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Acta Cryst. (2010). E66, o525-o526    [ doi:10.1107/S1600536810003995 ]

2-Azido-3,4;6,7-di-O-isopropylidene-[alpha]-D-glycero-D-talo-heptopyranose

S. F. Jenkinson, G. M. J. Lenagh-Snow, K. Izumori, G. W. J. Fleet, D. J. Watkin and A. L. Thompson

Abstract top

In the title compound, C13H21N3O6, the six-membered ring adopts a twist-boat conformation with the azide group in the bowsprit position. The azide group is disordered over two sets of sites in a 0.642 (10):0.358 (10) ratio. The crystal structure consists of O-H...O hydrogen-bonded trimer units. The absolute configuration was determined from the use of D-mannose as the starting material.

Comment top

The enzymatic interconversion of monosaccharides has been developed by Izumori (2002, 2006) and has been seen to be generally applicable for the 1-deoxy ketohexoses (Yoshihara et al., 2008, Gullapalli et al., 2010; Rao et al., 2009) and branched sugars (Rao et al., 2008; Jones et al., 2008). The methodology has also been applied to azido heptitols (Jenkinson et al., 2009) and thus to the synthesis of 2,6-dideoxy-2,6-iminoheptitols (homonojirimycins), seven carbon imino sugars (Compain et al., 2009; Asano et al., 2009; Watson et al., 2001) which are a family of glycosidase inhibitors. A number of homonojrimycins have been isolated as natural products from medicinal plants (Ikeda et al., 2000; Asano et al., 1998; Kite et al., 1988).

A Kiliani cyanide reaction on diacetone mannose gave the lactone diacetonide 1 (Beacham et al., 1991; Myerscough et al., 1992). Esterification of 1 (Fig. 1) with triflic anhydride in pyridine followed by reaction with sodium azide in DMF gave the azide 2 with retention of configuration at C2; the stereochemistry of 2 was established by X-ray crystallographic analysis (Bruce et al., 1990). Reduction of the lactone 2 afforded the lactol 3, a key intermediate for the synthesis of four of the possible sixteen iminoheptitols 4 by Izumoring techniques. The reported crystal structure of 3 determines the configuration of both the azide at C2 and the anomeric position.

The X-ray structure shows that the six-membered ring in the title compound adopts a twist boat conformation with the azide in the bowsprit position and the anomeric alcohol group in the less hindered α-position (Fig. 2). There is significant disorder in the structure with the azide occupying two possible sites. The compound exists as repeating hydrogen bonded trimer units (Fig.3, Fig. 4, Fig. 5). The absolute configuration was determined from the use of D-mannose as the starting material. Only classical hydrogen bonding was considered.

Related literature top

For Izumoring techniques, see: Izumori (2002, 2006); Yoshihara et al. (2008); Gullapalli et al. (2010); Rao et al. (2008, 2009); Jones et al. (2008); Jenkinson et al. (2009). For the synthesis of homonojirimycins, see: Compain et al. (2009); Asano et al. (2009); Watson et al. (2001) and for their isolation, see: Ikeda et al. (2000); Asano et al. (1998); Kite et al. (1988). For the synthesis of the azidoheptitol, see: Beacham et al. (1991); Bruce et al. (1990); Myerscough et al. (1992). For the weighting scheme, see: Prince (1982); Watkin (1994).

Experimental top

The title compound was recrystallised from diethyl ether: m.p. 397-398 K; [α]D25 +41.3 (c, 1.0 in CHCl3) {Lit. (Myerscough et al., 1992) m.p. 387-388 K; [α]D20 +41.0 (c, 1.0 in CHCl3).

Refinement top

In the absence of significant anomalous scattering, Friedel pairs were merged and the absolute configuration was assigned from the starting material D-mannose. Changes in illuminated volume were kept to a minimum, and were taken into account (Görbitz, 1999) by the multi-scan inter-frame scaling (DENZO/SCALEPACK, Otwinowski & Minor, 1997).

The H atoms were all located in a difference map, but those attached to carbon atoms were repositioned geometrically. The H atoms were initially refined with soft restraints on the bond lengths and angles to regularize their geometry (C—H in the range 0.93–0.98, O—H = 0.82 Å) and Uiso(H) (in the range 1.2–1.5 times Ueq of the parent atom), after which the positions were refined with riding constraints.

Computing details top

Data collection: COLLECT (Nonius, 2001); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS (Betteridge et al., 2003).

