(2S*,3S*,4R*,5R*)-3,4,5-Trihydr­oxy-6-(hydroxy­meth­yl)-3,4,5,6-tetra­hydro-2H-pyran-2-yl benzoate

He, X.-J.; Lobkovsky, E.; Liu, R.H.

doi:10.1107/S1600536805043114

(2S,3S,4R,5R)-3,4,5-Trihydroxy-6-(hydroxymethyl)-3,4,5,6-tetrahydro-2H-pyran-2-yl benzoate

The title compound, C₁₃H₁₆O₇, was extracted from fresh cranberries (Vaccinium macrocarpon). In the crystal structure, molecules are linked into a two-dimensional framework via O—H

O hydrogen bonds.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805043114/lh6594sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536805043114/lh6594Isup2.hkl Contains datablock I

CCDC reference: 298499

checkCIF report

Key indicators

Single-crystal X-ray study
T = 173 K
Mean (C-C) = 0.001 Å
Disorder in main residue
R factor = 0.032
wR factor = 0.092
Data-to-parameter ratio = 15.5

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT222_ALERT_3_A Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       5.36 Ratio

Author Response: This H atom is bonded to the minor component of the disordered O atom (O4A); it's occupancy being only 0.111(3).


Alert level B
PLAT417_ALERT_2_B Short Inter D-H..H-D       H1O    ..  H4AA    ..       2.09 Ang.
PLAT432_ALERT_2_B Short Inter X...Y Contact  O4     ..  C7      ..       2.90 Ang.

Alert level C
PLAT063_ALERT_3_C Crystal Probably too Large for Beam Size .......       0.70 mm
PLAT220_ALERT_2_C Large Non-Solvent    O     Ueq(max)/Ueq(min) ...       2.65 Ratio
PLAT301_ALERT_3_C Main Residue  Disorder .........................       5.00 Perc.
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........          5

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           37.78
           From the CIF: _reflns_number_total               3768
           Count of symmetry unique reflns         3858
           Completeness (_total/calc)             97.67%
           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

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

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

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT-Plus (Bruker, 2003); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Bruker, 1999); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

(2S,3S,4R,5R)-3,4,5-Trihydroxy-6-(hydroxymethyl)-tetrahydro-2H-pyran-2-yl benzoate top

Crystal data top

C₁₃H₁₆O₇	F(000) = 600
M_r = 284.26	D_x = 1.495 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 8636 reflections
a = 5.8022 (2) Å	θ = 2.7–37.4°
b = 7.6865 (3) Å	µ = 0.12 mm⁻¹
c = 28.3221 (12) Å	T = 173 K
V = 1263.13 (8) Å³	Block, colourless
Z = 4	0.70 × 0.60 × 0.50 mm

Data collection top

Bruker X8 APEX-II diffractometer	3768 independent reflections
Radiation source: fine-focus sealed tube	3448 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.024
φ and ω scans	θ_max = 37.8°, θ_min = 1.4°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −10→6
T_min = 0.919, T_max = 0.941	k = −13→7
15473 measured reflections	l = −48→39

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)] = 0.032	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.092	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ²(F_o²) + (0.0678P)²] where P = (F_o² + 2F_c²)/3
3768 reflections	(Δ/σ)_max = 0.001
243 parameters	Δρ_max = 0.41 e Å⁻³
0 restraints	Δρ_min = −0.21 e Å⁻³

