Syringin monohydrate

Yin, R.-J.; Wang, X.-B.; Kong, L.-Y.

doi:10.1107/S1600536806048008

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Syringin monohydrate

R.-J. Yin, X.-B. Wang and L.-Y. Kong

In the title compound, C₁₇H₂₄O₉·H₂O, the syringin [4-(3-hydroxy-1-propenyl)-2,6-dimethoxyphenyl-β-D-glucopyranoside] molecule contains a benzene ring, two methoxy groups, an allyl group and a D-glucose fragment which adopts a chair conformation. A molecular column running along the a axis is formed via O—H

O and C—H

O hydrogen bonds and C—H

π interactions. The columns are assembled into a three-dimensional framework by an O—H

O hydrogen bond.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536806048008/is2094sup1.cif Contains datablocks I, 060905c
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536806048008/is2094Isup2.hkl Contains datablock I

CCDC reference: 630022

checkCIF report

Key indicators

Single-crystal X-ray study
T = 298 K
Mean (C-C) = 0.009 Å
R factor = 0.057
wR factor = 0.168
Data-to-parameter ratio = 7.9

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax .LT. 18) .....       7.91
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          9
PLAT480_ALERT_4_C Long H...A H-Bond Reported H12    ..  O2      ..       2.63 Ang.

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           25.00
           From the CIF: _reflns_number_total               1986
           Count of symmetry unique reflns         1987
           Completeness (_total/calc)             99.95%
           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
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C12    = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C13    = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C14    = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C15    = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C16    = .          R

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

   6 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
   2 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 2000); software used to prepare material for publication: SHELXTL and PLATON (Spek, 2003).

4-(3-hydroxy-1-propenyl)-2,6-dimethoxyphenyl-β-D-glucopyranoside monohydrate top

Crystal data top

C₁₇H₂₄O₉·H₂O	F(000) = 832
M_r = 390.38	D_x = 1.362 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 1728 reflections
a = 4.855 (2) Å	θ = 2.3–25.3°
b = 19.519 (3) Å	µ = 0.11 mm⁻¹
c = 20.084 (3) Å	T = 298 K
V = 1903.3 (9) Å³	Prism, colourless
Z = 4	0.49 × 0.15 × 0.10 mm

Data collection top

Bruker SMART 1000 CCD area-detector diffractometer	1986 independent reflections
Radiation source: fine-focus sealed tube	1241 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.085
φ and ω scans	θ_max = 25.0°, θ_min = 1.5°
Absorption correction: multi-scan (SADABS; Bruker, 2000)	h = −5→5
T_min = 0.980, T_max = 0.989	k = −18→23
9643 measured reflections	l = −23→23

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)] = 0.057	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.168	H-atom parameters constrained
S = 1.02	w = 1/[σ²(F_o²) + (0.0605P)² + 3.1656P] where P = (F_o² + 2F_c²)/3
1986 reflections	(Δ/σ)_max < 0.001
251 parameters	Δρ_max = 0.25 e Å⁻³
0 restraints	Δρ_min = −0.33 e Å⁻³

Special details top

Experimental. UV λ_max (MeOH) (nm): 221,265; IR υ_max(cm^-1): 3450, 3431, 2890, 1590, 1510, 1463, 1421, 1100, 980, 968.

