organic compounds
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
In the title compound, C11H18O5S2, the six- and five-membered rings adopt a chair and an approximately planar conformation, respectively.
Experimental
Crystal data
|
Data collection: SMART (Bruker, 2001); cell 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
10.1107/S1600536808011458/wk2082sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536808011458/wk2082Isup2.hkl
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.
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).
Data collection: SMART (Bruker, 2001); cell
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).C11H18O5S2 | Dx = 1.360 Mg m−3 |
Mr = 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 |
Bruker APEX CCD diffractometer | 3115 independent reflections |
Radiation source: fine-focus sealed tube | 2487 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.098 |
ϕ scans | θmax = 27.0°, θmin = 2.3° |
Absorption correction: multi-scan (SADABS; Sheldrick, 2004) | h = −11→8 |
Tmin = 0.752, Tmax = 1.000 | k = −14→14 |
8467 measured reflections | l = −17→17 |
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(Fo2) + (0.0386P)2] where P = (Fo2 + 2Fc2)/3 |
S = 0.95 | (Δ/σ)max = 0.001 |
3115 reflections | Δρmax = 0.25 e Å−3 |
167 parameters | Δρmin = −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) |
C11H18O5S2 | V = 1438.2 (2) Å3 |
Mr = 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 |
Bruker APEX CCD diffractometer | 3115 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2004) | 2487 reflections with I > 2σ(I) |
Tmin = 0.752, Tmax = 1.000 | Rint = 0.098 |
8467 measured reflections |
R[F2 > 2σ(F2)] = 0.042 | H-atom parameters constrained |
wR(F2) = 0.099 | Δρmax = 0.25 e Å−3 |
S = 0.95 | Δρmin = −0.19 e Å−3 |
3115 reflections | Absolute structure: Flack (1983), 1306 Friedel pairs |
167 parameters | Absolute structure parameter: −0.05 (8) |
0 restraints |
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. |
x | y | z | Uiso*/Ueq | ||
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* |
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) |
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 |
Mr | 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) |
Tmin, Tmax | 0.752, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8467, 3115, 2487 |
Rint | 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 |
Δρmax, Δρmin (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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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.