Special details top

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	Occ. (<1)
O1	0.40391 (12)	0.10738 (9)	0.82186 (2)	0.01912 (12)
H1O	0.524 (5)	0.087 (3)	0.8451 (8)	0.059 (7)*
O2	0.52786 (12)	0.39486 (10)	0.76203 (2)	0.02045 (13)
H2O	0.515 (3)	0.462 (3)	0.7375 (6)	0.034 (4)*
O3	0.15978 (12)	0.64210 (9)	0.74963 (2)	0.01985 (13)
H3O	0.257 (3)	0.713 (2)	0.7415 (6)	0.027 (4)*
O4	0.13123 (19)	0.81961 (11)	0.86759 (3)	0.0269 (2)	0.889 (3)
H4A	0.1922	0.8978	0.8511	0.032*	0.889 (3)
O4A	−0.3093 (15)	0.7478 (16)	0.8523 (4)	0.044 (3)	0.111 (3)
H4AA	−0.3453	0.8442	0.8642	0.052*	0.111 (3)
O5	0.03348 (13)	0.45752 (8)	0.86545 (2)	0.01860 (12)
O6	0.11240 (11)	0.19852 (9)	0.89817 (2)	0.01658 (11)
O7	−0.25364 (12)	0.10427 (11)	0.88953 (3)	0.02285 (14)
C1	−0.05898 (15)	0.05058 (11)	0.96196 (3)	0.01553 (13)
C2	0.13580 (16)	0.08381 (12)	0.98951 (3)	0.01940 (15)
H2	0.263 (3)	0.135 (2)	0.9763 (6)	0.033 (4)*
C3	0.1439 (2)	0.02192 (14)	1.03566 (3)	0.02413 (18)
H3	0.281 (3)	0.050 (2)	1.0540 (5)	0.029 (4)*
C4	−0.0409 (2)	−0.07167 (14)	1.05400 (3)	0.02589 (19)
H4	−0.035 (3)	−0.114 (2)	1.0859 (6)	0.032 (4)*
C5	−0.2337 (2)	−0.10561 (14)	1.02653 (4)	0.02574 (18)
H5	−0.373 (4)	−0.162 (3)	1.0390 (6)	0.038 (5)*
C6	−0.24330 (16)	−0.04442 (13)	0.98054 (3)	0.02107 (16)
H6	−0.375 (3)	−0.073 (2)	0.9614 (5)	0.021 (3)*
C7	−0.08059 (14)	0.11741 (10)	0.91327 (3)	0.01511 (13)
C1'	0.09753 (15)	0.28600 (10)	0.85433 (3)	0.01498 (13)
H1'	−0.014 (3)	0.2258 (19)	0.8346 (5)	0.016 (3)*
C2'	0.33424 (14)	0.28294 (11)	0.83083 (3)	0.01481 (13)
H2'	0.448 (3)	0.339 (3)	0.8505 (6)	0.030 (4)*
C3'	0.30823 (14)	0.38250 (11)	0.78477 (3)	0.01448 (13)
H3'	0.202 (3)	0.317 (2)	0.7647 (5)	0.013 (3)*
C4'	0.21591 (13)	0.56429 (11)	0.79376 (3)	0.01420 (12)
H4'	0.330 (3)	0.6305 (19)	0.8094 (4)	0.012 (3)*
C5'	−0.00053 (14)	0.56366 (11)	0.82443 (3)	0.01630 (14)
H5'	−0.137 (2)	0.5198 (18)	0.8051 (4)	0.011 (3)*
C6'	−0.05862 (18)	0.74484 (12)	0.84241 (4)	0.02202 (16)
H6'1	−0.0990	0.8205	0.8154	0.026*	0.889 (3)
H6'2	−0.1943	0.7382	0.8635	0.026*	0.889 (3)
H6'3	0.0296	0.7705	0.8715	0.026*	0.111 (3)
H6'4	−0.0193	0.8332	0.8183	0.026*	0.111 (3)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0224 (3)	0.0168 (2)	0.0182 (3)	0.0038 (2)	−0.0011 (2)	−0.0002 (2)
O2	0.0186 (2)	0.0229 (3)	0.0198 (3)	0.0036 (2)	0.0066 (2)	0.0045 (2)
O3	0.0196 (3)	0.0223 (3)	0.0177 (3)	−0.0008 (2)	−0.0009 (2)	0.0076 (2)
O4	0.0393 (5)	0.0183 (3)	0.0232 (4)	−0.0027 (3)	0.0008 (3)	−0.0030 (3)
O4A	0.025 (4)	0.053 (6)	0.053 (6)	0.001 (4)	0.010 (4)	−0.018 (5)
O5	0.0249 (3)	0.0162 (2)	0.0147 (3)	0.0029 (2)	0.0043 (2)	0.00098 (19)
O6	0.0178 (2)	0.0195 (2)	0.0125 (2)	−0.0026 (2)	−0.00022 (19)	0.00327 (19)
O7	0.0183 (3)	0.0302 (3)	0.0201 (3)	−0.0017 (3)	−0.0036 (2)	0.0048 (3)
C1	0.0174 (3)	0.0155 (3)	0.0136 (3)	0.0003 (3)	0.0009 (2)	0.0007 (2)
C2	0.0222 (3)	0.0204 (3)	0.0156 (3)	−0.0020 (3)	−0.0013 (3)	0.0007 (3)
C3	0.0313 (4)	0.0253 (4)	0.0159 (4)	0.0001 (4)	−0.0036 (3)	0.0005 (3)
C4	0.0368 (5)	0.0253 (4)	0.0155 (3)	0.0035 (4)	0.0033 (4)	0.0030 (3)
C5	0.0292 (4)	0.0250 (4)	0.0230 (4)	−0.0014 (4)	0.0080 (3)	0.0061 (3)
C6	0.0209 (3)	0.0211 (4)	0.0212 (4)	−0.0022 (3)	0.0034 (3)	0.0033 (3)
C7	0.0156 (3)	0.0147 (3)	0.0150 (3)	0.0004 (3)	0.0010 (2)	0.0006 (2)
C1'	0.0187 (3)	0.0147 (3)	0.0116 (3)	−0.0011 (3)	0.0004 (2)	0.0014 (2)
C2'	0.0159 (3)	0.0150 (3)	0.0136 (3)	0.0005 (3)	−0.0001 (2)	−0.0002 (2)
C3'	0.0151 (3)	0.0159 (3)	0.0124 (3)	−0.0002 (3)	0.0011 (2)	0.0006 (2)
C4'	0.0142 (3)	0.0149 (3)	0.0135 (3)	−0.0003 (2)	−0.0004 (2)	0.0012 (2)
C5'	0.0166 (3)	0.0165 (3)	0.0159 (3)	0.0008 (3)	0.0016 (2)	0.0011 (2)
C6'	0.0260 (4)	0.0183 (3)	0.0218 (4)	0.0050 (3)	0.0035 (3)	0.0003 (3)
C6'A	0.0260 (4)	0.0183 (3)	0.0218 (4)	0.0050 (3)	0.0035 (3)	0.0003 (3)