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 (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.4406 (14)	0.2149 (2)	0.1672 (2)	0.0658 (17)
H1	0.4456	0.1877	0.1360	0.099*
O2	0.1102 (10)	0.5076 (2)	0.37876 (19)	0.0432 (12)
O3	0.3809 (9)	0.48704 (19)	0.49027 (19)	0.0352 (10)
O4	0.7253 (12)	0.3803 (2)	0.5063 (2)	0.0551 (14)
O5	0.6507 (9)	0.51822 (19)	0.57673 (18)	0.0344 (11)
O6	0.5074 (11)	0.6101 (2)	0.42269 (19)	0.0457 (13)
H6	0.3829	0.5843	0.4113	0.069*
O7	0.7343 (10)	0.71510 (19)	0.5040 (3)	0.0488 (13)
H7	0.8766	0.7373	0.4996	0.073*
O8	1.1187 (10)	0.6610 (2)	0.6061 (2)	0.0438 (12)
H8	1.0910	0.7001	0.6193	0.066*
O9	0.9502 (12)	0.4670 (2)	0.6876 (3)	0.0575 (14)
H9	0.8060	0.4464	0.6805	0.086*
O10	0.4528 (13)	0.3975 (2)	0.6482 (3)	0.0747 (18)
H18	0.3013	0.4180	0.6555	0.112*
H19	0.4971	0.4082	0.6086	0.112*
C1	0.642 (2)	0.1964 (4)	0.2152 (3)	0.077 (3)
H1A	0.8234	0.1979	0.1949	0.093*
H1B	0.6089	0.1499	0.2300	0.093*
C2	0.636 (2)	0.2436 (4)	0.2740 (4)	0.065 (3)
H2	0.7667	0.2369	0.3073	0.078*
C3	0.4587 (17)	0.2938 (3)	0.2816 (3)	0.0479 (19)
H3	0.3271	0.2991	0.2484	0.057*
C4	0.4474 (16)	0.3429 (3)	0.3382 (3)	0.0414 (17)
C5	0.2749 (16)	0.3989 (3)	0.3317 (3)	0.0418 (17)
H5	0.1665	0.4035	0.2938	0.050*
C6	0.2623 (15)	0.4485 (3)	0.3816 (3)	0.0342 (15)
C7	0.4160 (15)	0.4398 (3)	0.4392 (3)	0.0353 (15)
C8	0.5837 (16)	0.3833 (3)	0.4462 (3)	0.0387 (16)
C9	0.6067 (17)	0.3348 (3)	0.3955 (3)	0.0439 (17)
H9A	0.7257	0.2977	0.3998	0.053*
C10	−0.0512 (16)	0.5191 (4)	0.3190 (3)	0.053 (2)
H10A	0.0693	0.5216	0.2812	0.080*
H10B	−0.1511	0.5613	0.3232	0.080*
H10C	−0.1787	0.4820	0.3131	0.080*
C11	0.9154 (19)	0.3266 (3)	0.5171 (4)	0.064 (2)
H11A	0.8197	0.2836	0.5172	0.096*
H11B	1.0050	0.3331	0.5592	0.096*
H11C	1.0506	0.3267	0.4822	0.096*
C12	0.6166 (15)	0.5272 (3)	0.5070 (3)	0.0334 (14)
H12	0.7797	0.5114	0.4827	0.040*
C13	0.5606 (14)	0.6017 (3)	0.4929 (3)	0.0317 (14)
H13	0.3971	0.6159	0.5179	0.038*
C14	0.8008 (14)	0.6446 (3)	0.5145 (3)	0.0326 (15)
H14	0.9619	0.6326	0.4875	0.039*
C15	0.8645 (15)	0.6304 (3)	0.5878 (3)	0.0340 (15)
