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Acta Crystallogr Sect E Struct Rep Online. 2010 July 1; 66(Pt 7): o1724.
Published online 2010 June 23. doi:  10.1107/S1600536810022786
PMCID: PMC3007047

Methyl 6-de­oxy-6-iodo-α-d-galactoside

Abstract

In the crystal of the title compound, C7H13IO5, the molecules are linked by O—H(...)O hydrogen bonds, which build linkages around one screw axis of the cell. These C(5) and C(6) packing motifs expand to R 2 2(10) and C2 2(11) motifs and are similar to those found for closely related compounds. The galactoside ring has a 1 C 4 chair conformation.

Related literature

For the synthetic details, see Dangerfield et al. (2009 [triangle]); Stocker et al.(2010 [triangle]). For related structures, see Sikorski et al. (2009 [triangle]), Robertson & Sheldrick (1965 [triangle]). For ring conformations see: Cremer & Pople (1975 [triangle]) and for hydrogen-bond motifs, see: Bernstein et al. (1995 [triangle]).

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Object name is e-66-o1724-scheme1.jpg

Experimental

Crystal data

  • C7H13IO5
  • M r = 304.08
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o1724-efi5.jpg
  • a = 5.7745 (2) Å
  • b = 7.9055 (3) Å
  • c = 22.1835 (7) Å
  • V = 1012.68 (6) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 3.15 mm−1
  • T = 111 K
  • 0.51 × 0.30 × 0.02 mm

Data collection

  • Bruker APEXII CCD diffractometer
  • Absorption correction: multi-scan (Blessing, 1995 [triangle]) T min = 0.523, T max = 0.747
  • 30359 measured reflections
  • 4062 independent reflections
  • 3930 reflections with I > 2σ(I)
  • R int = 0.033

Refinement

  • R[F 2 > 2σ(F 2)] = 0.021
  • wR(F 2) = 0.050
  • S = 1.06
  • 4062 reflections
  • 122 parameters
  • H-atom parameters constrained
  • Δρmax = 1.45 e Å−3
  • Δρmin = −0.78 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1653 Friedel pairs
  • Flack parameter: 0.002 (13)

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT and SADABS (Bruker, 2005 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]), Mercury (Macrae et al., 2008 [triangle]) and PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: SHELXL97 and PLATON.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810022786/lh5062sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810022786/lh5062Isup2.hkl

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

Acknowledgments

This work was supported by a New Zealand Foundation for Research Science and Technology contract [No. C08X0701] (SAG & GJG), the Health Research Council of New Zealand (MSMT) and the Cancer Society of New Zealand (MSMT & BLS). We thank Dr J. Waikara of the University of Canterbury, New Zealand, for her assistance.

supplementary crystallographic information

Comment

Alkyl iodoglycosides such as the title compound (I) are versatile synthetic intermediates for the introduction of a wide array of functional groups, e.g. amines, ethers and esters, onto a carbohydrate scaffold. In addition, the chemical transformation of iodoglycosides have led to the synthesis of a wide array of biologically important molecules (Stocker et al., 2010; Dangerfield et al., 2009).

The asymmetric unit of the title compound (I) contains one independent methyl 6-deoxy-6-iodo-α-D-galactoside molecule (Fig. 1). The galactoside ring (C1–C5,O5) has a 1C4 chair conformation with Q 0.5902 (14) Å, θ & [var phi] 3.36 (15) & 279 (2)° respectively (Cremer & Pople, 1975) similar to that of the corresponding glucopyranoside 0.563 (5) Å, 4.8 (5)° & 310 (5)° (BOSLEB, Sikorski et al., 2009). The absolute configurations with C1(R), C2(R), C3(S), C4(R), C5(S) are consistent with that expected from the synthesis.

The reported data herein (see experimental) is for the default "conventional" model: isotropic hydrogen atoms riding on their parent atoms R[F2>2σ(F2)] (R1), 0.0214, with a total of 122 variables. For interest, a "fully refined" model was used with isotropic hydrogen atoms and anisotropic non-hydrogen atoms giving R1 0.0211, wR(F2) (wR2) 0.0482 for all 4062 data, using 170 variables. These coordinates are available from the designated author. The su values for the non-hydrogen atoms are similar for both models (0.0017–0.0023 Å), and no significant changes are found between the structural details of the two models. As an aside, we note the dominance of the iodine scattering seen in the refinement of a model with the iodine given anisotropic, and the non-hydrogen atoms isotropic, thermal parameters with the same restrained riding H atoms giving R1, wR2 of 0.0277, 0.0618 respectively for just 62 variables!

