Methyl 3,4-O-isopropyl­idene-2-O-[(methyl­sulfan­yl)thio­carbon­yl]-β-l-arabinoside

Li, H.; Song, Y.; Li, X.

doi:10.1107/S1600536808011458

organic compounds

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ISSN: 2056-9890

Volume 64| Part 5| May 2008| Page o933

doi:10.1107/S1600536808011458

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Methyl 3,4-O-isopropylidene-2-O-[(methylsulfanyl)thiocarbonyl]-β-L-arabinoside

Hongqi Li,^a ^* Yanxi Song ^b and Xiumei Li ^c

^aKey Laboratory of the Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, People's Republic of China, ^bCollege of Environmental Science and Engineering, Donghua University, Shanghai 201620, People's Republic of China, and ^cDepartment of Physics and Technology, Inner Mongolia Tongliao Vocational College, Tongliao 028000, People's Republic of China
^*Correspondence e-mail: hongqili@dhu.edu.cn

(Received 15 March 2008; accepted 22 April 2008; online 30 April 2008)

In the title compound, C₁₁H₁₈O₅S₂, the six- and five-membered rings adopt a chair and an approximately planar conformation, respectively.

Related literature

For related literature, see: Zhang et al. (1999 ).

Experimental

Crystal data

C₁₁H₁₈O₅S₂
M_r = 294.37
Orthorhombic, P 2₁ 2₁ 2₁
a = 9.1381 (9) Å
b = 11.2898 (11) Å
c = 13.9405 (14) Å
V = 1438.2 (2) Å³
Z = 4
Mo Kα radiation
μ = 0.38 mm⁻¹
T = 293 (2) K
0.50 × 0.41 × 0.39 mm

Data collection

Bruker APEX CCD diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 2004 ) T_min = 0.752, T_max = 1.000 (expected range = 0.649–0.863)
8467 measured reflections
3115 independent reflections
2487 reflections with I > 2σ(I)
R_int = 0.098

Refinement

R[F² > 2σ(F²)] = 0.042
wR(F²) = 0.099
S = 0.95
3115 reflections
167 parameters
H-atom parameters constrained
Δρ_max = 0.25 e Å⁻³
Δρ_min = −0.19 e Å⁻³
Absolute structure: Flack (1983 ), 1306 Friedel pairs
Flack parameter: −0.05 (8)

Data collection: SMART (Bruker, 2001 ); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808011458/wk2082sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536808011458/wk2082Isup2.hkl

checkCIF report

Comment top

The title compound is an important intermediate for synthesis of 2-deoxy-L-ribose and was synthesized starting from L-arabinose according to the procedures reported by Zhang et al. (1999). Herein we present the single-crystal structure of methyl 3,4-O-isopropylidene-2-O– [(methylthio)thiocarbonyl]-β-L-arabinoside.

Related literature top

For related literature, see: Zhang et al. (1999).

Experimental top

The title compound was prepared from L-arabinose according to the procedures reported by Zhang et al. (1999). Crystals suitable for X-ray diffraction were obtained by slow evaporation of a solution in ethyl acetate.

Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. A view of the molecule of the title compound. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii.
	Fig. 2. The crystal structure of the title compound, viewed along a axis.

Methyl 3,4-O-isopropylidene-2-O-[(methylsulfanyl)thiocarbonyl]-β-L-arabinoside top

Crystal data top

C₁₁H₁₈O₅S₂	D_x = 1.360 Mg m⁻³
M_r = 294.37	Melting point = 403–400 K
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
a = 9.1381 (9) Å	Cell parameters from 3384 reflections
b = 11.2898 (11) Å	θ = 4.6–47.9°
c = 13.9405 (14) Å	µ = 0.38 mm⁻¹
V = 1438.2 (2) Å³	T = 293 K
Z = 4	Prismatic, colorless
F(000) = 624	0.50 × 0.41 × 0.39 mm

Data collection top

Bruker APEX CCD diffractometer	3115 independent reflections
Radiation source: fine-focus sealed tube	2487 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.098
ϕ scans	θ_max = 27.0°, θ_min = 2.3°
Absorption correction: multi-scan (SADABS; Sheldrick, 2004)	h = −11→8
T_min = 0.752, T_max = 1.000	k = −14→14
8467 measured reflections	l = −17→17

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.042	H-atom parameters constrained
wR(F²) = 0.099	w = 1/[σ²(F_o²) + (0.0386P)²] where P = (F_o² + 2F_c²)/3
S = 0.95	(Δ/σ)_max = 0.001
3115 reflections	Δρ_max = 0.25 e Å⁻³
167 parameters	Δρ_min = −0.19 e Å⁻³
0 restraints	Absolute structure: Flack (1983), 1306 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: −0.05 (8)

