1,2-O-Isopropyl­idene-6-thio-α-D-glucofuran­ose

In the crystalline state, the title compound, C₉H₁₆O₅S, forms hydrogen-bonded chains.

Key indicators

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.006 Å
• R factor = 0.052
• wR factor = 0.130
• Data-to-parameter ratio = 15.5

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT222_ALERT_3_B Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       4.33 Ratio

Alert level C
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......       0.97
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          6
PLAT354_ALERT_3_C Short   O-H Bond (0.82A)   O5     -   H5O    ...       0.70 Ang.
PLAT420_ALERT_2_C D-H Without Acceptor       S1     -   H1S    ...          ?

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           27.55
           From the CIF: _reflns_number_total               2324
           Count of symmetry unique reflns         1369
           Completeness (_total/calc)            169.76%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured       955
           Fraction of Friedel pairs measured     0.698
           Are heavy atom types Z>Si present        yes
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C1     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C4     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C5     = .          S

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

   5 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   4 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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Computing details

Data collection: COLLECT (Nonius, 1998); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2003).

1,2-O-Isopropylidene-6-thio-α-D-glucofuranose

Crystal data

C9H16O5S	F(000) = 252
Mr = 236.28	Dx = 1.452 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 1135 reflections
a = 9.1655 (8) Å	θ = 1.0–27.5°
b = 5.8452 (5) Å	µ = 0.30 mm^−1
c = 10.5282 (9) Å	T = 100 K
β = 106.563 (4)°	Poor quality needle, colourless
V = 540.58 (8) Å^3	0.5 × 0.1 × 0.1 mm
Z = 2

Data collection

Nonius KappaCCD diffractometer	2020 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.060
Graphite monochromator	θmax = 27.6°, θmin = 2.6°
Detector resolution: 1242 (horizontal) x 1152 (vertical) pixels, CCD pixel size is 22.5 x 22.5 µm which gives at the imput a pixel of 110 x 110 µm (with 2 x 2 binning) pixels mm^-1	h = −11→11
128 frames via φ rotation (rotation angle 2.0°) and 2*200 s per frame scans	k = −7→7
3891 measured reflections	l = −13→13
2324 independent reflections

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.052	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.130	w = 1/[σ^2(Fo^2) + (0.0298P)^2 + 1.2765P] where P = (Fo^2 + 2Fc^2)/3
S = 1.07	(Δ/σ)max = 0.010
2324 reflections	Δρmax = 0.40 e Å^−3
150 parameters	Δρmin = −0.45 e Å^−3
1 restraint	Absolute structure: Flack (1983), 955 Freidel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: −0.04 (15)

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
S1	0.84545 (13)	−0.32232 (19)	0.48802 (9)	0.0282 (3)
O3	0.6188 (3)	0.1600 (5)	1.0033 (2)	0.0193 (6)
O1	0.8451 (3)	0.1534 (5)	0.8378 (2)	0.0203 (6)
O2	0.8766 (3)	0.2299 (4)	1.0650 (2)	0.0173 (6)
O5	0.5637 (3)	−0.1627 (5)	0.5813 (3)	0.0206 (6)
O4	0.5725 (4)	0.3961 (5)	0.6778 (3)	0.0213 (7)
C5	0.7066 (5)	−0.0447 (6)	0.6358 (4)	0.0156 (7)
H5	0.7115	0.0865	0.5793	0.019*
C3	0.5805 (5)	0.2177 (6)	0.7720 (3)	0.0173 (8)
H3	0.4813	0.1454	0.7615	0.021*
C4	0.7039 (4)	0.0423 (7)	0.7719 (4)	0.0166 (8)
H4	0.6911	−0.0891	0.8255	0.020*
C7	0.7571 (4)	0.1161 (6)	1.1057 (4)	0.0173 (8)
C1	0.8187 (5)	0.3089 (7)	0.9343 (3)	0.0178 (8)
H1	0.8594	0.4608	0.9244	0.021*
C2	0.6456 (4)	0.3191 (7)	0.9097 (3)	0.0165 (8)
H2	0.6077	0.4733	0.9187	0.020*
C8	0.7460 (5)	0.2190 (7)	1.2346 (4)	0.0235 (9)
H8A	0.7397	0.3825	1.2265	0.035*
H8B	0.8347	0.1780	1.3049	0.035*
H8C	0.6567	0.1616	1.2543	0.035*
C9	0.7878 (5)	−0.1397 (7)	1.1160 (4)	0.0210 (8)
H9A	0.7015	−0.2176	1.1301	0.032*
H9B	0.8761	−0.1697	1.1890	0.032*
H9C	0.8052	−0.1935	1.0354	0.032*
C6	0.8424 (5)	−0.1982 (7)	0.6456 (4)	0.0218 (9)
H6A	0.8420	−0.3208	0.7076	0.026*
H6B	0.9348	−0.1101	0.6810	0.026*
H5O	0.576 (6)	−0.263 (9)	0.620 (5)	0.028 (15)*
H4O	0.520 (5)	0.357 (7)	0.606 (4)	0.012 (10)*
H1S	0.721 (6)	−0.472 (10)	0.468 (5)	0.052 (16)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0343 (6)	0.0310 (6)	0.0181 (4)	0.0033 (5)	0.0057 (4)	−0.0076 (5)
O3	0.0207 (14)	0.0227 (14)	0.0130 (11)	−0.0012 (13)	0.0025 (10)	0.0025 (12)
O1	0.0207 (14)	0.0240 (15)	0.0141 (11)	−0.0014 (13)	0.0016 (10)	−0.0067 (12)
O2	0.0162 (14)	0.0211 (15)	0.0130 (11)	−0.0032 (11)	0.0015 (10)	0.0016 (10)
O5	0.0274 (17)	0.0172 (15)	0.0139 (13)	0.0003 (13)	0.0004 (12)	0.0022 (12)
O4	0.0303 (17)	0.0180 (14)	0.0108 (13)	0.0004 (12)	−0.0016 (13)	0.0003 (11)
C5	0.0214 (19)	0.0098 (15)	0.0140 (16)	−0.0037 (15)	0.0024 (15)	−0.0013 (13)
C3	0.021 (2)	0.016 (2)	0.0126 (16)	0.0017 (15)	0.0007 (14)	0.0021 (14)
C4	0.015 (2)	0.0207 (19)	0.0114 (16)	0.0040 (16)	0.0004 (14)	−0.0020 (14)
C7	0.019 (2)	0.019 (2)	0.0138 (16)	−0.0036 (15)	0.0028 (15)	0.0010 (13)
C1	0.025 (2)	0.0146 (18)	0.0107 (16)	−0.0078 (16)	−0.0004 (15)	−0.0031 (13)
C2	0.021 (2)	0.0150 (18)	0.0119 (16)	0.0074 (16)	0.0027 (14)	0.0003 (14)
C8	0.034 (2)	0.022 (2)	0.0159 (17)	0.0025 (17)	0.0086 (17)	−0.0015 (15)
C9	0.023 (2)	0.018 (2)	0.0225 (19)	0.0023 (17)	0.0064 (16)	0.0004 (16)
C6	0.024 (2)	0.026 (2)	0.0118 (17)	0.0013 (17)	−0.0012 (15)	−0.0071 (15)