H15	0.7165	0.6489	0.6156	0.041*
C16	0.8925 (15)	0.5538 (3)	0.6002 (3)	0.0358 (15)
H16	1.0560	0.5363	0.5772	0.043*
C17	0.9124 (19)	0.5378 (3)	0.6738 (3)	0.052 (2)
H17A	1.0653	0.5632	0.6926	0.063*
H17B	0.7454	0.5533	0.6956	0.063*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.114 (5)	0.040 (3)	0.044 (3)	0.003 (3)	−0.006 (3)	−0.011 (2)
O2	0.046 (3)	0.046 (3)	0.038 (2)	0.010 (3)	−0.008 (2)	−0.006 (2)
O3	0.034 (2)	0.033 (2)	0.038 (2)	−0.005 (2)	0.003 (2)	−0.0095 (18)
O4	0.072 (4)	0.040 (3)	0.053 (3)	0.015 (3)	−0.023 (3)	−0.003 (2)
O5	0.041 (3)	0.030 (2)	0.033 (2)	−0.005 (2)	−0.004 (2)	0.0037 (17)
O6	0.056 (4)	0.043 (3)	0.038 (2)	−0.002 (3)	−0.013 (2)	0.010 (2)
O7	0.036 (3)	0.024 (2)	0.086 (3)	0.000 (2)	−0.002 (3)	0.012 (2)
O8	0.036 (3)	0.038 (2)	0.057 (3)	−0.003 (2)	−0.004 (2)	−0.010 (2)
O9	0.065 (4)	0.053 (3)	0.054 (3)	−0.003 (3)	−0.007 (3)	0.018 (3)
O10	0.075 (4)	0.069 (4)	0.080 (4)	−0.010 (4)	0.013 (4)	0.022 (3)
C1	0.128 (10)	0.057 (5)	0.048 (4)	0.019 (6)	−0.016 (6)	−0.019 (4)
C2	0.094 (7)	0.047 (4)	0.055 (4)	0.013 (5)	−0.010 (5)	−0.023 (4)
C3	0.062 (6)	0.040 (4)	0.041 (4)	−0.001 (4)	−0.001 (4)	−0.009 (3)
C4	0.047 (5)	0.037 (4)	0.040 (4)	−0.007 (4)	0.000 (4)	−0.007 (3)
C5	0.045 (4)	0.040 (4)	0.040 (4)	0.000 (4)	−0.002 (3)	−0.006 (3)
C6	0.035 (4)	0.033 (3)	0.035 (3)	−0.002 (3)	−0.001 (3)	−0.008 (3)
C7	0.041 (4)	0.028 (3)	0.037 (3)	0.002 (3)	−0.002 (3)	−0.009 (3)
C8	0.048 (5)	0.034 (3)	0.035 (3)	0.005 (4)	−0.009 (3)	−0.004 (3)
C9	0.051 (5)	0.033 (3)	0.048 (4)	0.003 (4)	0.002 (4)	−0.006 (3)
C10	0.052 (5)	0.065 (5)	0.042 (4)	0.008 (5)	−0.019 (4)	−0.003 (3)
C11	0.061 (6)	0.045 (4)	0.087 (6)	0.014 (5)	−0.009 (5)	0.004 (4)
C12	0.036 (4)	0.032 (3)	0.032 (3)	−0.001 (3)	−0.002 (3)	0.004 (3)
C13	0.031 (4)	0.032 (3)	0.032 (3)	0.001 (3)	−0.003 (3)	0.004 (3)
C14	0.030 (4)	0.028 (3)	0.040 (3)	0.007 (3)	−0.005 (3)	0.001 (3)
C15	0.030 (4)	0.034 (3)	0.038 (3)	−0.005 (3)	−0.004 (3)	−0.002 (3)
C16	0.038 (4)	0.033 (3)	0.036 (3)	−0.003 (3)	0.000 (3)	0.000 (3)
C17	0.073 (6)	0.046 (4)	0.038 (3)	−0.001 (4)	−0.013 (4)	0.008 (3)

