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Acta Crystallogr Sect E Struct Rep Online. 2009 August 1; 65(Pt 8): o1999–o2000.
Published online 2009 July 25. doi:  10.1107/S1600536809029031
PMCID: PMC2977305

An ortho­rhom­bic polymorph of 6-de­oxy-6-iodo-1,2:3,4-di-O-isopropyl­idene-α-d-galactopyran­oside

Abstract

The title compound, C12H19IO5, is the ortho­rhom­bic polymorph of a previously reported monoclinic form [Krajewski et al. (1987 [triangle]). Bull. Pol. Acad. Sci. Chem. 35, 91–102]. The dihedral angles between the six-membered ring and the two five-membered rings are 67.66 (14) and 71.79 (13)°, whereas the dihedral angle between the five-membered rings is 74.41 (12)°, indicating that all three rings are twisted from each other. The six-membered ring has a twist-boat conformation while both of the five-membered rings have envelope conformations. The crystal structure is stabilized by a network of C—H(...)O contacts linking the mol­ecules into a two-dimensional array parallel to the ab plane.

Related literature

For the monoclinic polymorph of the title compound, see: Krajewski et al. (1987 [triangle]). For the synthesis and biological evaluation of 6-substituted purines, see: Gambogi Braga et al. (2007 [triangle]). For halogenation reagent systems, see: Classon et al. (1988 [triangle]). For the synthesis of perosamine derivatives, see: Stevens et al. (1970 [triangle]). For the synthesis of labilose, see: Westwood et al. (1967 [triangle]). For ring conformations and ring puckering analysis, see: Boeyens (1978 [triangle]); Cremer & Pople (1975 [triangle]). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1999-scheme1.jpg

Experimental

Crystal data

  • C12H19IO5
  • M r = 370.17
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1999-efi1.jpg
  • a = 7.3595 (1) Å
  • b = 11.5145 (2) Å
  • c = 16.9945 (2) Å
  • V = 1440.13 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 2.23 mm−1
  • T = 100 K
  • 0.17 × 0.11 × 0.11 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.703, T max = 0.785
  • 27359 measured reflections
  • 7509 independent reflections
  • 6211 reflections with I > 2σ(I)
  • R int = 0.046

Refinement

  • R[F 2 > 2σ(F 2)] = 0.035
  • wR(F 2) = 0.096
  • S = 1.07
  • 7509 reflections
  • 167 parameters
  • H-atom parameters constrained
  • Δρmax = 0.87 e Å−3
  • Δρmin = −1.24 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 3286 Friedel pairs
  • Flack parameter: −0.020 (19)

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809029031/tk2509sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809029031/tk2509Isup2.hkl

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

Acknowledgments

HKF and WCL thank Universiti Sains Malaysia (USM) for a Research University Golden Goose Grant (No. 1001/PFIZIK/811012). WCL thanks USM for a student assistantship. AMI is grateful to the Director, NITK, Surathkal, India, for providing research facilities

supplementary crystallographic information

Comment

Libilomycin, an antibiotic which inhibits the growth of Gram-positive bacteria (Westwood et al., 1967) and which is effective against certain tumor cells, is produced by the microorganism, streptomyces albosporeas (Stevens et al., 1970), and contains 6-iodo,6-deoxy-1,2,3,4-di-O-isopropylidine-α-D-galactopyranoside as a part of its structure (Classon et al., 1988). These intermediates are used for the synthesis of 6-substituted purines which show high activity against Leishmania amazonensis (Gambogi Braga et al., 2007). These results prompted us to synthesize the title compound, (I).

Compound (I), Fig. 1, crystallized in the orthorhombic space group P212121 but has been reported previously (Krajewski et al., 1987) in the monoclinic space group P21, with a = 11.157 (2) Å, b = 20.047 (4) Å, c = 14.188 (2) Å and β = 107.67 (1)°. The dihedral angles between the six-membered ring systems, ring A (C1/C3/C4/C6/C7/O5), and the five-membered ring systems [rings B (C1—C3/O1—O2) and C (C4—C6/O3—O4)] are 67.66 (14)° and 71.79 (13)°, repectively. Moreover, the dihedral angle between rings B and C is 74.41 (12)° indicating that all the three rings are twisted from each other. Ring A adopts the twist-boat conformation (Boeyens, 1978; Cremer & Pople, 1975) with puckering amplitude Q = 0.629 (2) Å, [var phi] = 75.3 (3)° and θ = 325.6 (2)°. On the other hand, each of rings B and C adopt an envelope conformation with flap atoms O2 and C5, respectively, but having different puckering parameters. For ring B, the puckering amplitude Q = 0.285 (2) Å and [var phi] = 294.9 (5)° whereas for ring C, the puckering amplitude Q = 0.323 (3) Å and [var phi] = 150.8 (4)°.

