1,6:3,4-Dian­hydro-2-azido-2-deoxy-β-D-galactopyran­ose

In the title compound, C₆H₇N₃O₃, the presence of the epoxide group modifies the bonding in the sugar ring so that the five C atoms within it are coplanar, with a shortening of the formally single C—C bonds to an average of 1.475 (8) Å.

Key indicators

• Single-crystal X-ray study
• T = 298 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.041
• wR factor = 0.111
• Data-to-parameter ratio = 6.5

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


 Alert Level C:



PLAT_710  Alert C Delete 1-2-3 or 2-3-4 (CIF) Linear Torsion Angle #      3
                   C2  -N1  -N2  -N3   -169.00  4.00   1.555   1.555   1.555   1.555

General Notes



REFLT_03
         From the CIF: _diffrn_reflns_theta_max           24.94
         From the CIF: _reflns_number_total                774
         Count of symmetry unique reflns          781
         Completeness (_total/calc)             99.10%
         TEST3: Check Friedels for noncentro structure
         Estimate of Friedel pairs measured         0
         Fraction of Friedel pairs measured     0.000
         Are heavy atom types Z>Si present           no
          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.


 0 Alert Level A = Potentially serious problem

 0 Alert Level B = Potential problem

 1 Alert Level C = Please check

---

S1. Comment

We have recently examined some 2,4-azido-2,4-dideoxy-β-D-glucopyranose derivatives (Barnes et al., 1996, 2002). Part of this study involved ring opening of the epoxide 1,6:3,4-dianhydro-2-azido-2-deoxy-β-D-galactopyranose, (III), with the azide ion. Compound (III) was prepared from the tosylate (II) by an intramolecular displacement with inversion at C4 (Williams, 1970). Compound (II) had been obtained by regioselective tosylation of the readily available diol (I) (Tailler et al., 1992). Although preferential tosylation of the (presumably) less hindered 4-OH group of (I) was anticipated, the ¹H NMR spectrum of (II) did not provide unequivocal structural information. The availability of good crystals of (III) gave the opportunity to confirm the structure and thus that of (II).

Since there are no atoms present with significant anomalous dispersion, the absolute configuration could not be determined using the Flack (1983) method. There was no reason to suppose that the remaining stereochemistry had reversed from that of (II) and refinement was carried out with Friedel pairs merged.

Fig. 1 shows that, as expected (Williams, 1970), the epoxy group has constrained C1, C2, C3, C4 and C5 into a plane (r.m.s. deviation 0.0154 Å), with significant shortening of the nominal single bonds C2—C3 [1.479 (5) Å], C3—C4 [1.455 (4) Å], C4—C5 [1.480 (4) Å] and C5—C6 [1.493 (5) Å Å]. Apparent bond shortening and ring flattening can occur as an artifact when positional disorder is overlooked during refinement but there is no evidence of disorder in (III).

The PLATON checking report in CHECKCIF draws attention to the unusual adp values for the azide group. The major axes of the ellipsoids of N1, N2 and to some extent N3 are parallel to that of the parent atom C2. However, the U_(eq) values [0.087 (1), 0.074 (1) and 0.140 (2) Ų] show that the azide is wagging about N2 and that N3 has considerably more freedom than N1 or N2. In a recent structure, which included an azide group on a glucopyranoside (Barnes et al., 2002). The anisotropic displacement parameters for the azide indicate a simple rocking motion about the parent C atom.

S2. Experimental

Details of the preparation of (I) will appear in a separate publication. (Brimacombe, Ferguson and Paterson, 2002)

S3. Refinement

H atoms were placed on calculated positions and allowed to ride on the adjacent C atom during refinement. Isotropic displacement parameters were constrained to be 1.3 times the U_eq of the adjacent C atom.

Computing details

Data collection: DENZO (Otwinowski & Minor, 1997); cell refinement: DENZO and COLLECT (Hooft, 1998); data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON and PLUTON (Spek, 1998); software used to prepare material for publication: SHELXL97.

Figures

Fig. 1. The structure of (I), showing 50% probability displacement ellipsoids.