Geometric parameters (Å, º) top

O1—C1	1.421 (10)	C4—C5	1.383 (9)
O1—H1	0.8200	C4—C9	1.396 (9)
O2—C6	1.370 (7)	C5—C6	1.395 (8)
O2—C10	1.450 (7)	C5—H5	0.9300
O3—C7	1.389 (6)	C6—C7	1.387 (8)
O3—C12	1.427 (7)	C7—C8	1.378 (8)
O4—C8	1.389 (7)	C8—C9	1.396 (8)
O4—C11	1.413 (8)	C9—H9A	0.9300
O5—C12	1.421 (6)	C10—H10A	0.9600
O5—C16	1.443 (8)	C10—H10B	0.9600
O6—C13	1.444 (7)	C10—H10C	0.9600
O6—H6	0.8200	C11—H11A	0.9600
O7—C14	1.430 (6)	C11—H11B	0.9600
O7—H7	0.8200	C11—H11C	0.9600
O8—C15	1.419 (8)	C12—C13	1.505 (7)
O8—H8	0.8200	C12—H12	0.9800
O9—C17	1.420 (7)	C13—C14	1.499 (8)
O9—H9	0.8200	C13—H13	0.9800
O10—H18	0.8500	C14—C15	1.529 (8)
O10—H19	0.8500	C14—H14	0.9800
C1—C2	1.498 (9)	C15—C16	1.523 (8)
C1—H1A	0.9700	C15—H15	0.9800
C1—H1B	0.9700	C16—C17	1.512 (8)
C2—C3	1.313 (10)	C16—H16	0.9800
C2—H2	0.9300	C17—H17A	0.9700
C3—C4	1.488 (8)	C17—H17B	0.9700
C3—H3	0.9300

C1—O1—H1	109.5	H10A—C10—H10C	109.5
C6—O2—C10	117.1 (5)	H10B—C10—H10C	109.5
C7—O3—C12	116.1 (5)	O4—C11—H11A	109.5
C8—O4—C11	119.2 (5)	O4—C11—H11B	109.5
C12—O5—C16	111.0 (5)	H11A—C11—H11B	109.5
C13—O6—H6	109.5	O4—C11—H11C	109.5
C14—O7—H7	109.5	H11A—C11—H11C	109.5
C15—O8—H8	109.5	H11B—C11—H11C	109.5
C17—O9—H9	109.5	O5—C12—O3	104.9 (5)
H18—O10—H19	105.4	O5—C12—C13	109.0 (5)
O1—C1—C2	111.5 (7)	O3—C12—C13	110.0 (5)
O1—C1—H1A	109.3	O5—C12—H12	110.9
C2—C1—H1A	109.3	O3—C12—H12	110.9
O1—C1—H1B	109.3	C13—C12—H12	110.9
C2—C1—H1B	109.3	O6—C13—C14	111.0 (5)
H1A—C1—H1B	108.0	O6—C13—C12	109.0 (5)
C3—C2—C1	124.2 (8)	C14—C13—C12	110.2 (5)
C3—C2—H2	117.9	O6—C13—H13	108.9
C1—C2—H2	117.9	C14—C13—H13	108.9
C2—C3—C4	126.4 (7)	C12—C13—H13	108.9
C2—C3—H3	116.8	O7—C14—C13	108.6 (5)
C4—C3—H3	116.8	O7—C14—C15	111.2 (5)
C5—C4—C9	120.2 (6)	C13—C14—C15	109.5 (5)
C5—C4—C3	117.4 (6)	O7—C14—H14	109.1
C9—C4—C3	122.4 (6)	C13—C14—H14	109.1
C4—C5—C6	120.5 (6)	C15—C14—H14	109.1
C4—C5—H5	119.7	O8—C15—C16	107.0 (5)
C6—C5—H5	119.7	O8—C15—C14	110.5 (5)
O2—C6—C7	115.3 (5)	C16—C15—C14	110.8 (5)
O2—C6—C5	125.3 (6)	O8—C15—H15	109.5
C7—C6—C5	119.4 (6)	C16—C15—H15	109.5
C8—C7—C6	120.1 (5)	C14—C15—H15	109.5
C8—C7—O3	121.9 (5)	O5—C16—C17	105.8 (6)
C6—C7—O3	117.9 (5)	O5—C16—C15	110.2 (5)
C7—C8—O4	114.5 (5)	C17—C16—C15	111.7 (5)
C7—C8—C9	121.0 (6)	O5—C16—H16	109.7
O4—C8—C9	124.5 (6)	C17—C16—H16	109.7
C8—C9—C4	118.7 (6)	C15—C16—H16	109.7
C8—C9—H9A	120.6	O9—C17—C16	113.6 (5)
C4—C9—H9A	120.6	O9—C17—H17A	108.8
O2—C10—H10A	109.5	C16—C17—H17A	108.8
O2—C10—H10B	109.5	O9—C17—H17B	108.8
H10A—C10—H10B	109.5	C16—C17—H17B	108.8
O2—C10—H10C	109.5	H17A—C17—H17B	107.7