The crystal packing (Fig. 2 & Fig. 3) is consolidated by C8—H8B···O2 and C12—H12C···O2 contacts (Table 1) that link the molecules into a 2-D array parallel to the ab plane.

Experimental

Triphenylphosphine (0.53 g, 1.9 mmol) and imidazole (0.4 g, 5.7 mmol) was added to the mixture of 1,2,3,4-di-O-isopropylidine-α-D-galactopyranoside (0.5 g, 1.9 mmol) in toluene: acetonitrile (2: 1, 10 ml). The mixture was heated to 70 °C. Iodine (0.6 g, 3.8 mmol) was then added portion-wise for a period of 30 min and mixture was further stirred for 2 hours. The completion of the reaction was confirmed by TLC (30% EtOAc/hexane, Rf - 0.6). The brown reaction mixture was concentrated under vacuum and the residue was purified by column chromatography using 25% ethylacetate in petroleum ether to get desired compound as white crystals. (Yield 600 mg, 83%, m.p. 334–336 K).

Refinement

C-bound H atoms were positioned geometrically [C—H = 0.96–0.98 Å] and refined using a riding model, with Uiso(H) = 1.2Ueq(C) and 1.5Ueq(methyl-C). A rotating group model was used for the methyl groups.

The maximum and minimum residual electron density peaks of 0.87 and -1.24 eÅ-3, respectively, were located 0.85 Å and 0.52 Å from the H8A and I1 atoms, respectively.

Figures

Fig. 1.
The molecular structure of (I), showing 50% probability displacement ellipsoids and the atom numbering scheme.
Fig. 2.
Crystal packing viewed along the a axis. The C-H···O contacts are shown as dashed lines.
Fig. 3.
Crystal packing viewed along the c axis. The C-H···O contacts are shown as dashed lines.

Crystal data

C12H19IO5F(000) = 736
Mr = 370.17Dx = 1.707 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 6517 reflections
a = 7.3595 (1) Åθ = 3.0–30.1°
b = 11.5145 (2) ŵ = 2.23 mm1
c = 16.9945 (2) ÅT = 100 K
V = 1440.13 (4) Å3Block, colourless
Z = 40.17 × 0.11 × 0.11 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer7509 independent reflections
Radiation source: fine-focus sealed tube6211 reflections with I > 2σ(I)
graphiteRint = 0.046
[var phi] and ω scansθmax = 37.5°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −12→12
Tmin = 0.703, Tmax = 0.785k = −19→17
27359 measured reflectionsl = −28→29

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.035H-atom parameters constrained
wR(F2) = 0.096w = 1/[σ2(Fo2) + (0.0418P)2 + 0.1348P] where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max = 0.003
7509 reflectionsΔρmax = 0.87 e Å3
167 parametersΔρmin = −1.24 e Å3
0 restraintsAbsolute structure: Flack (1983), 3286 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: −0.020 (19)

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.
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)

