1,5-Dimethyl citrate monohydrate from Dioscorea opposita Thunb.

The hydrated title compound, C₈H₁₂O₇·H₂O, was isolated from the Chinese yam Dioscorea opposita Thunb. An intra­molecular O—H...O hydrogen bond occurs in the organic mol­ecule. In the crystal structure, the mol­ecules are linked by inter­molecular O—H...O hydrogen bonds, thereby forming chains propagating in [010].

Key indicators

• Single-crystal X-ray study
• T = 296 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.033
• wR factor = 0.089
• Data-to-parameter ratio = 12.7

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT154_ALERT_1_C The su's on the Cell Angles are Equal  (x 10000)        100 Deg.
PLAT180_ALERT_3_C Check Cell Rounding: # of Values Ending with 0 =          3
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........          2

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

   2 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

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S1. Comment

The Chinese yam Dioscorea opposite Thunb is widely used in traditional medicine for the treatment of anorexia, chronic diarrhoea, diabetes, seminal emission and excessive leucorrhea. Up to now, many components have been successfully isolated and indentified from Dioscorea opposite Thumb. (Sautour et al., 2004). Herein we report the title compound, (I), isolated from the same plant (Fig. 1).

Within the organic molecule, an intra-molecular O—H···O hydrogen bond occurs (Table 1), thus constructing an S(5) ring. In the crystal, the 1,5-dimethyl citrate molecules and water molecules through intermolecular O—H···O hydrogen bonds and finally construct a one-dimensional chain (Fig. 2).

Related literature

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

S2. Experimental

Dried Dioscorea opposite Thumb (3 kg) was pulverized and extracted with EtOH three times, 3 h each time. Concentration of the EtOH extract was performed and further fractionated by addition of light petroleum, EtOAc and n-BuOH, sequentially. The n-BuOH-soluble fraction was then separated and purified on silica gel column using CHCl₃–MeOH mixtures with increasing polarity: 90:10; 85:15; 80:20; 75:25; 60:40; 50:50 to yield twelve fractions. After one week, colourless blocks of (I) were obtained from the seventh fraction.

S3. Refinement

The water H atoms were located in difference Fourier maps and freely refined. The other H atoms were positioned geometrically (O—H = 0.82 Å, C—H = 0.96–0.97 Å) and refined as riding with U_iso(H) = 1.2U_eq(C) or 1.5U_eq(O or methyl-C).

Computing details

Data collection: SMART (Bruker, 2001); cell refinement: SAINT-Plus (Bruker, 2001); data reduction: SAINT-Plus (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). Displacement ellipsoids are drawn at the 50% probability level. The hydrogen bonds are shown as dashed lines.
	Fig. 2. One-dimensional structure of (I), Hydrogen bonds are shown as dashed lines. For clarity, H atoms not involved in hydrogen bonds are omitted.

1,5-Dimethyl citrate monohydrate

Crystal data

C8H12O7·H2O	Z = 2
Mr = 238.19	F(000) = 252
Triclinic, P1	Dx = 1.462 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 7.8872 (5) Å	Cell parameters from 1584 reflections
b = 8.1304 (5) Å	θ = 2.7–28.2°
c = 9.5891 (6) Å	µ = 0.13 mm^−1
α = 94.569 (1)°	T = 296 K
β = 110.122 (1)°	Block, colourless
γ = 106.957 (1)°	0.18 × 0.16 × 0.12 mm
V = 541.07 (6) Å^3

Data collection

Bruker SMART CCD diffractometer	1993 independent reflections
Radiation source: fine-focus sealed tube	1729 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.011
ω scans	θmax = 25.5°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Sheldrick, 2001)	h = −9→9
Tmin = 0.977, Tmax = 0.984	k = −6→9
2932 measured reflections	l = −11→10