Lattice binding is provided by O—H···O hydrogen bonds (Table 1), which build linkages around the b screw axis of the cell (Figure 2). This binding is notably similar to that observed for the bromohydrin analogue (MGALBH, Robertson & Sheldrick, 1965), and the corresponding glucopyranoside (BOSLEB). The basic motif building blocks (Bernstein et al., 1995) are of C(6) & C(5) types, which combine to give 2R2(10) and 2C2(11) motifs. Minor packing differences are noted with the BOSLEB structure, which has similar cell dimensions, with two, rather than one C(6) motif, an additional C–H···O interaction and a different 2R2(10) motif.

Experimental

Synthetic details are given in Dangerfield et al. (2009). The title compound was recrystallized from a solution of 10% methanol in ethyl acetate

Refinement

One reflection (0,0,2) affected by the backstop and two clearly outlier reflections (ΔF2/σ(F2)>5) were removed from the refinment.

The methyl H atoms were constrained to an ideal geometry (C—H = 0.98 Å) with Uiso(H) = 1.5Ueq(C), but were allowed to rotate freely about the adjacent C—C bond. All other H atoms were placed in geometrically idealized positions and constrained to ride on their parent atoms with C—H distances of 1.00 (primary) or 0.99 (methylene) Å and O—H distances of 0.84 Å and with Uiso(H) = 1.5Ueq(C,O) (see Comment text).

Figures

Fig. 1.
Asymmetric unit contents of (I) (Farrugia, 1997) at the 30% thermal ellipsoid level.
Fig. 2.
A packing view (Mercury 2.3, Macrae et al. (2008)) of the cell highlighting major hydrogen bonds (dotted). Symmetry codes: (i) 1 - x, 1/2 + y, 1/2 - z (ii) 2 - x, 1/2 + y, 1/2 - z.

Crystal data

C7H13IO5F(000) = 592
Mr = 304.08Dx = 1.994 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 9870 reflections
a = 5.7745 (2) Åθ = 2.6–34.2°
b = 7.9055 (3) ŵ = 3.15 mm1
c = 22.1835 (7) ÅT = 111 K
V = 1012.68 (6) Å3Plate, colourless
Z = 40.51 × 0.30 × 0.02 mm

Data collection

Bruker APEXII CCD diffractometer4062 independent reflections
Radiation source: fine-focus sealed tube3930 reflections with I > 2σ(I)
graphiteRint = 0.033
Detector resolution: 8.333 pixels mm-1θmax = 35.0°, θmin = 2.7°
[var phi] and ω scansh = −8→9
Absorption correction: multi-scan (Blessing, 1995)k = −12→11
Tmin = 0.523, Tmax = 0.747l = −33→33
30359 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.021H-atom parameters constrained
wR(F2) = 0.050w = 1/[σ2(Fo2) + (0.0236P)2 + 0.4353P] where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.001
4062 reflectionsΔρmax = 1.45 e Å3
122 parametersΔρmin = −0.78 e Å3
0 restraintsAbsolute structure: Flack (1983), 1653 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.002 (13)

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 (Å2)

xyzUiso*/Ueq
I10.40872 (2)0.478714 (16)0.504464 (5)0.02898 (4)
O10.5838 (2)0.12645 (13)0.34021 (5)0.01598 (19)
O20.67433 (18)0.21293 (14)0.22048 (5)0.01352 (19)
H2O0.75810.13330.23280.020*
O31.03501 (17)0.45621 (14)0.24533 (5)0.01504 (19)
H3O1.07450.37810.22180.023*
O40.77547 (18)0.67940 (13)0.31887 (6)0.01447 (19)
H4O0.63410.67000.31060.022*
O50.47929 (18)0.40652 (14)0.36225 (5)0.01431 (19)
C10.4969 (2)0.27912 (17)0.31726 (7)0.0122 (2)
H10.33910.25790.30030.018*
C20.6547 (2)0.33786 (17)0.26630 (7)0.0107 (2)
H20.58290.44060.24780.016*
C30.8900 (2)0.38930 (17)0.29162 (7)0.0118 (2)
H30.96640.28720.30930.018*
C40.8602 (2)0.52225 (19)0.34128 (6)0.0131 (2)
H41.01470.54260.36030.020*
C50.6977 (2)0.44721 (18)0.38928 (7)0.0145 (2)
H50.76870.34230.40640.022*
C60.6533 (3)0.5722 (2)0.43929 (8)0.0239 (3)
H6A0.59360.67880.42170.036*
H6B0.80130.59800.45990.036*
C70.4228 (3)0.0461 (2)0.38037 (8)0.0239 (3)
H7A0.40690.11410.41710.036*
H7B0.4798−0.06680.39090.036*
H7C0.27170.03620.36060.036*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
I10.03654 (6)0.02910 (6)0.02130 (5)0.00409 (4)0.01094 (4)0.00063 (4)
O10.0168 (4)0.0098 (4)0.0213 (5)−0.0006 (4)0.0006 (4)0.0029 (3)
O20.0113 (4)0.0111 (4)0.0182 (5)0.0009 (3)−0.0005 (4)−0.0027 (4)
O30.0118 (4)0.0134 (4)0.0199 (5)−0.0024 (3)0.0043 (3)−0.0023 (4)
O40.0124 (4)0.0092 (4)0.0218 (5)−0.0001 (3)−0.0002 (4)0.0013 (4)
O50.0124 (4)0.0133 (5)0.0172 (5)0.0013 (3)0.0022 (4)−0.0012 (4)
C10.0096 (5)0.0103 (5)0.0168 (6)0.0000 (4)0.0004 (4)0.0003 (5)
C20.0079 (4)0.0101 (5)0.0141 (6)−0.0001 (4)−0.0002 (4)−0.0007 (4)
C30.0081 (5)0.0109 (5)0.0163 (6)−0.0009 (4)0.0005 (4)−0.0001 (4)
C40.0119 (5)0.0107 (5)0.0167 (6)−0.0003 (4)−0.0016 (4)0.0008 (5)
C50.0165 (6)0.0123 (6)0.0149 (6)−0.0004 (5)−0.0009 (5)0.0002 (5)
C60.0341 (8)0.0179 (7)0.0197 (8)−0.0040 (6)0.0073 (6)−0.0047 (6)
C70.0311 (8)0.0190 (7)0.0218 (7)−0.0062 (7)0.0037 (6)0.0055 (5)

