organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

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[Zhang, W., Ramasamy, K. & Averett, D. R. (1999). Nucleosides Nucleotides, 18, 2357-2365.]).

[Scheme 1]

Experimental

Crystal data
  • C11H18O5S2

  • Mr = 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[Sheldrick, G. M. (2004). SADABS. University of Göttingen, Germany.]) Tmin = 0.752, Tmax = 1.000 (expected range = 0.649–0.863)

  • 8467 measured reflections

  • 3115 independent reflections

  • 2487 reflections with I > 2σ(I)

  • Rint = 0.098

Refinement
  • R[F2 > 2σ(F2)] = 0.042

  • wR(F2) = 0.099

  • S = 0.95

  • 3115 reflections

  • 167 parameters

  • H-atom parameters constrained

  • Δρmax = 0.25 e Å−3

  • Δρmin = −0.19 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1306 Friedel pairs

  • Flack parameter: −0.05 (8)

Data collection: SMART (Bruker, 2001[Bruker (2001). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2001[Bruker (2001). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL software used to prepare material for publication: SHELXTL.

Supporting information


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.

Refinement top

All H atoms were placed at calculated positions using a riding model, with C—H = 0.96Å for methyl C—H, 0.97Å for methylene C—H, and 0.98Å for methine C—H and with Uiso(H) = 1.2Ueq(C) except for methyl groups Uiso(H) = 1.5Ueq(C).