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)] = 0.033	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.089	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	w = 1/[σ^2(Fo^2) + (0.0434P)^2 + 0.1209P] where P = (Fo^2 + 2Fc^2)/3
1993 reflections	(Δ/σ)max < 0.001
157 parameters	Δρmax = 0.19 e Å^−3
0 restraints	Δρmin = −0.15 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
O1	0.74007 (15)	1.12766 (14)	0.25191 (13)	0.0449 (3)
O2	0.66449 (16)	0.93114 (15)	0.39024 (12)	0.0463 (3)
O3	0.30961 (15)	0.57067 (13)	0.20264 (11)	0.0383 (3)
H3	0.3345	0.4988	0.2545	0.057*
O4	0.29657 (15)	0.70190 (13)	0.41154 (11)	0.0383 (3)
O5	0.24343 (15)	0.97566 (12)	0.29313 (11)	0.0355 (2)
H5	0.2747	0.9576	0.3798	0.053*
O6	−0.22748 (17)	0.79091 (17)	0.04817 (16)	0.0596 (4)
O7	−0.11049 (14)	0.59972 (14)	0.16700 (13)	0.0433 (3)
C1	0.9351 (2)	1.1961 (3)	0.3639 (2)	0.0605 (5)
H1A	0.9336	1.2305	0.4615	0.091*
H1B	1.0076	1.2961	0.3368	0.091*
H1C	0.9932	1.1071	0.3678	0.091*
C2	0.6206 (2)	0.99264 (18)	0.27822 (16)	0.0336 (3)
C3	0.4279 (2)	0.92440 (19)	0.15003 (15)	0.0346 (3)
H3A	0.4295	0.8363	0.0765	0.042*
H3B	0.4062	1.0200	0.1003	0.042*
C4	0.25973 (19)	0.84363 (16)	0.19763 (14)	0.0288 (3)
C5	0.0742 (2)	0.77648 (19)	0.05383 (15)	0.0347 (3)
H5A	0.0722	0.8670	−0.0062	0.042*
H5B	0.0745	0.6749	−0.0063	0.042*
C6	−0.1043 (2)	0.72700 (18)	0.08723 (16)	0.0365 (3)
C7	−0.2732 (3)	0.5434 (2)	0.2110 (2)	0.0578 (5)
H7A	−0.2883	0.6440	0.2578	0.087*
H7B	−0.2518	0.4669	0.2814	0.087*
H7C	−0.3872	0.4818	0.1228	0.087*
C8	0.29059 (18)	0.69683 (17)	0.28355 (15)	0.0293 (3)
O1W	0.4011 (2)	0.34048 (17)	0.34949 (16)	0.0595 (4)
H1AW	0.345 (3)	0.234 (3)	0.318 (2)	0.071 (7)*
H1BW	0.504 (4)	0.354 (3)	0.425 (3)	0.098 (9)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0359 (6)	0.0441 (6)	0.0536 (7)	0.0080 (5)	0.0192 (5)	0.0163 (5)
O2	0.0452 (6)	0.0510 (7)	0.0368 (6)	0.0127 (5)	0.0103 (5)	0.0159 (5)
O3	0.0492 (6)	0.0325 (5)	0.0390 (6)	0.0223 (5)	0.0161 (5)	0.0105 (4)
O4	0.0468 (6)	0.0426 (6)	0.0342 (5)	0.0211 (5)	0.0190 (5)	0.0162 (4)
O5	0.0485 (6)	0.0310 (5)	0.0321 (5)	0.0194 (4)	0.0164 (5)	0.0081 (4)
O6	0.0473 (7)	0.0609 (8)	0.0844 (9)	0.0345 (6)	0.0243 (6)	0.0323 (7)
O7	0.0359 (6)	0.0428 (6)	0.0592 (7)	0.0182 (5)	0.0214 (5)	0.0211 (5)
C1	0.0342 (9)	0.0655 (12)	0.0714 (12)	0.0059 (8)	0.0181 (9)	0.0107 (10)
C2	0.0373 (8)	0.0324 (7)	0.0371 (8)	0.0137 (6)	0.0197 (6)	0.0079 (6)
C3	0.0387 (8)	0.0358 (7)	0.0318 (7)	0.0126 (6)	0.0151 (6)	0.0128 (6)
C4	0.0337 (7)	0.0261 (6)	0.0286 (7)	0.0123 (5)	0.0122 (6)	0.0071 (5)
C5	0.0384 (8)	0.0337 (7)	0.0318 (7)	0.0158 (6)	0.0097 (6)	0.0098 (6)
C6	0.0356 (8)	0.0314 (7)	0.0374 (8)	0.0141 (6)	0.0062 (6)	0.0049 (6)
C7	0.0453 (10)	0.0548 (10)	0.0816 (13)	0.0163 (8)	0.0328 (9)	0.0235 (10)
C8	0.0268 (6)	0.0285 (7)	0.0324 (7)	0.0103 (5)	0.0101 (5)	0.0079 (5)
O1W	0.0611 (8)	0.0325 (7)	0.0639 (9)	0.0151 (6)	−0.0009 (7)	0.0144 (6)