Geometric parameters (Å, º)

S1—C6	1.818 (4)	C3—C4	1.527 (5)
S1—H1S	1.41 (6)	C3—H3	0.9800
O3—C2	1.426 (5)	C4—H4	0.9800
O3—C7	1.434 (5)	C7—C8	1.514 (5)
O1—C1	1.434 (4)	C7—C9	1.520 (5)
O1—C4	1.437 (5)	C1—C2	1.534 (5)
O2—C1	1.405 (4)	C1—H1	0.9800
O2—C7	1.447 (4)	C2—H2	0.9800
O5—C5	1.446 (5)	C8—H8A	0.9600
O5—H5O	0.71 (5)	C8—H8B	0.9600
O4—C3	1.427 (4)	C8—H8C	0.9600
O4—H4O	0.80 (4)	C9—H9A	0.9600
C5—C6	1.514 (6)	C9—H9B	0.9600
C5—C4	1.527 (5)	C9—H9C	0.9600
C5—H5	0.9800	C6—H6A	0.9700
C3—C2	1.522 (5)	C6—H6B	0.9700
C6—S1—H1S	99 (2)	O2—C1—O1	113.2 (3)
C2—O3—C7	110.3 (3)	O2—C1—C2	105.2 (3)
C1—O1—C4	108.5 (3)	O1—C1—C2	106.3 (3)
C1—O2—C7	109.6 (3)	O2—C1—H1	110.7
C5—O5—H5O	101 (4)	O1—C1—H1	110.7
C3—O4—H4O	110 (3)	C2—C1—H1	110.7
O5—C5—C6	112.2 (3)	O3—C2—C3	107.8 (3)
O5—C5—C4	106.1 (3)	O3—C2—C1	103.4 (3)
C6—C5—C4	111.5 (3)	C3—C2—C1	104.6 (3)
O5—C5—H5	109.0	O3—C2—H2	113.4
C6—C5—H5	109.0	C3—C2—H2	113.4
C4—C5—H5	109.0	C1—C2—H2	113.4
O4—C3—C2	107.8 (3)	C7—C8—H8A	109.5
O4—C3—C4	112.4 (3)	C7—C8—H8B	109.5
C2—C3—C4	100.0 (3)	H8A—C8—H8B	109.5
O4—C3—H3	112.0	C7—C8—H8C	109.5
C2—C3—H3	112.0	H8A—C8—H8C	109.5
C4—C3—H3	112.0	H8B—C8—H8C	109.5
O1—C4—C3	105.2 (3)	C7—C9—H9A	109.5
O1—C4—C5	110.5 (3)	C7—C9—H9B	109.5
C3—C4—C5	115.8 (3)	H9A—C9—H9B	109.5
O1—C4—H4	108.4	C7—C9—H9C	109.5
C3—C4—H4	108.4	H9A—C9—H9C	109.5
C5—C4—H4	108.4	H9B—C9—H9C	109.5
O3—C7—O2	106.1 (3)	C5—C6—S1	113.6 (3)
O3—C7—C8	109.4 (3)	C5—C6—H6A	108.8
O2—C7—C8	109.4 (3)	S1—C6—H6A	108.8
O3—C7—C9	109.6 (3)	C5—C6—H6B	108.8
O2—C7—C9	109.4 (3)	S1—C6—H6B	108.8
C8—C7—C9	112.7 (3)	H6A—C6—H6B	107.7