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
[Figure 1] 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.
[Figure 2] 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
C11H18O5S2Dx = 1.360 Mg m3
Mr = 294.37Melting point = 403–400 K
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
a = 9.1381 (9) ÅCell parameters from 3384 reflections
b = 11.2898 (11) Åθ = 4.6–47.9°
c = 13.9405 (14) ŵ = 0.38 mm1
V = 1438.2 (2) Å3T = 293 K
Z = 4Prismatic, colorless
F(000) = 6240.50 × 0.41 × 0.39 mm
Data collection top
Bruker APEX CCD
diffractometer
3115 independent reflections
Radiation source: fine-focus sealed tube2487 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.098
ϕ scansθmax = 27.0°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2004)
h = 118
Tmin = 0.752, Tmax = 1.000k = 1414
8467 measured reflectionsl = 1717
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.042H-atom parameters constrained
wR(F2) = 0.099 w = 1/[σ2(Fo2) + (0.0386P)2]
where P = (Fo2 + 2Fc2)/3
S = 0.95(Δ/σ)max = 0.001
3115 reflectionsΔρmax = 0.25 e Å3
167 parametersΔρmin = 0.19 e Å3
0 restraintsAbsolute structure: Flack (1983), 1306 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.05 (8)
Crystal data top
C11H18O5S2V = 1438.2 (2) Å3
Mr = 294.37Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 9.1381 (9) ŵ = 0.38 mm1
b = 11.2898 (11) ÅT = 293 K
c = 13.9405 (14) Å0.50 × 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)
Tmin = 0.752, Tmax = 1.000Rint = 0.098
8467 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.042H-atom parameters constrained
wR(F2) = 0.099Δρmax = 0.25 e Å3
S = 0.95Δρmin = 0.19 e Å3
3115 reflectionsAbsolute structure: Flack (1983), 1306 Friedel pairs
167 parametersAbsolute 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
xyzUiso*/Ueq
S10.98335 (7)1.00851 (6)0.84959 (5)0.0646 (2)
S20.91603 (8)0.75403 (5)0.89614 (5)0.0669 (2)
O10.72545 (17)0.90443 (12)0.86747 (11)0.0509 (4)
O20.5721 (2)1.16759 (15)0.75190 (13)0.0639 (5)
O30.51511 (18)1.00383 (13)1.00502 (12)0.0567 (4)
O40.44353 (18)1.18675 (13)0.95542 (11)0.0593 (4)
O50.5692 (2)0.97000 (14)0.70389 (12)0.0605 (4)
C10.8723 (3)0.90034 (18)0.86865 (16)0.0473 (5)
C20.6525 (2)1.01781 (17)0.85773 (15)0.0457 (5)
H20.70751.07760.89370.055*
C30.6417 (3)1.0560 (2)0.7547 (2)0.0544 (6)
H30.74081.06430.72860.065*
C40.4237 (3)1.1616 (3)0.78384 (19)0.0674 (7)
H4A0.36751.11620.73760.081*
H4B0.38371.24110.78520.081*
C50.4044 (3)1.1071 (2)0.88035 (19)0.0601 (6)
H50.30201.08330.88830.072*
C60.5033 (2)1.00210 (18)0.90391 (17)0.0522 (5)
H60.45820.92800.88240.063*
C70.4676 (3)1.1180 (2)1.03915 (17)0.0576 (6)
C80.5872 (3)1.1738 (2)1.0974 (2)0.0746 (8)
H8A0.67291.18311.05840.112*
H8B0.60971.12401.15130.112*
H8C0.55551.24991.12000.112*
C90.3288 (3)1.1016 (3)1.0968 (2)0.0898 (10)
H9A0.29231.17761.11630.115*
H9B0.34941.05461.15250.115*
H9C0.25671.06241.05810.115*
C100.5657 (3)0.9914 (3)0.60277 (18)0.0719 (7)
H10A0.49481.05170.58890.108*
H10B0.53950.91980.56990.108*
H10C0.66051.01710.58160.108*
C111.1125 (3)0.7582 (3)0.8980 (2)0.0867 (10)
H11A1.14830.77740.83510.110*
H11B1.14960.68220.91700.110*
H11C1.14460.81730.94280.110*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0495 (3)0.0544 (3)0.0899 (5)0.0063 (3)0.0028 (3)0.0012 (3)
S20.0618 (4)0.0451 (3)0.0938 (5)0.0156 (3)0.0026 (4)0.0094 (4)
O10.0464 (8)0.0338 (7)0.0726 (10)0.0039 (6)0.0027 (8)0.0054 (7)
O20.0733 (12)0.0430 (8)0.0754 (11)0.0076 (9)0.0087 (10)0.0124 (8)
O30.0616 (10)0.0418 (8)0.0667 (9)0.0057 (9)0.0069 (8)0.0086 (7)
O40.0588 (10)0.0438 (8)0.0753 (10)0.0135 (8)0.0043 (9)0.0031 (8)
O50.0642 (11)0.0504 (8)0.0668 (10)0.0004 (8)0.0101 (8)0.0006 (8)
C10.0475 (12)0.0417 (11)0.0526 (13)0.0062 (9)0.0033 (10)0.0031 (10)
C20.0447 (11)0.0299 (9)0.0626 (14)0.0015 (9)0.0038 (10)0.0039 (10)
C30.0484 (13)0.0420 (11)0.0726 (16)0.0007 (11)0.0045 (11)0.0051 (11)
