organic compounds
Methyl 6-azido-6-deoxy-α-D-galactoside
aSchool of Chemical and Physical Sciences, Victoria University of Welllington, PO Box 600, Wellington, New Zealand, bMalaghan Institute of Medical Research, PO Box 7060, Wellington, New Zealand, and cCarbohydrate Chemistry Group, Industrial Research Limited, PO Box 31-310, Lower Hutt, New Zealand
*Correspondence e-mail: g.gainsford@irl.cri.nz
The structure of the title compound, C7H13N3O5, was solved using data from a multiple fragment crystal. The galactoside ring adopts a 4C1 chair conformation. In the crystal, the molecules are linked by strong O—H⋯O hydrogen bonds, which build linkages around the screw axis of the cell in a similar way to the iodo analogue. These C-5 and C-6 packing motifs expand to R22(10), C22(7) and C222(8) motifs, as found in closely related compounds.
Related literature
For details of the synthesis, see Cheng et al. (2011). For related structures, see Sikorski et al. (2009), Robertson & Sheldrick (1965), Zhou et al. (2002), Kurhade et al.(2011). For the iodo derivative, see: Gulab et al. (2010). For ring conformations, see: Cremer & Pople (1975) and for hydrogen-bond motifs, see: Bernstein et al. (1995). For the Hooft parameter, see: Hooft et al. (2008).
Experimental
Crystal data
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Data collection: CrystalClear (Rigaku, 2005); cell FSProcess in PROCESS-AUTO (Rigaku, 1998); data reduction: FSProcess in PROCESS-AUTO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP in WinGX (Farrugia, 1997) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009).
Supporting information
10.1107/S1600536811025323/fj2434sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536811025323/fj2434Isup2.hkl
Methyl 6-azido-6-deoxy-α-D-galactopyranoside was prepared as described in Cheng et al. (2011) from methyl 6-deoxy-6-iodo-α-D-galactopyranoside as reported in Gulab et al. (2010). The title compound was recrystallized from methanol.
The crystals were predominantly multiple-fragment blocks up to ~0.7 x 0.6 x 0.2 mm in size. The minute crystal which was finally selected consisted of one major fragment with some minor fragments along the long (needle) axis. In addition, the data collection was partially marred by crystal movement initiated by ice buildup. The dataset arises from processing the remaining 155 screens of data after removing the affected 66 slices which were identified by the screen review statistics; this was verified by visual inspection of the screens which showed misalignment and ice rings. In the (automatic) processing, a further 209 outliers were detected and removed. High angle data was also recognized as being weak or suffering from misalignent, so the data outside the 0.92 Å shell was omitted using the SHEL command. A further 20 outlier reflections (ΔF2/σ(F2)>4.2) were removed from the some of these could be identified as being affected by ice-diffracted scattering or behind the goniometer shadow. As a result, the final dataset is significantly less than 100% complete but is adequate for defining the structure; defining the known from the synthetic procedure, is not possible.
The hydroxyl atom HO4 on oxygen O4 was not placed correctly using the usual SHELX (AFIX 147) command, as determined by packing analysis inspection. It was placed, and then freely refined, on the basis of careful difference mapping around the O4 site and restrained to be 0.84 (3) Å from O4 using DFIX. The other hydroxyl H atoms were refined by automatic placement at positions indicated by a difference
and their positions were constrained to refine on their parent O atoms with O–H 0.84 Å (using AFIX 147). The hydroxyl H atoms were refined with Uiso(H) = 1.5Ueq(O).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 and with Uiso(H) = 1.2Ueq(C).
