1,2,3-Tri-O-acetyl-5-de­oxy-5-methyl­thio-β-D-ribofuran­ose

In the structure of the title compound, C₁₂H₁₈O₇S, no alteration of the relative configuration compared with D-(−)-ribose is observed.

Key indicators

• Single-crystal X-ray study
• T = 296 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.035
• wR factor = 0.087
• Data-to-parameter ratio = 15.5

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        C31

Alert level G
REFLT03_ALERT_4_G  WARNING: Large fraction of Friedel related reflns may
                     be needed to determine absolute structure
           From the CIF: _diffrn_reflns_theta_max           27.87
           From the CIF: _reflns_number_total               2912
           Count of symmetry unique reflns         1946
           Completeness (_total/calc)            149.64%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured       966
           Fraction of Friedel pairs measured     0.496
           Are heavy atom types Z>Si present        yes

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   1 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
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion

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Computing details

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

1,2,3-Tri-O-acetyl-5-deoxy-5-methylthio-β-D-ribofuranose

Crystal data

C12H18O7S	F(000) = 324
Mr = 306.32	Dx = 1.317 Mg m^−3 Dm = 1.31 (1) Mg m^−3 Dm measured by flotation
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 1624 reflections
a = 8.6831 (4) Å	θ = 2.3–22.2°
b = 9.8249 (5) Å	µ = 0.24 mm^−1
c = 9.6824 (5) Å	T = 296 K
β = 110.766 (2)°	Prism, colourless
V = 772.35 (7) Å^3	0.43 × 0.30 × 0.16 mm
Z = 2

Data collection

Siemens SMART 1K CCD area-detector diffractometer	2912 independent reflections
Radiation source: fine-focus sealed tube	2272 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.015
ω scans	θmax = 27.9°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −11→11
Tmin = 0.853, Tmax = 0.963	k = −12→11
4361 measured reflections	l = −12→11

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)] = 0.035	H-atom parameters constrained
wR(F^2) = 0.087	w = 1/[σ^2(Fo^2) + (0.0424P)^2 + 0.0345P] where P = (Fo^2 + 2Fc^2)/3
S = 1.04	(Δ/σ)max = 0.008
2912 reflections	Δρmax = 0.11 e Å^−3
188 parameters	Δρmin = −0.14 e Å^−3
1 restraint	Absolute structure: Flack (1983), with 1136 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.04 (8)