Crystal data top

C₁₁H₁₈O₅S₂	V = 1438.2 (2) Å³
M_r = 294.37	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 9.1381 (9) Å	µ = 0.38 mm⁻¹
b = 11.2898 (11) Å	T = 293 K
c = 13.9405 (14) Å	0.50 × 0.41 × 0.39 mm

Data collection top

Bruker APEX CCD diffractometer	3115 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 2004)	2487 reflections with I > 2σ(I)
T_min = 0.752, T_max = 1.000	R_int = 0.098
8467 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.042	H-atom parameters constrained
wR(F²) = 0.099	Δρ_max = 0.25 e Å⁻³
S = 0.95	Δρ_min = −0.19 e Å⁻³
3115 reflections	Absolute structure: Flack (1983), 1306 Friedel pairs
167 parameters	Absolute structure parameter: −0.05 (8)
0 restraints

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
S1	0.98335 (7)	1.00851 (6)	0.84959 (5)	0.0646 (2)
S2	0.91603 (8)	0.75403 (5)	0.89614 (5)	0.0669 (2)
O1	0.72545 (17)	0.90443 (12)	0.86747 (11)	0.0509 (4)
O2	0.5721 (2)	1.16759 (15)	0.75190 (13)	0.0639 (5)
O3	0.51511 (18)	1.00383 (13)	1.00502 (12)	0.0567 (4)
O4	0.44353 (18)	1.18675 (13)	0.95542 (11)	0.0593 (4)
O5	0.5692 (2)	0.97000 (14)	0.70389 (12)	0.0605 (4)
C1	0.8723 (3)	0.90034 (18)	0.86865 (16)	0.0473 (5)
C2	0.6525 (2)	1.01781 (17)	0.85773 (15)	0.0457 (5)
H2	0.7075	1.0776	0.8937	0.055*
C3	0.6417 (3)	1.0560 (2)	0.7547 (2)	0.0544 (6)
H3	0.7408	1.0643	0.7286	0.065*
C4	0.4237 (3)	1.1616 (3)	0.78384 (19)	0.0674 (7)
H4A	0.3675	1.1162	0.7376	0.081*
H4B	0.3837	1.2411	0.7852	0.081*
C5	0.4044 (3)	1.1071 (2)	0.88035 (19)	0.0601 (6)
H5	0.3020	1.0833	0.8883	0.072*
C6	0.5033 (2)	1.00210 (18)	0.90391 (17)	0.0522 (5)
H6	0.4582	0.9280	0.8824	0.063*
C7	0.4676 (3)	1.1180 (2)	1.03915 (17)	0.0576 (6)
C8	0.5872 (3)	1.1738 (2)	1.0974 (2)	0.0746 (8)
H8A	0.6729	1.1831	1.0584	0.112*
H8B	0.6097	1.1240	1.1513	0.112*
H8C	0.5555	1.2499	1.1200	0.112*
C9	0.3288 (3)	1.1016 (3)	1.0968 (2)	0.0898 (10)
H9A	0.2923	1.1776	1.1163	0.115*
H9B	0.3494	1.0546	1.1525	0.115*
H9C	0.2567	1.0624	1.0581	0.115*
C10	0.5657 (3)	0.9914 (3)	0.60277 (18)	0.0719 (7)
H10A	0.4948	1.0517	0.5889	0.108*
H10B	0.5395	0.9198	0.5699	0.108*
H10C	0.6605	1.0171	0.5816	0.108*
C11	1.1125 (3)	0.7582 (3)	0.8980 (2)	0.0867 (10)
H11A	1.1483	0.7774	0.8351	0.110*
H11B	1.1496	0.6822	0.9170	0.110*
H11C	1.1446	0.8173	0.9428	0.110*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0495 (3)	0.0544 (3)	0.0899 (5)	−0.0063 (3)	−0.0028 (3)	0.0012 (3)
S2	0.0618 (4)	0.0451 (3)	0.0938 (5)	0.0156 (3)	0.0026 (4)	0.0094 (4)
O1	0.0464 (8)	0.0338 (7)	0.0726 (10)	0.0039 (6)	−0.0027 (8)	0.0054 (7)
O2	0.0733 (12)	0.0430 (8)	0.0754 (11)	0.0076 (9)	−0.0087 (10)	0.0124 (8)
O3	0.0616 (10)	0.0418 (8)	0.0667 (9)	0.0057 (9)	0.0069 (8)	0.0086 (7)
O4	0.0588 (10)	0.0438 (8)	0.0753 (10)	0.0135 (8)	−0.0043 (9)	0.0031 (8)
O5	0.0642 (11)	0.0504 (8)	0.0668 (10)	0.0004 (8)	−0.0101 (8)	−0.0006 (8)
C1	0.0475 (12)	0.0417 (11)	0.0526 (13)	0.0062 (9)	−0.0033 (10)	−0.0031 (10)
C2	0.0447 (11)	0.0299 (9)	0.0626 (14)	0.0015 (9)	−0.0038 (10)	0.0039 (10)
C3	0.0484 (13)	0.0420 (11)	0.0726 (16)	0.0007 (11)	−0.0045 (11)	0.0051 (11)
C4	0.0679 (17)	0.0574 (14)	0.0767 (18)	0.0202 (15)	−0.0196 (15)	0.0030 (13)
C5	0.0428 (12)	0.0521 (12)	0.0854 (18)	0.0067 (11)	−0.0077 (13)	0.0011 (13)
C6	0.0465 (12)	0.0382 (10)	0.0719 (15)	−0.0009 (11)	−0.0028 (11)	0.0009 (11)
C7	0.0583 (16)	0.0469 (12)	0.0676 (15)	0.0092 (11)	0.0070 (13)	0.0079 (11)
C8	0.0845 (19)	0.0596 (15)	0.0799 (18)	0.0064 (16)	−0.0079 (17)	−0.0018 (14)
C9	0.070 (2)	0.095 (2)	0.104 (2)	0.0147 (18)	0.0279 (18)	0.005 (2)
C10	0.0788 (18)	0.0741 (17)	0.0629 (15)	0.0076 (16)	−0.0103 (15)	−0.0025 (14)
C11	0.0576 (16)	0.085 (2)	0.117 (2)	0.0362 (16)	0.0070 (16)	0.017 (2)