Geometric parameters (Å, º) top

O1—C2'	1.4314 (11)	C3—C4	1.3913 (16)
O1—H1O	0.97 (3)	C3—H3	0.975 (18)
O2—C3'	1.4309 (10)	C4—C5	1.3876 (17)
O2—H2O	0.869 (18)	C4—H4	0.961 (18)
O3—C4'	1.4232 (10)	C5—C6	1.3857 (14)
O3—H3O	0.82 (2)	C5—H5	0.98 (2)
O4—C6'	1.4327 (15)	C6—H6	0.964 (17)
O4—H4A	0.8400	C1'—C2'	1.5264 (12)
O4A—H4AA	0.8400	C1'—H1'	0.971 (15)
O5—C1'	1.4055 (10)	C2'—C3'	1.5200 (11)
O5—C5'	1.4334 (11)	C2'—H2'	0.965 (19)
O6—C7	1.3511 (10)	C3'—C4'	1.5180 (12)
O6—C1'	1.4146 (10)	C3'—H3'	0.977 (14)
O7—C7	1.2126 (10)	C4'—C5'	1.5270 (12)
C1—C2	1.3969 (12)	C4'—H4'	0.946 (14)
C1—C6	1.3979 (12)	C5'—C6'	1.5206 (13)
C1—C7	1.4769 (11)	C5'—H5'	1.019 (14)
C2—C3	1.3919 (13)	C6'—H6'1	0.9900
C2—H2	0.92 (2)	C6'—H6'2	0.9900