Data collection: CrystalClear (Rigaku, 2005); cell
FSProcess in PROCESS-AUTO (Rigaku, 1998); data reduction: FSProcess in PROCESS-AUTO (Rigaku, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP in WinGX (Farrugia, 1997) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).C7H13N3O5 | F(000) = 232 |
Mr = 219.20 | Dx = 1.477 Mg m−3 |
Monoclinic, P21 | Cu Kα radiation, λ = 1.54178 Å |
Hall symbol: P 2yb | Cell parameters from 4158 reflections |
a = 5.8272 (5) Å | θ = 7.0–66.7° |
b = 7.8358 (6) Å | µ = 1.09 mm−1 |
c = 11.0387 (10) Å | T = 123 K |
β = 102.117 (7)° | Plate, colourless |
V = 492.81 (7) Å3 | 0.20 × 0.10 × 0.02 mm |
Z = 2 |
Rigaku Spider diffractometer | 1114 independent reflections |
Radiation source: Rigaku MM007 rotating anode | 1039 reflections with I > 2σ(I) |
Rigaku VariMax-HF Confocal Optical System monochromator | Rint = 0.048 |
Detector resolution: 10 pixels mm-1 | θmax = 56.9°, θmin = 7.0° |
ω scans | h = −6→3 |
Absorption correction: multi-scan (ABSCOR; Higashi, 1995) | k = −8→8 |
Tmin = 0.581, Tmax = 1.0 | l = −11→11 |
4122 measured reflections |
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.047 | w = 1/[σ2(Fo2) + (0.0786P)2 + 0.1967P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.125 | (Δ/σ)max < 0.001 |
S = 1.04 | Δρmax = 0.21 e Å−3 |
1114 reflections | Δρmin = −0.24 e Å−3 |
143 parameters | Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
2 restraints | Extinction coefficient: 0.020 (4) |
Primary atom site location: structure-invariant direct methods | Absolute structure: Flack (1983), 491 Friedel pairs |
Secondary atom site location: difference Fourier map | Absolute structure parameter: 0.1 (5) |
C7H13N3O5 | V = 492.81 (7) Å3 |
Mr = 219.20 | Z = 2 |
Monoclinic, P21 | Cu Kα radiation |
a = 5.8272 (5) Å | µ = 1.09 mm−1 |
b = 7.8358 (6) Å | T = 123 K |
c = 11.0387 (10) Å | 0.20 × 0.10 × 0.02 mm |
β = 102.117 (7)° |
Rigaku Spider diffractometer | 1114 independent reflections |
Absorption correction: multi-scan (ABSCOR; Higashi, 1995) | 1039 reflections with I > 2σ(I) |
Tmin = 0.581, Tmax = 1.0 | Rint = 0.048 |
4122 measured reflections | θmax = 56.9° |
R[F2 > 2σ(F2)] = 0.047 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.125 | Δρmax = 0.21 e Å−3 |
S = 1.04 | Δρmin = −0.24 e Å−3 |
1114 reflections | Absolute structure: Flack (1983), 491 Friedel pairs |
143 parameters | Absolute structure parameter: 0.1 (5) |
2 restraints |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.9756 (5) | 0.6454 (3) | 0.6831 (2) | 0.0291 (8) | |
O2 | 0.8027 (5) | 0.5541 (3) | 0.4390 (2) | 0.0276 (8) | |
H2O | 0.7366 | 0.6378 | 0.4647 | 0.041* | |
O3 | 0.4659 (5) | 0.3064 (4) | 0.4887 (3) | 0.0292 (8) | |