xyzUiso*/Ueq
I10.48767 (2)−0.062287 (16)0.585388 (10)0.02322 (5)
O10.3941 (3)0.30650 (19)0.54871 (11)0.0202 (4)
O20.4126 (2)0.41053 (17)0.66190 (11)0.0174 (4)
O3−0.0095 (3)0.31453 (16)0.74636 (10)0.0169 (3)
O40.0869 (3)0.13209 (18)0.77122 (12)0.0181 (4)
O50.2158 (2)0.16776 (16)0.61095 (11)0.0162 (3)
C10.2269 (3)0.2856 (2)0.58845 (16)0.0166 (4)
H1A0.12560.30410.55320.020*
C20.4873 (3)0.4031 (2)0.58404 (14)0.0167 (4)
C30.2281 (3)0.3722 (2)0.65788 (15)0.0166 (4)
H3A0.14760.43790.64660.020*
C40.1835 (3)0.3209 (3)0.73797 (15)0.0167 (4)
H4A0.23350.37100.77930.020*
C5−0.0464 (3)0.2160 (2)0.79401 (15)0.0165 (4)
C60.2485 (3)0.1941 (2)0.75132 (13)0.0152 (5)
H6A0.33590.19070.79480.018*
C70.3309 (3)0.1412 (2)0.67660 (15)0.0165 (5)
H7A0.45220.17370.66770.020*
C80.3433 (4)0.0106 (3)0.68407 (16)0.0194 (5)
H8A0.2220−0.02210.68640.023*
H8B0.4059−0.00920.73250.023*
C90.4481 (4)0.5139 (3)0.53734 (17)0.0235 (6)
H9A0.31930.52670.53530.035*
H9B0.49450.50570.48480.035*
H9C0.50580.57870.56260.035*
C100.6874 (4)0.3785 (3)0.59115 (18)0.0220 (5)
H10A0.70490.30320.61420.033*
H10B0.74300.43640.62400.033*
H10C0.74210.38040.53990.033*
C11−0.0254 (4)0.2444 (3)0.88146 (15)0.0241 (5)
H11A0.09460.27390.89100.036*
H11B−0.04400.17530.91200.036*
H11C−0.11360.30180.89630.036*
C12−0.2321 (4)0.1723 (3)0.77260 (18)0.0205 (5)
H12A−0.23070.14350.71960.031*
H12B−0.31830.23460.77660.031*
H12C−0.26620.11090.80780.031*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
I10.02406 (8)0.02602 (9)0.01959 (7)0.00713 (7)0.00446 (7)0.00100 (6)
O10.0212 (9)0.0223 (10)0.0170 (8)−0.0053 (8)0.0033 (7)−0.0029 (8)
O20.0136 (7)0.0220 (10)0.0167 (8)−0.0033 (6)0.0016 (6)−0.0022 (7)
O30.0124 (7)0.0161 (7)0.0222 (7)−0.0003 (6)0.0014 (6)0.0023 (6)
O40.0133 (8)0.0188 (9)0.0223 (9)0.0002 (6)0.0036 (7)0.0023 (7)
O50.0169 (8)0.0149 (9)0.0166 (7)−0.0011 (6)−0.0038 (6)0.0004 (7)
C10.0177 (9)0.0178 (12)0.0143 (9)−0.0010 (8)−0.0028 (9)−0.0001 (9)
C20.0173 (9)0.0193 (10)0.0134 (8)−0.0026 (8)0.0025 (11)0.0023 (8)
C30.0145 (10)0.0180 (12)0.0172 (10)−0.0018 (8)0.0006 (8)−0.0008 (9)
C40.0127 (9)0.0207 (13)0.0167 (10)−0.0020 (8)0.0012 (8)−0.0009 (9)
C50.0150 (10)0.0179 (12)0.0166 (10)0.0003 (8)0.0014 (8)0.0017 (8)
C60.0125 (9)0.0197 (13)0.0135 (10)−0.0002 (8)−0.0011 (7)0.0007 (9)
C70.0127 (10)0.0218 (13)0.0149 (10)−0.0004 (8)−0.0003 (8)0.0005 (9)
C80.0186 (11)0.0227 (14)0.0170 (11)0.0044 (9)0.0011 (9)0.0041 (10)
C90.0251 (13)0.0236 (14)0.0218 (12)−0.0012 (10)0.0004 (10)0.0054 (11)
C100.0175 (10)0.0292 (15)0.0193 (11)0.0012 (9)0.0031 (10)0.0007 (11)
C110.0227 (13)0.0313 (15)0.0182 (10)0.0003 (11)0.0021 (10)−0.0010 (10)
C120.0170 (11)0.0200 (14)0.0245 (13)−0.0021 (9)0.0014 (9)0.0036 (11)

Geometric parameters (Å, °)