1,6:3,4-di-anhydro-2-azido-2-deoxygalactopyranose

Crystal data

C6H7N3O3	Dx = 1.526 Mg m^−3
Mr = 169.15	Melting point = 83–84 K
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
a = 5.9011 (2) Å	Cell parameters from 5109 reflections
b = 7.2728 (4) Å	θ = 3.0–24.9°
c = 17.1567 (10) Å	µ = 0.13 mm^−1
V = 736.32 (6) Å^3	T = 298 K
Z = 4	Needle, colourless
F(000) = 352	0.4 × 0.3 × 0.15 mm

Data collection

Enraf–Nonius KappaCCD area-detector diffractometer	774 independent reflections
Radiation source: Enraf–Nonius FR591 rotating anode	670 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.030
Detector resolution: 9.091 pixels/mm pixels mm^-1	θmax = 24.9°, θmin = 3.0°
ϕ and ω scans to fill Ewald sphere	h = −6→6
Absorption correction: empirical (using intensity measurements) (SORTAV; Blessing, 1997)	k = −8→8
Tmin = 0.943, Tmax = 0.982	l = −20→20
5109 measured reflections

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F^2 > 2σ(F^2)] = 0.041	w = 1/[σ^2(Fo^2) + (0.0568P)^2 + 0.1579P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.111	(Δ/σ)max = 0.001
S = 1.08	Δρmax = 0.15 e Å^−3
774 reflections	Δρmin = −0.11 e Å^−3
119 parameters	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
0 restraints	Extinction coefficient: 0.081 (19)
Primary atom site location: structure-invariant direct methods	Absolute structure: No significant anomalous dispersion - Friedel pairs merged
Secondary atom site location: difference Fourier map

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. Hydrogen atoms were placed on calculated positions and allowed to ride on the adjacent carbon atom during refinement. Isotropic adps were constrained to be 1.3 times the U(eq) of the adjacent carbon atom.

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
C1	0.9375 (7)	0.3286 (5)	0.58714 (17)	0.0737 (10)
H1	0.9840	0.4151	0.5463	0.096*
C2	0.6997 (6)	0.3743 (4)	0.61485 (18)	0.0642 (9)
H2	0.5881	0.3377	0.5755	0.083*
C3	0.6470 (6)	0.2864 (4)	0.6904 (2)	0.0623 (8)
H3	0.524 (6)	0.344 (5)	0.7228 (18)	0.081*
C4	0.8216 (6)	0.1766 (4)	0.72813 (16)	0.0604 (8)
H4	0.832 (6)	0.168 (5)	0.784 (2)	0.078*
C5	1.0437 (5)	0.1638 (5)	0.68836 (19)	0.0638 (8)
H5	1.163 (7)	0.158 (6)	0.719 (2)	0.083*
C6	1.0442 (7)	0.0359 (5)	0.6203 (2)	0.0839 (12)
H6A	1.1970	−0.0030	0.6075	0.109*
H6B	0.9519	−0.0719	0.6305	0.109*
N1	0.6930 (7)	0.5773 (4)	0.62682 (17)	0.0871 (11)
N2	0.5697 (5)	0.6612 (4)	0.58404 (16)	0.0742 (8)
N3	0.4647 (9)	0.7546 (6)	0.5470 (3)	0.140 (2)
O3	0.6336 (4)	0.0896 (3)	0.68981 (16)	0.0762 (8)
O5	1.0897 (4)	0.3372 (3)	0.65022 (14)	0.0721 (7)
O6	0.9482 (6)	0.1463 (4)	0.55862 (12)	0.0957 (10)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.115 (3)	0.0560 (18)	0.0503 (14)	−0.006 (2)	0.0181 (17)	0.0031 (15)
C2	0.081 (2)	0.0502 (17)	0.0617 (16)	0.0032 (16)	−0.0281 (16)	−0.0031 (13)
C3	0.0561 (17)	0.0556 (19)	0.0751 (19)	0.0030 (14)	0.0063 (17)	0.0009 (16)
C4	0.0767 (19)	0.0549 (17)	0.0496 (14)	0.0006 (18)	0.0029 (14)	0.0060 (14)
C5	0.0562 (17)	0.0559 (18)	0.0792 (19)	0.0042 (16)	−0.0108 (15)	0.0029 (19)
C6	0.087 (3)	0.067 (2)	0.098 (3)	0.019 (2)	0.025 (2)	−0.005 (2)
N1	0.127 (3)	0.0509 (16)	0.0829 (18)	0.0115 (17)	−0.045 (2)	0.0022 (14)
N2	0.0908 (19)	0.0646 (17)	0.0672 (15)	0.0263 (18)	−0.0062 (15)	−0.0022 (15)
N3	0.183 (5)	0.108 (3)	0.128 (3)	0.081 (3)	−0.050 (3)	−0.008 (3)
O3	0.0629 (14)	0.0596 (14)	0.1060 (18)	−0.0110 (10)	0.0089 (15)	0.0107 (12)
O5	0.0546 (12)	0.0601 (13)	0.1016 (16)	−0.0094 (11)	0.0065 (11)	0.0050 (13)
O6	0.157 (3)	0.0699 (15)	0.0602 (12)	0.0087 (19)	0.0290 (16)	−0.0113 (12)

