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

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.

Key indicators

• Single-crystal X-ray study
• T = 111 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.021
• wR factor = 0.050
• Data-to-parameter ratio = 33.3

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) .....          1
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600          2
PLAT915_ALERT_3_C Low Friedel Pair Coverage ......................      87.18 Perc.
PLAT912_ALERT_4_C Missing # of FCF Reflections Above STh/L=  0.600        151
PLAT952_ALERT_1_C Reported and Calculated Lmax Values Differ by ..          2

Alert level G
REFLT03_ALERT_1_G ALERT: Expected hkl max differ from CIF values
           From the CIF: _diffrn_reflns_theta_max           35.03
           From the CIF: _reflns_number_total               4062
           From the CIF: _diffrn_reflns_limit_ max hkl    9.   11.   33.
           From the CIF: _diffrn_reflns_limit_ min hkl   -8.  -12.  -33.
           TEST1: Expected hkl limits for theta max
           Calculated maximum hkl    9.   12.   35.
           Calculated minimum hkl   -9.  -12.  -35.
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           35.03
           From the CIF: _reflns_number_total               4062
           Count of symmetry unique reflns         2581
           Completeness (_total/calc)            157.38%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured      1481
           Fraction of Friedel pairs measured     0.574
           Are heavy atom types Z>Si present        yes
PLAT791_ALERT_4_G Note: The Model has Chirality at C2     (Verify)          R
PLAT791_ALERT_4_G Note: The Model has Chirality at C3     (Verify)          S
PLAT791_ALERT_4_G Note: The Model has Chirality at C4     (Verify)          R
PLAT791_ALERT_4_G Note: The Model has Chirality at C5     (Verify)          S

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   5 ALERT level C = Check and explain
   6 ALERT level G = General alerts; check

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   3 ALERT type 3 Indicator that the structure quality may be low
   6 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. 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 & 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

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).

S2. Experimental

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

S3. 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 U_iso(H) = 1.5U_eq(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 U_iso(H) = 1.5U_eq(C,O) (see Comment text).

Computing details

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

	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.

Methyl 6-deoxy-6-iodo-α-D-galactoside

Crystal data

C7H13IO5	F(000) = 592
Mr = 304.08	Dx = 1.994 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 9870 reflections
a = 5.7745 (2) Å	θ = 2.6–34.2°
b = 7.9055 (3) Å	µ = 3.15 mm^−1
c = 22.1835 (7) Å	T = 111 K
V = 1012.68 (6) Å^3	Plate, colourless
Z = 4	0.51 × 0.30 × 0.02 mm

Data collection

Bruker APEXII CCD diffractometer	4062 independent reflections
Radiation source: fine-focus sealed tube	3930 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.033
Detector resolution: 8.333 pixels mm^-1	θmax = 35.0°, θmin = 2.7°
ϕ and ω scans	h = −8→9
Absorption correction: multi-scan (Blessing, 1995)	k = −12→11
Tmin = 0.523, Tmax = 0.747	l = −33→33
30359 measured reflections

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.021	H-atom parameters constrained
wR(F^2) = 0.050	w = 1/[σ^2(Fo^2) + (0.0236P)^2 + 0.4353P] where P = (Fo^2 + 2Fc^2)/3
S = 1.06	(Δ/σ)max = 0.001
4062 reflections	Δρmax = 1.45 e Å^−3
122 parameters	Δρmin = −0.78 e Å^−3
0 restraints	Absolute structure: Flack (1983), 1653 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure 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 (Ų)

	x	y	z	Uiso*/Ueq
I1	0.40872 (2)	0.478714 (16)	0.504464 (5)	0.02898 (4)
O1	0.5838 (2)	0.12645 (13)	0.34021 (5)	0.01598 (19)
O2	0.67433 (18)	0.21293 (14)	0.22048 (5)	0.01352 (19)
H2O	0.7581	0.1333	0.2328	0.020*
O3	1.03501 (17)	0.45621 (14)	0.24533 (5)	0.01504 (19)
H3O	1.0745	0.3781	0.2218	0.023*
O4	0.77547 (18)	0.67940 (13)	0.31887 (6)	0.01447 (19)
H4O	0.6341	0.6700	0.3106	0.022*
O5	0.47929 (18)	0.40652 (14)	0.36225 (5)	0.01431 (19)
C1	0.4969 (2)	0.27912 (17)	0.31726 (7)	0.0122 (2)
H1	0.3391	0.2579	0.3003	0.018*
C2	0.6547 (2)	0.33786 (17)	0.26630 (7)	0.0107 (2)
H2	0.5829	0.4406	0.2478	0.016*
C3	0.8900 (2)	0.38930 (17)	0.29162 (7)	0.0118 (2)
H3	0.9664	0.2872	0.3093	0.018*
C4	0.8602 (2)	0.52225 (19)	0.34128 (6)	0.0131 (2)
H4	1.0147	0.5426	0.3603	0.020*
C5	0.6977 (2)	0.44721 (18)	0.38928 (7)	0.0145 (2)
H5	0.7687	0.3423	0.4064	0.022*
C6	0.6533 (3)	0.5722 (2)	0.43929 (8)	0.0239 (3)
H6A	0.5936	0.6788	0.4217	0.036*
H6B	0.8013	0.5980	0.4599	0.036*
C7	0.4228 (3)	0.0461 (2)	0.38037 (8)	0.0239 (3)
H7A	0.4069	0.1141	0.4171	0.036*
H7B	0.4798	−0.0668	0.3909	0.036*
H7C	0.2717	0.0362	0.3606	0.036*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
I1	0.03654 (6)	0.02910 (6)	0.02130 (5)	0.00409 (4)	0.01094 (4)	0.00063 (4)
O1	0.0168 (4)	0.0098 (4)	0.0213 (5)	−0.0006 (4)	0.0006 (4)	0.0029 (3)
O2	0.0113 (4)	0.0111 (4)	0.0182 (5)	0.0009 (3)	−0.0005 (4)	−0.0027 (4)
O3	0.0118 (4)	0.0134 (4)	0.0199 (5)	−0.0024 (3)	0.0043 (3)	−0.0023 (4)
O4	0.0124 (4)	0.0092 (4)	0.0218 (5)	−0.0001 (3)	−0.0002 (4)	0.0013 (4)
O5	0.0124 (4)	0.0133 (5)	0.0172 (5)	0.0013 (3)	0.0022 (4)	−0.0012 (4)
C1	0.0096 (5)	0.0103 (5)	0.0168 (6)	0.0000 (4)	0.0004 (4)	0.0003 (5)
C2	0.0079 (4)	0.0101 (5)	0.0141 (6)	−0.0001 (4)	−0.0002 (4)	−0.0007 (4)
C3	0.0081 (5)	0.0109 (5)	0.0163 (6)	−0.0009 (4)	0.0005 (4)	−0.0001 (4)
C4	0.0119 (5)	0.0107 (5)	0.0167 (6)	−0.0003 (4)	−0.0016 (4)	0.0008 (5)
C5	0.0165 (6)	0.0123 (6)	0.0149 (6)	−0.0004 (5)	−0.0009 (5)	0.0002 (5)
C6	0.0341 (8)	0.0179 (7)	0.0197 (8)	−0.0040 (6)	0.0073 (6)	−0.0047 (6)
C7	0.0311 (8)	0.0190 (7)	0.0218 (7)	−0.0062 (7)	0.0037 (6)	0.0055 (5)