H3O | 0.4068 | 0.3842 | 0.4397 | 0.044* | |
O4 | 0.7817 (5) | 0.0839 (3) | 0.6441 (3) | 0.0287 (9) | |
H4O | 0.913 (5) | 0.091 (8) | 0.632 (5) | 0.043* | |
O5 | 1.1064 (5) | 0.3653 (3) | 0.7346 (2) | 0.0286 (8) | |
N1 | 1.1494 (9) | 0.2908 (5) | 0.9995 (3) | 0.0449 (12) | |
N2 | 1.3424 (9) | 0.3419 (5) | 0.9860 (4) | 0.0449 (12) | |
N3 | 1.5248 (10) | 0.3958 (7) | 0.9855 (4) | 0.0634 (16) | |
C1 | 1.0514 (9) | 0.4929 (5) | 0.6392 (4) | 0.0263 (12) | |
H1 | 1.1946 | 0.5161 | 0.6053 | 0.032* | |
C2 | 0.8568 (7) | 0.4282 (5) | 0.5348 (4) | 0.0241 (11) | |
H2 | 0.9169 | 0.3246 | 0.4986 | 0.029* | |
C3 | 0.6484 (8) | 0.3764 (5) | 0.5835 (4) | 0.0248 (11) | |
H3 | 0.5851 | 0.4800 | 0.6182 | 0.030* | |
C4 | 0.7136 (8) | 0.2439 (5) | 0.6880 (4) | 0.0251 (11) | |
H4 | 0.5733 | 0.2246 | 0.7252 | 0.030* | |
C5 | 0.9054 (8) | 0.3214 (5) | 0.7856 (4) | 0.0320 (12) | |
H5 | 0.8442 | 0.4269 | 0.8188 | 0.038* | |
C6 | 0.9996 (9) | 0.2007 (6) | 0.8927 (4) | 0.0342 (12) | |
H6A | 0.8662 | 0.1461 | 0.9203 | 0.041* | |
H6B | 1.0927 | 0.1096 | 0.8636 | 0.041* | |
C7 | 1.1589 (9) | 0.7300 (6) | 0.7705 (4) | 0.0389 (13) | |
H7A | 1.2933 | 0.7506 | 0.7320 | 0.058* | |
H7B | 1.2077 | 0.6577 | 0.8439 | 0.058* | |
H7C | 1.1001 | 0.8391 | 0.7951 | 0.058* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.034 (2) | 0.0158 (14) | 0.0364 (15) | 0.0004 (13) | 0.0049 (15) | −0.0036 (13) |
O2 | 0.0303 (19) | 0.0160 (15) | 0.0353 (16) | 0.0039 (13) | 0.0038 (15) | 0.0044 (12) |
O3 | 0.0261 (18) | 0.0200 (14) | 0.0387 (16) | −0.0024 (13) | 0.0004 (13) | 0.0018 (12) |
O4 | 0.0276 (18) | 0.0178 (15) | 0.0398 (17) | 0.0018 (15) | 0.0045 (17) | −0.0030 (13) |
O5 | 0.0264 (17) | 0.0206 (14) | 0.0393 (15) | −0.0028 (14) | 0.0083 (15) | 0.0041 (14) |
N1 | 0.051 (3) | 0.041 (2) | 0.036 (2) | −0.004 (2) | −0.007 (2) | −0.0040 (19) |
N2 | 0.046 (3) | 0.039 (3) | 0.042 (2) | 0.003 (3) | −0.009 (3) | 0.001 (2) |
N3 | 0.039 (3) | 0.080 (4) | 0.061 (3) | −0.013 (3) | −0.014 (3) | 0.015 (3) |
C1 | 0.034 (3) | 0.016 (2) | 0.029 (2) | 0.0015 (18) | 0.009 (2) | 0.0030 (17) |
C2 | 0.024 (2) | 0.0133 (19) | 0.034 (2) | 0.0015 (18) | 0.005 (2) | 0.0042 (17) |
C3 | 0.026 (2) | 0.0115 (19) | 0.035 (2) | 0.0000 (19) | 0.003 (2) | −0.0067 (19) |
C4 | 0.026 (3) | 0.018 (2) | 0.033 (2) | 0.0044 (18) | 0.009 (2) | 0.0015 (19) |
C5 | 0.039 (3) | 0.014 (2) | 0.039 (2) | −0.0002 (19) | −0.002 (2) | −0.0067 (19) |
C6 | 0.040 (3) | 0.024 (3) | 0.036 (2) | −0.0039 (19) | 0.003 (2) | 0.0008 (18) |
C7 | 0.049 (3) | 0.024 (2) | 0.038 (2) | −0.005 (2) | −0.005 (2) | −0.004 (2) |
O1—C1 | 1.395 (5) | C1—H1 | 1.0000 |
O1—C7 | 1.441 (5) | C2—C3 | 1.484 (6) |
