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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 66| Part 7| July 2010| Page o1724
doi:10.1107/S1600536810022786

Methyl 6-de­­oxy-6-iodo-α-D-galactoside

Shivali A. Gulab,a Janice M. H. Cheng,b,c Mattie S. M. Timmer,b Bridget L. Stockerb and Graeme J. Gainsforda*

aCarbohydrate Chemistry Group, Industrial Research Limited, PO Box 31-310, Lower Hutt, New Zealand, bSchool of Chemical and Physical Sciences, Victoria University of Welllington, PO Box 600, Wellington, New Zealand, and cMalaghan Institute of Medical Research, PO Box 7060, Wellington, New Zealand
*Correspondence e-mail: g.gainsford@irl.cri.nz

(Received 2 June 2010; accepted 14 June 2010; online 23 June 2010)

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 R22(10) and C22(11) motifs and are similar to those found for closely related compounds. The galactoside ring has a 1C4 chair conformation.

Related literature

For the synthetic details, see Dangerfield et al. (2009[Dangerfield, E. M., Timmer, M. S. M. & Stocker, B. L. (2009). Org. Lett. 11, 535-538.]); Stocker et al.(2010[Stocker, B. L., Dangerfield, E. M., Win-Mason, A. L., Haslett, G. W. & Timmer, M. S. M. (2010). Eur. J. Org. Chem. 9, 1615-1637.]). For related structures, see Sikorski et al. (2009[Sikorski, A., Tuwalska, D., Matjasik, B. & Liberek, B. (2009). Carbohydr. Res. 344, 830-833.]), Robertson & Sheldrick (1965[Robertson, J. H. & Sheldrick, B. (1965). Acta Cryst. 19, 820-826.]). For ring conformations see: Cremer & Pople (1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358.]) and for hydrogen-bond motifs, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data

  • C7H13IO5

  • Mr = 304.08

  • Orthorhombic, P 21 21 21

  • 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[Blessing, R. H. (1995). Acta Cryst. A51, 33-38.]) Tmin = 0.523, Tmax = 0.747

  • 30359 measured reflections

  • 4062 independent reflections

  • 3930 reflections with I > 2σ(I)

  • Rint = 0.033
Refinement

  • R[F2 > 2σ(F2)] = 0.021

  • wR(F2) = 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[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1653 Friedel pairs

  • Flack parameter: 0.002 (13)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O2—H2O⋯O3i 0.84 1.90 2.7407 (15) 175
O3—H3O⋯O4i 0.84 2.01 2.8310 (16) 166
O4—H4O⋯O2ii 0.84 1.94 2.7529 (15) 163
Symmetry codes: (i) [-x+2, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) [-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2005[Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2005[Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT and SADABS (Bruker, 2005[Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]), Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]); software used to prepare material for publication: SHELXL97 and PLATON.

Supporting information

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

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

checkCIF report


Comment top

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 & ϕ 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.

Related literature top

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

Experimental top

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

Refinement top

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).

Computing details top

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

Figures top
[Figure 1] Fig. 1. Asymmetric unit contents of (I) (Farrugia, 1997) at the 30% thermal ellipsoid level.
[Figure 2] 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.
Methyl 6-deoxy-6-iodo-α-D-galactoside top
Crystal data top
C7H13IO5F(000) = 592
Mr = 304.08Dx = 1.994 Mg m−3
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 mm−1
c = 22.1835 (7) ÅT = 111 K
V = 1012.68 (6) Å3Plate, colourless
Z = 40.51 × 0.30 × 0.02 mm
Data collection top
Bruker APEXII CCD
diffractometer		4062 independent reflections
Radiation source: fine-focus sealed tube3930 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.033
Detector resolution: 8.333 pixels mm-1θmax = 35.0°, θmin = 2.7°
ϕ 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 top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.021H-atom parameters constrained
wR(F2) = 0.050 w = 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 Å−3
122 parametersΔρmin = −0.78 e Å−3
0 restraintsAbsolute structure: Flack (1983), 1653 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.002 (13)
Crystal data top
C7H13IO5V = 1012.68 (6) Å3
Mr = 304.08Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 5.7745 (2) ŵ = 3.15 mm−1
b = 7.9055 (3) ÅT = 111 K
c = 22.1835 (7) Å0.51 × 0.30 × 0.02 mm
Data collection top
Bruker APEXII CCD
diffractometer		4062 independent reflections
Absorption correction: multi-scan
(Blessing, 1995)		3930 reflections with I > 2σ(I)
Tmin = 0.523, Tmax = 0.747Rint = 0.033
30359 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.021H-atom parameters constrained
wR(F2) = 0.050Δρmax = 1.45 e Å−3
S = 1.06Δρmin = −0.78 e Å−3
4062 reflectionsAbsolute structure: Flack (1983), 1653 Friedel pairs
122 parametersAbsolute structure parameter: 0.002 (13)
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
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) top
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, º) top
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, º) top
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.

Experimental details

Crystal data
Chemical formulaC7H13IO5
Mr304.08
Crystal system, space groupOrthorhombic, P212121
Temperature (K)111
a, b, c (Å)5.7745 (2), 7.9055 (3), 22.1835 (7)
V (Å3)1012.68 (6)
Z4
Radiation typeMo Kα
µ (mm−1)3.15
Crystal size (mm)0.51 × 0.30 × 0.02
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correctionMulti-scan
(Blessing, 1995)
Tmin, Tmax0.523, 0.747
No. of measured, independent and
observed [I > 2σ(I)] reflections		30359, 4062, 3930
Rint0.033
(sin θ/λ)max (Å−1)0.808
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.021, 0.050, 1.06
No. of reflections4062
No. of parameters122
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)1.45, −0.78
Absolute structureFlack (1983), 1653 Friedel pairs
Absolute structure parameter0.002 (13)

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SAINT and SADABS (Bruker, 2005), SHELXS97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997), Mercury (Macrae et al., 2008) and PLATON (Spek, 2009), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
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.
 

Acknowledgements

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.

References

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ISSN: 2056-9890
Volume 66| Part 7| July 2010| Page o1724
doi:10.1107/S1600536810022786
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