Geometric parameters (Å, º)

C1—O5	1.408 (4)	C4—C5	1.480 (5)
C1—O6	1.415 (5)	C4—H4	0.96 (4)
C1—C2	1.518 (5)	C5—O5	1.447 (4)
C1—H1	0.9800	C5—C6	1.493 (5)
C2—C3	1.479 (5)	C5—H5	0.89 (4)
C2—N1	1.491 (4)	C6—O6	1.444 (4)
C2—H2	0.9800	C6—H6A	0.9700
C3—O3	1.434 (4)	C6—H6B	0.9700
C3—C4	1.455 (4)	N1—N2	1.200 (4)
C3—H3	1.01 (4)	N2—N3	1.118 (4)
C4—O3	1.437 (4)
O5—C1—O6	106.2 (3)	O3—C4—H4	118 (2)
O5—C1—C2	109.8 (2)	C3—C4—H4	122 (2)
O6—C1—C2	110.8 (3)	C5—C4—H4	114 (2)
O5—C1—H1	110.0	O5—C5—C4	108.7 (3)
O6—C1—H1	110.0	O5—C5—C6	100.9 (3)
C2—C1—H1	110.0	C4—C5—C6	113.7 (3)
C3—C2—N1	107.5 (3)	O5—C5—H5	100 (3)
C3—C2—C1	112.0 (3)	C4—C5—H5	116 (2)
N1—C2—C1	106.5 (3)	C6—C5—H5	116 (3)
C3—C2—H2	110.2	O6—C6—C5	103.1 (3)
N1—C2—H2	110.2	O6—C6—H6A	111.2
C1—C2—H2	110.2	C5—C6—H6A	111.2
O3—C3—C4	59.6 (2)	O6—C6—H6B	111.2
O3—C3—C2	115.9 (3)	C5—C6—H6B	111.2
C4—C3—C2	118.5 (3)	H6A—C6—H6B	109.1
O3—C3—H3	112 (2)	N2—N1—C2	115.8 (3)
C4—C3—H3	119.6 (19)	N3—N2—N1	173.1 (4)
C2—C3—H3	117 (2)	C3—O3—C4	60.9 (2)
O3—C4—C3	59.44 (19)	C1—O5—C5	100.9 (2)
O3—C4—C5	116.4 (3)	C1—O6—C6	106.6 (3)
C3—C4—C5	117.2 (3)
C4—C3—C2—N1	−115.2 (3)	C2—C3—C4—C5	1.2 (5)
C3—C2—N1—N2	−125.4 (3)	C3—C4—C5—O5	34.8 (4)
C2—N1—N2—N3	−169 (4)	C4—C5—O5—C1	−73.2 (3)
O3—C4—C5—O5	102.2 (3)	C5—O5—C1—C2	78.2 (3)
C1—C2—C3—C4	1.5 (4)	O5—C1—C2—C3	−42.0 (4)