O1—C1—C2—C3	2.9 (14)	C3—C4—C9—C8	179.9 (7)
C1—C2—C3—C4	−178.6 (8)	C16—O5—C12—O3	177.2 (4)
C2—C3—C4—C5	169.5 (8)	C16—O5—C12—C13	−65.1 (6)
C2—C3—C4—C9	−9.3 (12)	C7—O3—C12—O5	−126.7 (5)
C9—C4—C5—C6	1.4 (10)	C7—O3—C12—C13	116.3 (5)
C3—C4—C5—C6	−177.4 (7)	O5—C12—C13—O6	−176.1 (5)
C10—O2—C6—C7	179.3 (6)	O3—C12—C13—O6	−61.6 (7)
C10—O2—C6—C5	0.2 (10)	O5—C12—C13—C14	61.9 (7)
C4—C5—C6—O2	176.4 (6)	O3—C12—C13—C14	176.4 (5)
C4—C5—C6—C7	−2.7 (10)	O6—C13—C14—O7	62.5 (6)
O2—C6—C7—C8	−177.8 (6)	C12—C13—C14—O7	−176.7 (5)
C5—C6—C7—C8	1.4 (10)	O6—C13—C14—C15	−175.9 (5)
O2—C6—C7—O3	6.3 (9)	C12—C13—C14—C15	−55.0 (6)
C5—C6—C7—O3	−174.6 (6)	O7—C14—C15—O8	−70.1 (7)
C12—O3—C7—C8	67.6 (8)	C13—C14—C15—O8	169.8 (5)
C12—O3—C7—C6	−116.5 (6)	O7—C14—C15—C16	171.5 (6)
C6—C7—C8—O4	−179.7 (6)	C13—C14—C15—C16	51.4 (7)
O3—C7—C8—O4	−3.9 (10)	C12—O5—C16—C17	−177.6 (5)
C6—C7—C8—C9	1.3 (11)	C12—O5—C16—C15	61.5 (6)
O3—C7—C8—C9	177.0 (6)	O8—C15—C16—O5	−174.5 (5)
C11—O4—C8—C7	−176.3 (6)	C14—C15—C16—O5	−54.0 (7)
C11—O4—C8—C9	2.7 (11)	O8—C15—C16—C17	68.1 (8)
C7—C8—C9—C4	−2.6 (11)	C14—C15—C16—C17	−171.3 (7)
O4—C8—C9—C4	178.4 (7)	O5—C16—C17—O9	62.5 (9)
C5—C4—C9—C8	1.2 (10)	C15—C16—C17—O9	−177.5 (7)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O6—H6···O2	0.82	2.10	2.916 (7)	172
O6—H6···O3	0.82	2.47	2.827 (5)	107
O9—H9···O10	0.82	2.07	2.881 (8)	172
O10—H18···O9ⁱ	0.85	2.06	2.902 (9)	172
O10—H19···O5	0.85	2.36	2.921 (6)	124
C3—H3···O1	0.93	2.38	2.768 (7)	105
C13—H13···O8ⁱ	0.98	2.40	3.334 (8)	160
C12—H12···O2ⁱⁱ	0.98	2.63	3.538 (8)	154
C16—H16···O3ⁱⁱ	0.98	2.54	3.493 (8)	163
C17—H17A···O8	0.97	2.59	2.938 (8)	101
O8—H8···O1ⁱⁱⁱ	0.82	1.92	2.730 (6)	168
C10—H10C···Cgⁱ	0.96	3.00	3.805 (6)	142
C11—H11C···Cgⁱⁱ	0.96	2.92	3.812 (9)	155

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

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