—C4	1.532 (2)	C7—H7C	0.9600
C3—C6	1.534 (2)	O1—H1	0.8200
C4—C5	1.492 (2)	O3—H2	0.8200
C4—H4A	0.9700	O4—H4	0.8200
C4—H4B	0.9700
O2—C1—O1	123.71 (17)	C3—C4—H4B	109.2
O2—C1—C2	124.04 (16)	H4A—C4—H4B	107.9
O1—C1—C2	112.21 (16)	O5—C5—O4	122.53 (17)
C1—C2—C3	113.13 (15)	O5—C5—C4	123.44 (17)
C1—C2—H2A	109.0	O4—C5—C4	114.01 (14)
C3—C2—H2A	109.0	O6—C6—O7	124.30 (16)
C1—C2—H2B	109.0	O6—C6—C3	124.53 (16)
C3—C2—H2B	109.0	O7—C6—C3	111.18 (13)
H2A—C2—H2B	107.8	O7—C7—H7A	109.5
O3—C3—C2	112.32 (13)	O7—C7—H7B	109.5
O3—C3—C4	105.67 (13)	H7A—C7—H7B	109.5
C2—C3—C4	107.13 (13)	O7—C7—H7C	109.5
O3—C3—C6	110.67 (13)	H7A—C7—H7C	109.5
C2—C3—C6	110.02 (14)	H7B—C7—H7C	109.5
C4—C3—C6	110.91 (12)	C1—O1—H1	109.5
C5—C4—C3	112.03 (13)	C3—O3—H2	109.5
C5—C4—H4A	109.2	C5—O4—H4	109.5
C3—C4—H4A	109.2	C6—O7—C7	116.36 (14)
C5—C4—H4B	109.2

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O6^i	0.82	1.89	2.7011 (19)	171
O3—H2···O2^ii	0.82	2.03	2.8164 (18)	162
O4—H4···O5^iii	0.82	1.87	2.6854 (19)	176

Symmetry codes: (i) x+1/2, −y+3/2, −z+1; (ii) x−1/2, −y+3/2, −z+1; (iii) x−1/2, −y+1/2, −z+1.