I1—C82.155 (3)C5—C111.530 (4)
O1—C11.424 (3)C6—C71.533 (4)
O1—C21.438 (3)C6—H6A0.9800
O2—C31.430 (3)C7—C81.512 (4)
O2—C21.435 (3)C7—H7A0.9800
O3—C51.420 (3)C8—H8A0.9700
O3—C41.429 (3)C8—H8B0.9700
O4—C61.428 (3)C9—H9A0.9600
O4—C51.431 (3)C9—H9B0.9600
O5—C11.412 (3)C9—H9C0.9600
O5—C71.434 (3)C10—H10A0.9600
C1—C31.545 (4)C10—H10B0.9600
C1—H1A0.9800C10—H10C0.9600
C2—C101.505 (4)C11—H11A0.9600
C2—C91.530 (4)C11—H11B0.9600
C3—C41.519 (4)C11—H11C0.9600
C3—H3A0.9800C12—H12A0.9600
C4—C61.554 (4)C12—H12B0.9600
C4—H4A0.9800C12—H12C0.9600
C5—C121.501 (4)
C1—O1—C2110.17 (19)C7—C6—H6A110.4
C3—O2—C2107.52 (19)C4—C6—H6A110.4
C5—O3—C4106.8 (2)O5—C7—C8108.2 (2)
C6—O4—C5107.3 (2)O5—C7—C6109.1 (2)
C1—O5—C7112.42 (19)C8—C7—C6110.4 (2)
O5—C1—O1109.9 (2)O5—C7—H7A109.7
O5—C1—C3114.4 (2)C8—C7—H7A109.7
O1—C1—C3104.4 (2)C6—C7—H7A109.7
O5—C1—H1A109.3C7—C8—I1110.61 (18)
O1—C1—H1A109.3C7—C8—H8A109.5
C3—C1—H1A109.3I1—C8—H8A109.5
O2—C2—O1104.41 (18)C7—C8—H8B109.5
O2—C2—C10108.2 (2)I1—C8—H8B109.5
O1—C2—C10110.8 (2)H8A—C8—H8B108.1
O2—C2—C9110.8 (2)C2—C9—H9A109.5
O1—C2—C9109.8 (2)C2—C9—H9B109.5
C10—C2—C9112.5 (2)H9A—C9—H9B109.5
O2—C3—C4106.4 (2)C2—C9—H9C109.5
O2—C3—C1104.0 (2)H9A—C9—H9C109.5
C4—C3—C1115.6 (2)H9B—C9—H9C109.5
O2—C3—H3A110.2C2—C10—H10A109.5
C4—C3—H3A110.2C2—C10—H10B109.5
C1—C3—H3A110.2H10A—C10—H10B109.5
O3—C4—C3108.9 (2)C2—C10—H10C109.5
O3—C4—C6104.1 (2)H10A—C10—H10C109.5
C3—C4—C6115.4 (2)H10B—C10—H10C109.5
O3—C4—H4A109.4C5—C11—H11A109.5
C3—C4—H4A109.4C5—C11—H11B109.5
C6—C4—H4A109.4H11A—C11—H11B109.5
O3—C5—O4104.70 (19)C5—C11—H11C109.5
O3—C5—C12107.7 (2)H11A—C11—H11C109.5
O4—C5—C12109.4 (2)H11B—C11—H11C109.5
O3—C5—C11111.4 (2)C5—C12—H12A109.5
O4—C5—C11109.8 (2)C5—C12—H12B109.5
C12—C5—C11113.5 (2)H12A—C12—H12B109.5
O4—C6—C7109.1 (2)C5—C12—H12C109.5
O4—C6—C4104.4 (2)H12A—C12—H12C109.5
C7—C6—C4112.0 (2)H12B—C12—H12C109.5
O4—C6—H6A110.4

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C8—H8B···O2i0.972.423.377 (3)169
C12—H12C···O2ii0.962.603.477 (4)152

Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) −x, y−1/2, −z+3/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: TK2509).

References

  • Boeyens, J. C. A. (1978). J. Cryst. Mol. Struct.8, 317–320.
  • Bruker (2005). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Classon, B., Liu, Z. & Samuelsson, B. (1988). J. Org. Chem.53, 6126–6130.
  • Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst.19, 105–107.
  • Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc.97, 1354–1358.
  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  • Gambogi Braga, F., Soares Coimbra, E., De Oliveira Matos, M., Lino Carmo, A. M., Damato Cancio, M. & Da Silva, A. D. (2007). Eur. J. Med. Chem.42, 530–537. [PubMed]
  • Krajewski, J. W., Gluzinski, P., Jarosz, S., Bleidelis, J., Mishnyov, A. & Kemme, A. (1987). Bull. Pol. Acad. Sci. Chem.35, 91–102.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst D65, 148–155. [PMC free article] [PubMed]
  • Stevens, C. L., Glinski, P. R., Taylor, K. G., Blumberg, P. & Gupta, S. K. (1970). J. Am. Chem. Soc 92, 3160–3168. [PubMed]
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