C2'—O1—H1O	103.7 (16)	C2'—C1'—H1'	109.9 (9)
C3'—O2—H2O	108.6 (13)	O1—C2'—C3'	110.51 (7)
C4'—O3—H3O	111.6 (12)	O1—C2'—C1'	110.24 (7)
C6'—O4—H4A	109.5	C3'—C2'—C1'	106.09 (6)
C1'—O5—C5'	112.87 (6)	O1—C2'—H2'	109.3 (12)
C7—O6—C1'	116.52 (7)	C3'—C2'—H2'	109.9 (11)
C2—C1—C6	120.27 (8)	C1'—C2'—H2'	110.8 (10)
C2—C1—C7	121.78 (8)	O2—C3'—C4'	109.18 (7)
C6—C1—C7	117.93 (8)	O2—C3'—C2'	109.34 (6)
C3—C2—C1	119.29 (9)	C4'—C3'—C2'	110.76 (6)
C3—C2—H2	120.1 (12)	O2—C3'—H3'	109.5 (8)
C1—C2—H2	120.2 (11)	C4'—C3'—H3'	110.5 (9)
C4—C3—C2	120.09 (10)	C2'—C3'—H3'	107.5 (9)
C4—C3—H3	123.1 (9)	O3—C4'—C3'	108.68 (7)
C2—C3—H3	116.8 (10)	O3—C4'—C5'	108.22 (6)
C5—C4—C3	120.61 (9)	C3'—C4'—C5'	112.50 (7)
C5—C4—H4	119.4 (12)	O3—C4'—H4'	110.2 (8)
C3—C4—H4	120.0 (12)	C3'—C4'—H4'	109.0 (9)
C6—C5—C4	119.70 (9)	C5'—C4'—H4'	108.2 (8)
C6—C5—H5	117.1 (11)	O5—C5'—C6'	106.28 (7)
C4—C5—H5	123.0 (11)	O5—C5'—C4'	110.47 (7)
C5—C6—C1	120.03 (9)	C6'—C5'—C4'	111.71 (7)
C5—C6—H6	118.9 (10)	O5—C5'—H5'	110.7 (8)
C1—C6—H6	121.0 (10)	C6'—C5'—H5'	108.1 (8)
O7—C7—O6	123.31 (7)	C4'—C5'—H5'	109.5 (7)
O7—C7—C1	123.99 (8)	O4—C6'—C5'	111.33 (8)
O6—C7—C1	112.69 (7)	O4—C6'—H6'1	109.4
O5—C1'—O6	105.38 (6)	C5'—C6'—H6'1	109.4
O5—C1'—C2'	110.49 (7)	O4—C6'—H6'2	109.4
O6—C1'—C2'	108.69 (7)	C5'—C6'—H6'2	109.4
O5—C1'—H1'	113.6 (9)	H6'1—C6'—H6'2	108.0
O6—C1'—H1'	108.5 (9)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1O···O7ⁱ	0.97 (3)	1.81 (3)	2.7607 (10)	166 (2)
O3—H3O···O2ⁱⁱ	0.82 (2)	1.88 (2)	2.6774 (10)	166.1 (16)
O4—H4A···O1ⁱⁱⁱ	0.84	2.19	3.0121 (12)	167
O4A—H4AA···O7ⁱⁱⁱ	0.84	2.19	2.953 (11)	151

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

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(2S*,3S*,4R*,5R*)-3,4,5-Trihydr­oxy-6-(hydroxy­meth­yl)-3,4,5,6-tetra­hydro-2H-pyran-2-yl benzoate

Supporting information

Key indicators

checkCIF/PLATON results

(2S,3S,4R,5R)-3,4,5-Trihydroxy-6-(hydroxymethyl)-3,4,5,6-tetrahydro-2H-pyran-2-yl benzoate