O2—C2 | 1.432 (5) | C2—H2 | 1.0000 |
O2—H2O | 0.8400 | C3—C4 | 1.540 (6) |
O3—C3 | 1.435 (5) | C3—H3 | 1.0000 |
O3—H3O | 0.8400 | C4—C5 | 1.508 (5) |
O4—C4 | 1.430 (5) | C4—H4 | 1.0000 |
O4—H4O | 0.81 (3) | C5—C6 | 1.523 (5) |
O5—C1 | 1.439 (5) | C5—H5 | 1.0000 |
O5—C5 | 1.444 (6) | C6—H6A | 0.9900 |
N1—N2 | 1.232 (6) | C6—H6B | 0.9900 |
N1—C6 | 1.489 (5) | C7—H7A | 0.9800 |
N2—N3 | 1.144 (7) | C7—H7B | 0.9800 |
C1—C2 | 1.524 (6) | C7—H7C | 0.9800 |
C1—O1—C7 | 112.5 (3) | O4—C4—C5 | 112.2 (3) |
C2—O2—H2O | 109.5 | O4—C4—C3 | 112.3 (3) |
C3—O3—H3O | 109.5 | C5—C4—C3 | 107.0 (3) |
C4—O4—H4O | 110 (4) | O4—C4—H4 | 108.4 |
C1—O5—C5 | 112.1 (3) | C5—C4—H4 | 108.4 |
N2—N1—C6 | 117.2 (4) | C3—C4—H4 | 108.4 |
N3—N2—N1 | 173.1 (5) | O5—C5—C4 | 110.9 (3) |
O1—C1—O5 | 112.3 (3) | O5—C5—C6 | 105.1 (4) |
O1—C1—C2 | 108.0 (4) | C4—C5—C6 | 113.4 (3) |
O5—C1—C2 | 109.8 (3) | O5—C5—H5 | 109.1 |
O1—C1—H1 | 108.9 | C4—C5—H5 | 109.1 |
O5—C1—H1 | 108.9 | C6—C5—H5 | 109.1 |
C2—C1—H1 | 108.9 | N1—C6—C5 | 112.1 (4) |
O2—C2—C3 | 112.7 (3) | N1—C6—H6A | 109.2 |
O2—C2—C1 | 110.0 (3) | C5—C6—H6A | 109.2 |
C3—C2—C1 | 110.7 (3) | N1—C6—H6B | 109.2 |
O2—C2—H2 | 107.8 | C5—C6—H6B | 109.2 |
C3—C2—H2 | 107.8 | H6A—C6—H6B | 107.9 |
C1—C2—H2 | 107.8 | O1—C7—H7A | 109.5 |
O3—C3—C2 | 112.2 (3) | O1—C7—H7B | 109.5 |
O3—C3—C4 | 108.5 (3) | H7A—C7—H7B | 109.5 |
C2—C3—C4 | 111.3 (3) | O1—C7—H7C | 109.5 |
O3—C3—H3 | 108.2 | H7A—C7—H7C | 109.5 |
C2—C3—H3 | 108.2 | H7B—C7—H7C | 109.5 |
C4—C3—H3 | 108.2 | ||
C7—O1—C1—O5 | 66.9 (5) | C2—C3—C4—O4 | −67.6 (4) |
C7—O1—C1—C2 | −172.0 (4) | O3—C3—C4—C5 | 179.9 (4) |
C5—O5—C1—O1 | 60.9 (4) | C2—C3—C4—C5 | 56.0 (4) |
C5—O5—C1—C2 | −59.1 (4) | C1—O5—C5—C4 | 62.8 (4) |
O1—C1—C2—O2 | 57.9 (4) | C1—O5—C5—C6 | −174.3 (3) |
O5—C1—C2—O2 | −179.5 (3) | O4—C4—C5—O5 | 65.1 (4) |
O1—C1—C2—C3 | −67.3 (4) | C3—C4—C5—O5 | −58.6 (4) |
O5—C1—C2—C3 | 55.3 (5) | O4—C4—C5—C6 | −53.0 (5) |
O2—C2—C3—O3 | 59.4 (4) | C3—C4—C5—C6 | −176.6 (4) |
C1—C2—C3—O3 | −177.0 (3) | N2—N1—C6—C5 | −70.3 (5) |
O2—C2—C3—C4 | −178.8 (3) | O5—C5—C6—N1 | 71.0 (4) |
C1—C2—C3—C4 | −55.2 (4) | C4—C5—C6—N1 | −167.6 (4) |
O3—C3—C4—O4 | 56.3 (5) |
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2O···O3i | 0.84 | 1.91 | 2.742 (4) | 170 |
O4—H4O···O2ii | 0.81 (3) | 2.00 (4) | 2.774 (4) | 162 (6) |
O3—H3O···O4i | 0.84 | 2.02 | 2.841 (4) | 165 |
Symmetry codes: (i) −x+1, y+1/2, −z+1; (ii) −x+2, y−1/2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C7H13N3O5 |
Mr | 219.20 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 123 |
a, b, c (Å) | 5.8272 (5), 7.8358 (6), 11.0387 (10) |
β (°) | 102.117 (7) |
V (Å3) | 492.81 (7) |
Z | 2 |
Radiation type | Cu Kα |
