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

Abstract

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,

• a = 9.1381 (9) Å

• b = 11.2898 (11) Å

• c = 13.9405 (14) Å

• V = 1438.2 (2) ų

• 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[F ² > 2σ(F ²)] = 0.042

• wR(F ²) = 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.

Supplementary Material

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Comment

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.

Experimental

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

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 U_iso(H) = 1.2U_eq(C) except for methyl groups U_iso(H) = 1.5U_eq(C).

Figures

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.

Crystal data

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 = 4.6–47.9º
c = 13.9405 (14) Å	µ = 0.38 mm−1
V = 1438.2 (2) Å3	T = 293 (2) K
Z = 4	Prismatic, colorless
F000 = 624	0.50 × 0.41 × 0.39 mm

Data collection

Bruker APEX CCD diffractometer	3115 independent reflections
Radiation source: fine-focus sealed tube	2487 reflections with I > 2σ(I)
Monochromator: graphite	Rint = 0.098
T = 293(2) K	θmax = 27.0º
φ scans	θmin = 2.3º
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

Refinement on F2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F2 > 2σ(F2)] = 0.042	w = 1/[σ2(Fo2) + (0.0386P)2] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.099	(Δ/σ)max = 0.001
S = 0.95	Δρmax = 0.25 e Å−3
3115 reflections	Δρmin = −0.19 e Å−3
167 parameters	Extinction correction: none
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), 1306 Friedel pairs
Secondary atom site location: difference Fourier map	Flack parameter: −0.05 (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	0.98335 (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 (Ų)

	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, °)

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)