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	0.19384 (8)	0.75437 (7)	0.03250 (8)	0.0723 (2)
C5	0.2831 (3)	0.6148 (3)	0.1563 (3)	0.0597 (6)
H5A	0.3343	0.5522	0.1080	0.065 (5)*
H5B	0.3688	0.6499	0.2436	0.065 (5)*
C4	0.1593 (3)	0.5375 (2)	0.2035 (2)	0.0506 (5)
H4	0.0754	0.4980	0.1161	0.054 (3)*
C1	0.2258 (3)	0.4460 (3)	0.4402 (2)	0.0542 (5)
H1	0.2201	0.3582	0.4863	0.054 (3)*
C2	0.0693 (3)	0.5276 (3)	0.4103 (2)	0.0534 (5)
H2	0.0674	0.5769	0.4977	0.054 (3)*
C3	0.0749 (2)	0.6226 (2)	0.2877 (2)	0.0508 (5)
H3	0.1390	0.7046	0.3289	0.054 (3)*
C6	0.0631 (4)	0.6651 (4)	−0.1265 (3)	0.1006 (11)
H61	0.1274	0.6014	−0.1584	0.140 (4)*
H62	0.0119	0.7289	−0.2045	0.140 (4)*
H63	−0.0202	0.6172	−0.1022	0.140 (4)*
C22	−0.3336 (3)	0.3579 (3)	0.3057 (4)	0.0844 (9)
H22A	−0.4372	0.3855	0.3115	0.140 (4)*
H22B	−0.2976	0.2754	0.3607	0.140 (4)*
H22C	−0.3464	0.3427	0.2042	0.140 (4)*
C32	−0.3218 (4)	0.7952 (4)	0.1060 (4)	0.1014 (12)
H32A	−0.3887	0.7209	0.1163	0.140 (4)*
H32B	−0.3210	0.7965	0.0071	0.140 (4)*
H32C	−0.3662	0.8793	0.1258	0.140 (4)*
C12	0.6272 (3)	0.5646 (3)	0.6968 (4)	0.0891 (9)
H12A	0.7328	0.5208	0.7337	0.140 (4)*
H12B	0.5971	0.5945	0.7783	0.140 (4)*
H12C	0.6325	0.6416	0.6377	0.140 (4)*
O32	−0.08760 (18)	0.65758 (18)	0.18895 (17)	0.0587 (4)
O22	−0.06344 (17)	0.43190 (16)	0.35570 (17)	0.0569 (4)
O12	0.35531 (19)	0.52964 (17)	0.53538 (17)	0.0614 (4)
O	0.24376 (18)	0.42903 (16)	0.30300 (16)	0.0569 (4)
C31	−0.1494 (3)	0.7776 (3)	0.2131 (3)	0.0662 (7)
O31	−0.0761 (3)	0.8554 (2)	0.3066 (3)	0.0914 (6)
O21	−0.2294 (2)	0.5722 (2)	0.4220 (3)	0.0901 (6)
C21	−0.2081 (3)	0.4676 (3)	0.3689 (3)	0.0663 (7)
O11	0.5234 (2)	0.3494 (2)	0.5904 (2)	0.0857 (6)
C11	0.5014 (3)	0.4665 (3)	0.6049 (3)	0.0643 (7)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0781 (4)	0.0596 (4)	0.0804 (4)	−0.0068 (4)	0.0296 (3)	0.0057 (4)
C5	0.0496 (13)	0.0631 (15)	0.0637 (14)	−0.0044 (11)	0.0168 (11)	−0.0048 (12)
C4	0.0466 (12)	0.0501 (13)	0.0503 (12)	0.0010 (10)	0.0114 (10)	−0.0017 (10)
C1	0.0515 (12)	0.0498 (13)	0.0567 (13)	−0.0019 (11)	0.0135 (10)	0.0009 (11)
C2	0.0514 (13)	0.0538 (13)	0.0534 (12)	0.0021 (11)	0.0167 (10)	−0.0062 (10)
C3	0.0449 (12)	0.0462 (13)	0.0563 (12)	−0.0005 (10)	0.0118 (10)	−0.0035 (10)
C6	0.105 (2)	0.090 (2)	0.079 (2)	−0.0152 (19)	−0.0026 (17)	0.0172 (18)
C22	0.0554 (15)	0.092 (2)	0.109 (2)	−0.0062 (15)	0.0328 (15)	0.0082 (19)
C32	0.0707 (19)	0.110 (3)	0.117 (2)	0.0336 (18)	0.0261 (18)	0.030 (2)
C12	0.0624 (16)	0.093 (2)	0.0884 (19)	−0.0076 (15)	−0.0017 (15)	−0.0056 (17)
O32	0.0486 (9)	0.0611 (10)	0.0624 (10)	0.0081 (7)	0.0146 (7)	0.0015 (8)
O22	0.0479 (8)	0.0576 (9)	0.0668 (9)	−0.0017 (8)	0.0222 (7)	−0.0008 (8)
O12	0.0525 (9)	0.0540 (10)	0.0657 (10)	0.0003 (8)	0.0062 (8)	−0.0024 (8)
O	0.0573 (9)	0.0508 (9)	0.0632 (9)	0.0077 (8)	0.0221 (8)	0.0016 (8)
C31	0.0682 (16)	0.069 (2)	0.0689 (16)	0.0190 (14)	0.0330 (13)	0.0165 (15)
O31	0.1061 (17)	0.0692 (13)	0.0951 (15)	0.0220 (12)	0.0309 (13)	−0.0080 (12)
O21	0.0870 (14)	0.0775 (15)	0.1274 (17)	0.0128 (11)	0.0646 (13)	−0.0010 (13)
C21	0.0594 (16)	0.0689 (18)	0.0778 (17)	0.0098 (13)	0.0334 (14)	0.0161 (14)
O11	0.0711 (12)	0.0625 (13)	0.1028 (15)	0.0113 (10)	0.0055 (11)	0.0068 (11)
C11	0.0562 (15)	0.0601 (17)	0.0667 (15)	0.0016 (12)	0.0097 (12)	0.0068 (12)

Geometric parameters (Å, º)