µ (mm−1) | 1.09 |
Crystal size (mm) | 0.20 × 0.10 × 0.02 |
Data collection | |
Diffractometer | Rigaku Spider diffractometer |
Absorption correction | Multi-scan (ABSCOR; Higashi, 1995) |
Tmin, Tmax | 0.581, 1.0 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4122, 1114, 1039 |
Rint | 0.048 |
θmax (°) | 56.9 |
(sin θ/λ)max (Å−1) | 0.543 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.047, 0.125, 1.04 |
No. of reflections | 1114 |
No. of parameters | 143 |
No. of restraints | 2 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.21, −0.24 |
Absolute structure | Flack (1983), 491 Friedel pairs |
Absolute structure parameter | 0.1 (5) |
Computer programs: CrystalClear (Rigaku, 2005), FSProcess in PROCESS-AUTO (Rigaku, 1998), SHELXS97 (Sheldrick, 2008), ORTEP in WinGX (Farrugia, 1997) and Mercury (Macrae et al., 2008), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2O···O3i | 0.84 | 1.91 | 2.742 (4) | 170 |
O4—H4O···O2ii | 0.81 (3) | 2.00 (4) | 2.774 (4) | 162 (6) |
O3—H3O···O4i | 0.84 | 2.02 | 2.841 (4) | 165 |
Symmetry codes: (i) −x+1, y+1/2, −z+1; (ii) −x+2, y−1/2, −z+1. |
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 and BLS). We thank the MacDiarmid Institute for Advanced Materials and Nanotechnology for funding of the diffractometer equipment.
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
Alkyl azidoglycosides such as the title compound (I) are versatile synthetic intermediates for the synthesis of a wide array of biologically important molecules (Cheng et al., 2011; Kurhade et al.,2011; Zhou et al.,2002).
The asymmetric unit of the title compound (I) contains one independent methyl 6-deoxy-6-azido-α-D-galactoside molecule (Fig. 1). The galactoside ring (C1–C5,O5) has a 4C1 chair conformation with Q 0.581 (4) Å, θ & ϕ 2.5 (5) & 288 (9)° respectively (Cremer & Pople, 1975) identical to that of the iodo-analogues (Gulab et al., 2010) and similar to that of the corresponding glucopyranoside 0.563 (5) Å, 4.8 (5)° & 310 (5)° (BOSLEB, Sikorski et al., 2009), The absolute configurations known from the synthesis of C1(R), C2(R), C3(S), C4(R) and C5(S) are consistent with the weak indications given by the Hooft parameter (0.0 (2), Hooft et al., (2008)), compared with the indeterminate Flack value of 0.1 (5).
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 iodo derivative (Gulab et al., 2010), 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), 2C2(7) & 2C2(8) motifs. Close similarity with the iodo analogue is observed: the major difference concerns the approximately doubled c axis length and the presence of the two additional 21 screw axes in the latter orthorhombic crystal.