Geometric parameters (Å, º) top

S1—C1	1.610 (2)	C4—H4B	0.9700
S2—C1	1.742 (2)	C5—C6	1.526 (3)
S2—C11	1.796 (3)	C5—H5	0.9800
O1—C1	1.343 (3)	C6—H6	0.9800
O1—C2	1.450 (2)	C7—C8	1.501 (4)
O2—C3	1.412 (3)	C7—C9	1.513 (4)
O2—C4	1.429 (3)	C8—H8A	0.9600
O3—C6	1.414 (3)	C8—H8B	0.9600
O3—C7	1.441 (3)	C8—H8C	0.9600
O4—C7	1.419 (3)	C9—H9A	0.9600
O4—C5	1.426 (3)	C9—H9B	0.9600
O5—C3	1.372 (3)	C9—H9C	0.9600
O5—C10	1.431 (3)	C10—H10A	0.9600
C2—C3	1.503 (3)	C10—H10B	0.9600
C2—C6	1.518 (3)	C10—H10C	0.9600
C2—H2	0.9800	C11—H11A	0.9600
C3—H3	0.9800	C11—H11B	0.9600
C4—C5	1.490 (4)	C11—H11C	0.9600
C4—H4A	0.9700

C1—S2—C11	101.97 (14)	C2—C6—C5	110.47 (18)
C1—O1—C2	119.41 (16)	O3—C6—H6	110.4
C3—O2—C4	112.1 (2)	C2—C6—H6	110.4
C6—O3—C7	108.58 (16)	C5—C6—H6	110.4
C7—O4—C5	107.30 (18)	O4—C7—O3	105.34 (18)
C3—O5—C10	113.5 (2)	O4—C7—C8	109.2 (2)
O1—C1—S1	127.00 (16)	O3—C7—C8	109.6 (2)
O1—C1—S2	105.33 (15)	O4—C7—C9	111.9 (2)
S1—C1—S2	127.66 (14)	O3—C7—C9	108.6 (2)
O1—C2—C3	111.91 (17)	C8—C7—C9	112.0 (2)
O1—C2—C6	105.68 (16)	C7—C8—H8A	109.5
C3—C2—C6	112.33 (18)	C7—C8—H8B	109.5
O1—C2—H2	108.9	H8A—C8—H8B	109.5
C3—C2—H2	108.9	C7—C8—H8C	109.5
C6—C2—H2	108.9	H8A—C8—H8C	109.5
O5—C3—O2	113.57 (19)	H8B—C8—H8C	109.5
O5—C3—C2	108.75 (18)	C7—C9—H9A	109.5
O2—C3—C2	108.2 (2)	C7—C9—H9B	109.5
O5—C3—H3	108.8	H9A—C9—H9B	109.5
O2—C3—H3	108.8	C7—C9—H9C	109.5
C2—C3—H3	108.8	H9A—C9—H9C	109.5
O2—C4—C5	114.4 (2)	H9B—C9—H9C	109.5
O2—C4—H4A	108.7	O5—C10—H10A	109.5
C5—C4—H4A	108.7	O5—C10—H10B	109.5
O2—C4—H4B	108.7	H10A—C10—H10B	109.5
C5—C4—H4B	108.7	O5—C10—H10C	109.5
H4A—C4—H4B	107.6	H10A—C10—H10C	109.5
O4—C5—C4	111.9 (2)	H10B—C10—H10C	109.5
O4—C5—C6	100.59 (17)	S2—C11—H11A	109.5
C4—C5—C6	116.4 (2)	S2—C11—H11B	109.5
O4—C5—H5	109.2	H11A—C11—H11B	109.5
C4—C5—H5	109.2	S2—C11—H11C	109.5
C6—C5—H5	109.2	H11A—C11—H11C	109.5
O3—C6—C2	110.65 (18)	H11B—C11—H11C	109.5
O3—C6—C5	104.42 (18)

