Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807055535/hb2628sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807055535/hb2628Isup2.hkl |
CCDC reference: 672885
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.
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 Uiso(H) = 1.2Ueq(C) or 1.5Ueq(O or methyl-C).
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).
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) Å3 |
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 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)] = 0.033 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.089 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.07 | w = 1/[σ2(Fo2) + (0.0434P)2 + 0.1209P] where P = (Fo2 + 2Fc2)/3 |
1993 reflections | (Δ/σ)max < 0.001 |
157 parameters | Δρmax = 0.19 e Å−3 |
0 restraints | Δρmin = −0.15 e Å−3 |
C8H12O7·H2O | γ = 106.957 (1)° |
Mr = 238.19 | V = 541.07 (6) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.8872 (5) Å | Mo Kα radiation |
b = 8.1304 (5) Å | µ = 0.13 mm−1 |
c = 9.5891 (6) Å | T = 296 K |
α = 94.569 (1)° | 0.18 × 0.16 × 0.12 mm |
β = 110.122 (1)° |
Bruker SMART CCD diffractometer | 1993 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2001) | 1729 reflections with I > 2σ(I) |
Tmin = 0.977, Tmax = 0.984 | Rint = 0.011 |
2932 measured reflections |
R[F2 > 2σ(F2)] = 0.033 | 0 restraints |
wR(F2) = 0.089 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.07 | Δρmax = 0.19 e Å−3 |
1993 reflections | Δρmin = −0.15 e Å−3 |
157 parameters |
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. |
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)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
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) |
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) |
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···O2i | 0.82 | 2.15 | 2.8487 (14) | 144 |
O1W—H1AW···O5ii | 0.82 (2) | 1.98 (2) | 2.7869 (16) | 167 (2) |
O1W—H1BW···O4iii | 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. |
Experimental details
Crystal data | |
Chemical formula | C8H12O7·H2O |
Mr | 238.19 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 296 |
a, b, c (Å) | 7.8872 (5), 8.1304 (5), 9.5891 (6) |
α, β, γ (°) | 94.569 (1), 110.122 (1), 106.957 (1) |
V (Å3) | 541.07 (6) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.13 |
Crystal size (mm) | 0.18 × 0.16 × 0.12 |
Data collection | |
Diffractometer | Bruker SMART CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2001) |
Tmin, Tmax | 0.977, 0.984 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2932, 1993, 1729 |
Rint | 0.011 |
(sin θ/λ)max (Å−1) | 0.606 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.033, 0.089, 1.07 |
No. of reflections | 1993 |
No. of parameters | 157 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.19, −0.15 |
Computer programs: SMART (Bruker, 2001), SAINT-Plus (Bruker, 2001), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003).
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···O2i | 0.82 | 2.15 | 2.8487 (14) | 144 |
O1W—H1AW···O5ii | 0.82 (2) | 1.98 (2) | 2.7869 (16) | 167 (2) |
O1W—H1BW···O4iii | 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. |
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).