Geometric parameters (Å, °)

I1—C62.1521 (18)C2—C31.5252 (18)
O1—C11.4027 (17)C2—H21.0000
O1—C71.436 (2)C3—C41.532 (2)
O2—C21.4219 (18)C3—H31.0000
O2—H2O0.8400C4—C51.538 (2)
O3—C31.4268 (17)C4—H41.0000
O3—H3O0.8400C5—C61.508 (2)
O4—C41.4248 (17)C5—H51.0000
O4—H4O0.8400C6—H6A0.9900
O5—C11.4217 (18)C6—H6B0.9900
O5—C51.4332 (18)C7—H7A0.9800
C1—C21.524 (2)C7—H7B0.9800
C1—H11.0000C7—H7C0.9800
C1—O1—C7111.98 (12)O4—C4—C5111.62 (11)
C2—O2—H2O109.5C3—C4—C5107.55 (11)
C3—O3—H3O109.5O4—C4—H4108.3
C4—O4—H4O109.5C3—C4—H4108.3
C1—O5—C5112.93 (11)C5—C4—H4108.3
O1—C1—O5112.36 (12)O5—C5—C6107.77 (12)
O1—C1—C2108.51 (11)O5—C5—C4109.50 (11)
O5—C1—C2110.34 (11)C6—C5—C4111.12 (12)
O1—C1—H1108.5O5—C5—H5109.5
O5—C1—H1108.5C6—C5—H5109.5
C2—C1—H1108.5C4—C5—H5109.5
O2—C2—C1111.48 (11)C5—C6—I1112.39 (11)
O2—C2—C3112.18 (11)C5—C6—H6A109.1
C1—C2—C3109.92 (11)I1—C6—H6A109.1
O2—C2—H2107.7C5—C6—H6B109.1
C1—C2—H2107.7I1—C6—H6B109.1
C3—C2—H2107.7H6A—C6—H6B107.9
O3—C3—C2110.89 (12)O1—C7—H7A109.5
O3—C3—C4109.21 (11)O1—C7—H7B109.5
C2—C3—C4110.34 (10)H7A—C7—H7B109.5
O3—C3—H3108.8O1—C7—H7C109.5
C2—C3—H3108.8H7A—C7—H7C109.5
C4—C3—H3108.8H7B—C7—H7C109.5
O4—C4—C3112.69 (11)
C7—O1—C1—O568.74 (15)O3—C3—C4—O454.99 (14)
C7—O1—C1—C2−168.99 (12)C2—C3—C4—O4−67.15 (14)
C5—O5—C1—O160.32 (15)O3—C3—C4—C5178.43 (11)
C5—O5—C1—C2−60.91 (15)C2—C3—C4—C556.30 (14)
O1—C1—C2—O256.83 (14)C1—O5—C5—C6−175.45 (12)
O5—C1—C2—O2−179.68 (11)C1—O5—C5—C463.56 (15)
O1—C1—C2—C3−68.21 (14)O4—C4—C5—O564.63 (14)
O5—C1—C2—C355.28 (14)C3—C4—C5—O5−59.47 (14)
O2—C2—C3—O359.55 (14)O4—C4—C5—C6−54.31 (16)
C1—C2—C3—O3−175.82 (11)C3—C4—C5—C6−178.41 (13)
O2—C2—C3—C4−179.31 (11)O5—C5—C6—I156.19 (15)
C1—C2—C3—C4−54.68 (14)C4—C5—C6—I1176.16 (10)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O2—H2O···O3i0.841.902.7407 (15)175
O3—H3O···O4i0.842.012.8310 (16)166
O4—H4O···O2ii0.841.942.7529 (15)163

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH5062).

References

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