Geometric parameters (Å, º)

O1—C2	1.3269 (17)	C2—C3	1.497 (2)
O1—C1	1.448 (2)	C3—C4	1.5349 (18)
O2—C2	1.2060 (17)	C3—H3A	0.9700
O3—C8	1.3113 (16)	C3—H3B	0.9700
O3—H3	0.8200	C4—C8	1.5332 (18)
O4—C8	1.2088 (16)	C4—C5	1.5385 (19)
O5—C4	1.4186 (15)	C5—C6	1.499 (2)
O5—H5	0.8200	C5—H5A	0.9700
O6—C6	1.1956 (18)	C5—H5B	0.9700
O7—C6	1.3345 (18)	C7—H7A	0.9600
O7—C7	1.4469 (19)	C7—H7B	0.9600
C1—H1A	0.9600	C7—H7C	0.9600
C1—H1B	0.9600	O1W—H1AW	0.82 (2)
C1—H1C	0.9600	O1W—H1BW	0.85 (3)
C2—O1—C1	116.12 (13)	O5—C4—C5	107.74 (11)
C8—O3—H3	109.5	C8—C4—C5	111.81 (11)
C4—O5—H5	109.5	C3—C4—C5	107.94 (11)
C6—O7—C7	116.87 (12)	C6—C5—C4	113.12 (11)
O1—C1—H1A	109.5	C6—C5—H5A	109.0
O1—C1—H1B	109.5	C4—C5—H5A	109.0
H1A—C1—H1B	109.5	C6—C5—H5B	109.0
O1—C1—H1C	109.5	C4—C5—H5B	109.0
H1A—C1—H1C	109.5	H5A—C5—H5B	107.8
H1B—C1—H1C	109.5	O6—C6—O7	123.30 (14)
O2—C2—O1	123.76 (14)	O6—C6—C5	125.41 (14)
O2—C2—C3	124.70 (13)	O7—C6—C5	111.29 (12)
O1—C2—C3	111.52 (12)	O7—C7—H7A	109.5
C2—C3—C4	114.33 (11)	O7—C7—H7B	109.5
C2—C3—H3A	108.7	H7A—C7—H7B	109.5
C4—C3—H3A	108.7	O7—C7—H7C	109.5
C2—C3—H3B	108.7	H7A—C7—H7C	109.5
C4—C3—H3B	108.7	H7B—C7—H7C	109.5
H3A—C3—H3B	107.6	O4—C8—O3	125.61 (12)
O5—C4—C8	108.85 (10)	O4—C8—C4	122.10 (12)
O5—C4—C3	109.34 (10)	O3—C8—C4	112.29 (11)
C8—C4—C3	111.07 (11)	H1AW—O1W—H1BW	107 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3···O1W	0.82	1.74	2.5523 (15)	173
O5—H5···O4	0.82	2.17	2.6530 (13)	118
O5—H5···O2^i	0.82	2.15	2.8487 (14)	144
O1W—H1AW···O5^ii	0.82 (2)	1.98 (2)	2.7869 (16)	167 (2)
O1W—H1BW···O4^iii	0.85 (3)	1.99 (3)	2.8111 (17)	160 (2)

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