C1—O	1.402 (3)	C6—H63	0.9600
C1—O12	1.433 (3)	C22—C21	1.500 (4)
C1—C2	1.514 (3)	C22—H22A	0.9600
C2—C3	1.524 (3)	C22—H22B	0.9600
C3—C4	1.525 (3)	C22—H22C	0.9600
C4—O	1.450 (3)	C32—C31	1.499 (4)
S1—C6	1.786 (3)	C32—H32A	0.9600
S1—C5	1.806 (3)	C32—H32B	0.9600
C5—C4	1.513 (3)	C32—H32C	0.9600
C5—H5A	0.9700	C12—C11	1.491 (4)
C5—H5B	0.9700	C12—H12A	0.9600
C4—H4	0.9800	C12—H12B	0.9600
C1—H1	0.9800	C12—H12C	0.9600
C2—O22	1.435 (3)	O32—C31	1.350 (3)
C2—H2	0.9800	O22—C21	1.353 (3)
C3—O32	1.437 (2)	O12—C11	1.357 (3)
C3—H3	0.9800	C31—O31	1.183 (3)
C6—H61	0.9600	O21—C21	1.192 (3)
C6—H62	0.9600	O11—C11	1.183 (3)
C6—S1—C5	101.05 (14)	S1—C6—H63	109.5
C4—C5—S1	113.42 (15)	H61—C6—H63	109.5
C4—C5—H5A	108.9	H62—C6—H63	109.5
S1—C5—H5A	108.9	C21—C22—H22A	109.5
C4—C5—H5B	108.9	C21—C22—H22B	109.5
S1—C5—H5B	108.9	H22A—C22—H22B	109.5
H5A—C5—H5B	107.7	C21—C22—H22C	109.5
O—C4—C5	108.85 (17)	H22A—C22—H22C	109.5
O—C4—C3	105.86 (17)	H22B—C22—H22C	109.5
C5—C4—C3	114.50 (19)	C31—C32—H32A	109.5
O—C4—H4	109.2	C31—C32—H32B	109.5
C5—C4—H4	109.2	H32A—C32—H32B	109.5
C3—C4—H4	109.2	C31—C32—H32C	109.5
O—C1—O12	110.60 (18)	H32A—C32—H32C	109.5
O—C1—C2	106.01 (17)	H32B—C32—H32C	109.5
O12—C1—C2	105.43 (19)	C11—C12—H12A	109.5
O—C1—H1	111.5	C11—C12—H12B	109.5
O12—C1—H1	111.5	H12A—C12—H12B	109.5
C2—C1—H1	111.5	C11—C12—H12C	109.5
O22—C2—C1	105.81 (19)	H12A—C12—H12C	109.5
O22—C2—C3	110.92 (18)	H12B—C12—H12C	109.5
C1—C2—C3	101.47 (18)	C31—O32—C3	116.8 (2)
O22—C2—H2	112.6	C21—O22—C2	116.5 (2)
C1—C2—H2	112.6	C11—O12—C1	116.1 (2)
C3—C2—H2	112.6	C1—O—C4	110.02 (16)
O32—C3—C2	111.71 (17)	O31—C31—O32	123.9 (2)
O32—C3—C4	108.66 (17)	O31—C31—C32	126.1 (3)
C2—C3—C4	103.60 (18)	O32—C31—C32	109.9 (3)
O32—C3—H3	110.9	O21—C21—O22	123.7 (3)
C2—C3—H3	110.9	O21—C21—C22	126.4 (3)
C4—C3—H3	110.9	O22—C21—C22	109.9 (3)
S1—C6—H61	109.5	O11—C11—O12	123.2 (2)
S1—C6—H62	109.5	O11—C11—C12	125.7 (3)
H61—C6—H62	109.5	O12—C11—C12	111.0 (2)
O12—C1—O—C4	−88.8 (2)	C5—C4—C3—C2	−138.93 (18)
C4—O—C1—C2	25.0 (2)	C2—C3—O32—C31	97.5 (2)
O—C1—C2—C3	−35.7 (2)	C4—C3—O32—C31	−148.77 (19)
C1—C2—C3—C4	32.5 (2)	C1—C2—O22—C21	157.84 (19)
C2—C3—C4—O	−19.0 (2)	C3—C2—O22—C21	−92.9 (2)
C3—C4—O—C1	−3.5 (2)	O—C1—O12—C11	−80.6 (2)
C6—S1—C5—C4	−66.1 (2)	C2—C1—O12—C11	165.26 (19)
S1—C5—C4—O	−179.55 (14)	C2—C1—O—C4	25.0 (2)
S1—C5—C4—C3	−61.3 (2)	C5—C4—O—C1	120.09 (19)
O—C1—C2—O22	80.2 (2)	C3—O32—C31—O31	2.3 (4)
O12—C1—C2—O22	−162.51 (17)	C3—O32—C31—C32	−177.2 (2)
O12—C1—C2—C3	81.6 (2)	C2—O22—C21—O21	0.2 (3)
O22—C2—C3—O32	37.2 (3)	C2—O22—C21—C22	179.4 (2)
C1—C2—C3—O32	149.27 (18)	C1—O12—C11—O11	−0.4 (4)
O22—C2—C3—C4	−79.6 (2)	C1—O12—C11—C12	178.3 (2)
O—C4—C3—O32	−137.92 (17)	O—C1—C2—C3	−35.7 (2)
C5—C4—C3—O32	102.2 (2)	C1—C2—C3—C4	32.5 (2)
O—C4—C3—C2	−19.0 (2)	C3—C4—O—C1	−3.5 (2)