Methyl 6-azido-6-de-oxy-α-d-galactoside.

The structure of the title compound, C(7)H(13)N(3)O(5), was solved using data from a multiple fragment crystal. The galactoside ring adopts a (4)C(1) 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 R(2) (2)(10), C(2) (2)(7) and C(2) (2) (2)(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

C7H13N3O5

M = 219.20

Monoclinic,

a = 5.8272 (5) Å

b = 7.8358 (6) Å

c = 11.0387 (10) Å

β = 102.117 (7)°

V = 492.81 (7) Å3

Z = 2

Cu Kα radiation

μ = 1.09 mm−1

T = 123 K

0.20 × 0.10 × 0.02 mm

Data collection

Rigaku Spider diffractometer

Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ▶) T min = 0.581, T max = 1.0

4122 measured reflections

1114 independent reflections

1039 reflections with I > 2σ(I)

R int = 0.048

θmax = 56.9°

Refinement

R[F 2 > 2σ(F 2)] = 0.047

wR(F 2) = 0.125

S = 1.04

1114 reflections

143 parameters

2 restraints

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.21 e Å−3

Δρmin = −0.24 e Å−3

Absolute structure: Flack (1983 ▶), 491 Friedel pairs

Flack parameter: 0.1 (5)

Data collection: CrystalClear (Rigaku, 2005 ▶); cell refinement: 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 ▶).

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536811025323/fj2434sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811025323/fj2434Isup2.hkl

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

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	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	Flack parameter: 0.1 (5)

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

Table 1

Hydrogen-bond geometry (Å, °)

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) ; (ii) .