Geometric parameters (Å, º)

I1—C6	2.1521 (18)	C2—C3	1.5252 (18)
O1—C1	1.4027 (17)	C2—H2	1.0000
O1—C7	1.436 (2)	C3—C4	1.532 (2)
O2—C2	1.4219 (18)	C3—H3	1.0000
O2—H2O	0.8400	C4—C5	1.538 (2)
O3—C3	1.4268 (17)	C4—H4	1.0000
O3—H3O	0.8400	C5—C6	1.508 (2)
O4—C4	1.4248 (17)	C5—H5	1.0000
O4—H4O	0.8400	C6—H6A	0.9900
O5—C1	1.4217 (18)	C6—H6B	0.9900
O5—C5	1.4332 (18)	C7—H7A	0.9800
C1—C2	1.524 (2)	C7—H7B	0.9800
C1—H1	1.0000	C7—H7C	0.9800
C1—O1—C7	111.98 (12)	O4—C4—C5	111.62 (11)
C2—O2—H2O	109.5	C3—C4—C5	107.55 (11)
C3—O3—H3O	109.5	O4—C4—H4	108.3
C4—O4—H4O	109.5	C3—C4—H4	108.3
C1—O5—C5	112.93 (11)	C5—C4—H4	108.3
O1—C1—O5	112.36 (12)	O5—C5—C6	107.77 (12)
O1—C1—C2	108.51 (11)	O5—C5—C4	109.50 (11)
O5—C1—C2	110.34 (11)	C6—C5—C4	111.12 (12)
O1—C1—H1	108.5	O5—C5—H5	109.5
O5—C1—H1	108.5	C6—C5—H5	109.5
C2—C1—H1	108.5	C4—C5—H5	109.5
O2—C2—C1	111.48 (11)	C5—C6—I1	112.39 (11)
O2—C2—C3	112.18 (11)	C5—C6—H6A	109.1
C1—C2—C3	109.92 (11)	I1—C6—H6A	109.1
O2—C2—H2	107.7	C5—C6—H6B	109.1
C1—C2—H2	107.7	I1—C6—H6B	109.1
C3—C2—H2	107.7	H6A—C6—H6B	107.9
O3—C3—C2	110.89 (12)	O1—C7—H7A	109.5
O3—C3—C4	109.21 (11)	O1—C7—H7B	109.5
C2—C3—C4	110.34 (10)	H7A—C7—H7B	109.5
O3—C3—H3	108.8	O1—C7—H7C	109.5
C2—C3—H3	108.8	H7A—C7—H7C	109.5
C4—C3—H3	108.8	H7B—C7—H7C	109.5
O4—C4—C3	112.69 (11)
C7—O1—C1—O5	68.74 (15)	O3—C3—C4—O4	54.99 (14)
C7—O1—C1—C2	−168.99 (12)	C2—C3—C4—O4	−67.15 (14)
C5—O5—C1—O1	60.32 (15)	O3—C3—C4—C5	178.43 (11)
C5—O5—C1—C2	−60.91 (15)	C2—C3—C4—C5	56.30 (14)
O1—C1—C2—O2	56.83 (14)	C1—O5—C5—C6	−175.45 (12)
O5—C1—C2—O2	−179.68 (11)	C1—O5—C5—C4	63.56 (15)
O1—C1—C2—C3	−68.21 (14)	O4—C4—C5—O5	64.63 (14)
O5—C1—C2—C3	55.28 (14)	C3—C4—C5—O5	−59.47 (14)
O2—C2—C3—O3	59.55 (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—I1	56.19 (15)
C1—C2—C3—C4	−54.68 (14)	C4—C5—C6—I1	176.16 (10)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2O···O3^i	0.84	1.90	2.7407 (15)	175
O3—H3O···O4^i	0.84	2.01	2.8310 (16)	166
O4—H4O···O2^ii	0.84	1.94	2.7529 (15)	163

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