C2—O1—C1—S1	−6.7 (3)	O2—C4—C5—C6	−38.1 (3)
C2—O1—C1—S2	172.78 (14)	C7—O3—C6—C2	102.62 (19)
C11—S2—C1—O1	−179.09 (17)	C7—O3—C6—C5	−16.2 (2)
C11—S2—C1—S1	0.4 (2)	O1—C2—C6—O3	76.4 (2)
C1—O1—C2—C3	83.2 (2)	C3—C2—C6—O3	−161.29 (17)
C1—O1—C2—C6	−154.27 (19)	O1—C2—C6—C5	−168.44 (17)
C10—O5—C3—O2	65.6 (3)	C3—C2—C6—C5	−46.1 (2)
C10—O5—C3—C2	−173.94 (19)	O4—C5—C6—O3	32.2 (2)
C4—O2—C3—O5	55.4 (3)	C4—C5—C6—O3	153.3 (2)
C4—O2—C3—C2	−65.4 (2)	O4—C5—C6—C2	−86.8 (2)
O1—C2—C3—O5	57.3 (2)	C4—C5—C6—C2	34.3 (3)
C6—C2—C3—O5	−61.4 (2)	C5—O4—C7—O3	28.4 (2)
O1—C2—C3—O2	−178.93 (17)	C5—O4—C7—C8	146.0 (2)
C6—C2—C3—O2	62.4 (2)	C5—O4—C7—C9	−89.5 (3)
C3—O2—C4—C5	54.0 (3)	C6—O3—C7—O4	−6.3 (2)
C7—O4—C5—C4	−161.4 (2)	C6—O3—C7—C8	−123.6 (2)
C7—O4—C5—C6	−37.1 (2)	C6—O3—C7—C9	113.8 (2)
O2—C4—C5—O4	76.8 (3)

Experimental details

Crystal data
Chemical formula	C₁₁H₁₈O₅S₂
M_r	294.37
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	293
a, b, c (Å)	9.1381 (9), 11.2898 (11), 13.9405 (14)
V (Å³)	1438.2 (2)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.38
Crystal size (mm)	0.50 × 0.41 × 0.39

Data collection
Diffractometer	Bruker APEX CCD diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 2004)
T_min, T_max	0.752, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	8467, 3115, 2487
R_int	0.098
(sin θ/λ)_max (Å⁻¹)	0.639

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.042, 0.099, 0.95
No. of reflections	3115
No. of parameters	167
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.25, −0.19
Absolute structure	Flack (1983), 1306 Friedel pairs
Absolute structure parameter	−0.05 (8)

Computer programs: SMART (Bruker, 2001), SAINT (Bruker, 2001), SHELXTL (Sheldrick, 2008).

Acknowledgements

Financial support of this project by the Program for Changjiang Scholars and Innovative Research Team in Universities (No. IRT0526) and Shanghai Natural Science Foundation (No. 06ZR14001) is acknowledged.

References

Bruker (2001). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Flack, H. D. (1983). Acta Cryst. A39, 876–881. CrossRef CAS Web of Science IUCr Journals Google Scholar
Sheldrick, G. M. (2004). SADABS. University of Göttingen, Germany. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Zhang, W., Ramasamy, K. & Averett, D. R. (1999). Nucleosides Nucleotides, 18, 2357–2365. Web of Science CrossRef CAS Google Scholar

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