C40.0679 (17)0.0574 (14)0.0767 (18)0.0202 (15)0.0196 (15)0.0030 (13)
C50.0428 (12)0.0521 (12)0.0854 (18)0.0067 (11)0.0077 (13)0.0011 (13)
C60.0465 (12)0.0382 (10)0.0719 (15)0.0009 (11)0.0028 (11)0.0009 (11)
C70.0583 (16)0.0469 (12)0.0676 (15)0.0092 (11)0.0070 (13)0.0079 (11)
C80.0845 (19)0.0596 (15)0.0799 (18)0.0064 (16)0.0079 (17)0.0018 (14)
C90.070 (2)0.095 (2)0.104 (2)0.0147 (18)0.0279 (18)0.005 (2)
C100.0788 (18)0.0741 (17)0.0629 (15)0.0076 (16)0.0103 (15)0.0025 (14)
C110.0576 (16)0.085 (2)0.117 (2)0.0362 (16)0.0070 (16)0.017 (2)
Geometric parameters (Å, º) top
S1—C11.610 (2)C4—H4B0.9700
S2—C11.742 (2)C5—C61.526 (3)
S2—C111.796 (3)C5—H50.9800
O1—C11.343 (3)C6—H60.9800
O1—C21.450 (2)C7—C81.501 (4)
O2—C31.412 (3)C7—C91.513 (4)
O2—C41.429 (3)C8—H8A0.9600
O3—C61.414 (3)C8—H8B0.9600
O3—C71.441 (3)C8—H8C0.9600
O4—C71.419 (3)C9—H9A0.9600
O4—C51.426 (3)C9—H9B0.9600
O5—C31.372 (3)C9—H9C0.9600
O5—C101.431 (3)C10—H10A0.9600
C2—C31.503 (3)C10—H10B0.9600
C2—C61.518 (3)C10—H10C0.9600
C2—H20.9800C11—H11A0.9600
C3—H30.9800C11—H11B0.9600
C4—C51.490 (4)C11—H11C0.9600
C4—H4A0.9700
C1—S2—C11101.97 (14)C2—C6—C5110.47 (18)
C1—O1—C2119.41 (16)O3—C6—H6110.4
C3—O2—C4112.1 (2)C2—C6—H6110.4
C6—O3—C7108.58 (16)C5—C6—H6110.4
C7—O4—C5107.30 (18)O4—C7—O3105.34 (18)
C3—O5—C10113.5 (2)O4—C7—C8109.2 (2)
O1—C1—S1127.00 (16)O3—C7—C8109.6 (2)
O1—C1—S2105.33 (15)O4—C7—C9111.9 (2)
S1—C1—S2127.66 (14)O3—C7—C9108.6 (2)
O1—C2—C3111.91 (17)C8—C7—C9112.0 (2)
O1—C2—C6105.68 (16)C7—C8—H8A109.5
C3—C2—C6112.33 (18)C7—C8—H8B109.5
O1—C2—H2108.9H8A—C8—H8B109.5
C3—C2—H2108.9C7—C8—H8C109.5
C6—C2—H2108.9H8A—C8—H8C109.5
O5—C3—O2113.57 (19)H8B—C8—H8C109.5
O5—C3—C2108.75 (18)C7—C9—H9A109.5
O2—C3—C2108.2 (2)C7—C9—H9B109.5
O5—C3—H3108.8H9A—C9—H9B109.5
O2—C3—H3108.8C7—C9—H9C109.5
C2—C3—H3108.8H9A—C9—H9C109.5
O2—C4—C5114.4 (2)H9B—C9—H9C109.5
O2—C4—H4A108.7O5—C10—H10A109.5
C5—C4—H4A108.7O5—C10—H10B109.5
O2—C4—H4B108.7H10A—C10—H10B109.5
C5—C4—H4B108.7O5—C10—H10C109.5
H4A—C4—H4B107.6H10A—C10—H10C109.5
O4—C5—C4111.9 (2)H10B—C10—H10C109.5
O4—C5—C6100.59 (17)S2—C11—H11A109.5
C4—C5—C6116.4 (2)S2—C11—H11B109.5
O4—C5—H5109.2H11A—C11—H11B109.5
C4—C5—H5109.2S2—C11—H11C109.5
C6—C5—H5109.2H11A—C11—H11C109.5
O3—C6—C2110.65 (18)H11B—C11—H11C109.5
O3—C6—C5104.42 (18)
C2—O1—C1—S16.7 (3)O2—C4—C5—C638.1 (3)
C2—O1—C1—S2172.78 (14)C7—O3—C6—C2102.62 (19)
C11—S2—C1—O1179.09 (17)C7—O3—C6—C516.2 (2)
C11—S2—C1—S10.4 (2)O1—C2—C6—O376.4 (2)
C1—O1—C2—C383.2 (2)C3—C2—C6—O3161.29 (17)
C1—O1—C2—C6154.27 (19)O1—C2—C6—C5168.44 (17)
C10—O5—C3—O265.6 (3)C3—C2—C6—C546.1 (2)
C10—O5—C3—C2173.94 (19)O4—C5—C6—O332.2 (2)
C4—O2—C3—O555.4 (3)C4—C5—C6—O3153.3 (2)
C4—O2—C3—C265.4 (2)O4—C5—C6—C286.8 (2)
O1—C2—C3—O557.3 (2)C4—C5—C6—C234.3 (3)
C6—C2—C3—O561.4 (2)C5—O4—C7—O328.4 (2)
O1—C2—C3—O2178.93 (17)C5—O4—C7—C8146.0 (2)
C6—C2—C3—O262.4 (2)C5—O4—C7—C989.5 (3)
C3—O2—C4—C554.0 (3)C6—O3—C7—O46.3 (2)
C7—O4—C5—C4161.4 (2)C6—O3—C7—C8123.6 (2)
C7—O4—C5—C637.1 (2)C6—O3—C7—C9113.8 (2)
O2—C4—C5—O476.8 (3)

Experimental details

Crystal data
Chemical formulaC11H18O5S2
Mr294.37
Crystal system, space groupOrthorhombic, P212121
Temperature (K)293
a, b, c (Å)9.1381 (9), 11.2898 (11), 13.9405 (14)
V3)1438.2 (2)
Z4
Radiation typeMo Kα
µ (mm1)0.38
Crystal size (mm)0.50 × 0.41 × 0.39
Data collection
DiffractometerBruker APEX CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2004)
Tmin, Tmax0.752, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections
8467, 3115, 2487
Rint0.098
(sin θ/λ)max1)0.639
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.099, 0.95
No. of reflections3115
No. of parameters167
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.25, 0.19
Absolute structureFlack (1983), 1306 Friedel pairs
Absolute structure parameter0.05 (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

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

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