Figures top
[Figure 1] Fig. 1. Synthetic Scheme
[Figure 2] Fig. 2. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
[Figure 3] Fig. 3. Hydrogen bonded trimer unit. Hydrogen bonds are shown as dotted lines.
[Figure 4] Fig. 4. Packing diagram for the title compound projected along the c-axis. Hydrogen bonds are shown by dotted lines.
[Figure 5] Fig. 5. Packing diagram for the title compound projected along the b-axis. Hydrogen bonds are shown by dotted lines.
2-Azido-3,4;6,7-di-O-isopropylidene-α-D-glycero- D-talo-heptopyranose top
Crystal data top
C13H21N3O6Dx = 1.264 Mg m−3
Mr = 315.33Mo Kα radiation, λ = 0.71073 Å
Trigonal, R3Cell parameters from 1885 reflections
Hall symbol: R 3θ = 5–28°
a = 16.8793 (2) ŵ = 0.10 mm−1
c = 15.1043 (3) ÅT = 150 K
V = 3726.83 (10) Å3Plate, colourless
Z = 90.70 × 0.50 × 0.30 mm
F(000) = 1512
Data collection top
Nonius KappaCCD
diffractometer		1770 reflections with I > 2σ(I)
graphiteRint = 0.034
ω scansθmax = 27.5°, θmin = 5.2°
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)		h = −21→21
Tmin = 0.63, Tmax = 0.97k = −21→21
23870 measured reflectionsl = −19→19
1889 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.027H-atom parameters constrained
wR(F2) = 0.070 Method, part 1, Chebychev polynomial, (Watkin, 1994, Prince, 1982) [weight] = 1.0/[A0*T0(x) + A1*T1(x) ··· + An-1]*Tn-1(x)]
where Ai are the Chebychev coefficients listed below and x = F /Fmax Method = Robust Weighting (Prince, 1982) W = [weight] * [1-(deltaF/6*sigmaF)2]2 Ai are: 35.7 56.9 32.2 12.2 2.39
S = 0.87(Δ/σ)max = 0.0004
1889 reflectionsΔρmax = 0.16 e Å−3
227 parametersΔρmin = −0.16 e Å−3
43 restraints
Crystal data top
C13H21N3O6Z = 9
Mr = 315.33Mo Kα radiation
Trigonal, R3µ = 0.10 mm−1
a = 16.8793 (2) ÅT = 150 K
c = 15.1043 (3) Å0.70 × 0.50 × 0.30 mm
V = 3726.83 (10) Å3
Data collection top
Nonius KappaCCD
diffractometer		1889 independent reflections
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)		1770 reflections with I > 2σ(I)
Tmin = 0.63, Tmax = 0.97Rint = 0.034
23870 measured reflectionsθmax = 27.5°
Refinement top
R[F2 > 2σ(F2)] = 0.027H-atom parameters constrained
wR(F2) = 0.070Δρmax = 0.16 e Å−3
S = 0.87Δρmin = −0.16 e Å−3
1889 reflectionsAbsolute structure: ?
227 parametersFlack parameter: ?
43 restraintsRogers parameter: ?
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
O10.73085 (8)0.56052 (8)0.60278 (11)0.0388
C20.71163 (11)0.63258 (11)0.58727 (14)0.0334
C30.60997 (11)0.59051 (10)0.56713 (13)0.0348
O40.55748 (8)0.55027 (8)0.64559 (12)0.0420
C50.49780 (12)0.45418 (11)0.63308 (14)0.0398
O60.53523 (9)0.43128 (8)0.55852 (11)0.0414
C70.57940 (12)0.51014 (10)0.50233 (14)0.0370
C90.72913 (13)0.51340 (12)0.52439 (14)0.0407
O100.81499 (10)0.55590 (10)0.48357 (13)0.0511
C140.50399 (17)0.40362 (15)0.71240 (16)0.0540
C150.40195 (14)0.43489 (16)0.61352 (17)0.0544
C160.74277 (12)0.69311 (12)0.66864 (14)0.0376
O170.72041 (8)0.76403 (8)0.65905 (12)0.0420
C180.80336 (12)0.84914 (11)0.63848 (14)0.0408
O190.87138 (8)0.82461 (9)0.62410 (12)0.0457
C200.84636 (13)0.74546 (14)0.67731 (16)0.0468
C210.79042 (17)0.88864 (16)0.55377 (18)0.0588
C220.82716 (16)0.91340 (13)0.71627 (16)0.0519
H210.74700.66870.53530.0391*
H310.59780.63780.54360.0413*
H710.53610.50930.45800.0446*
H910.71230.45080.54150.0490*
H1410.46820.33790.70270.0810*
H1420.48040.41990.76370.0803*
H1430.56830.42140.72190.0805*
H1520.36320.36980.60470.0812*
H1530.37730.45410.66300.0797*
H1510.40110.46640.56070.0801*
H1610.71340.65690.72080.0440*
H2010.86480.76290.73920.0552*
H2020.87390.71010.65560.0567*
H2120.84550.94660.54250.0887*
H2130.73960.90010.56010.0886*
H2110.77930.84730.50540.0875*
H2220.88520.96820.70490.0781*
H2230.83090.88350.77000.0772*
H2210.78020.93020.72290.0777*
H1010.84470.53360.50650.0762*
C800.66053 (13)0.51225 (11)0.45706 (13)0.03990.642 (10)
N1100.6365 (5)0.4337 (5)0.3965 (5)0.04590.642 (10)
N1200.6176 (3)0.4422 (3)0.3203 (3)0.04850.642 (10)
N1300.5963 (4)0.4412 (3)0.2497 (2)0.08240.642 (10)
C810.66053 (13)0.51225 (11)0.45706 (13)0.03990.358 (10)
N1110.6151 (11)0.4225 (12)0.4122 (11)0.06170.358 (10)
N1210.6429 (6)0.4295 (6)0.3378 (7)0.05100.358 (10)
N1310.6661 (7)0.4252 (6)0.2652 (4)0.09360.358 (10)
H8010.69100.56800.42220.0469*0.642 (10)
H8110.68980.56450.41710.0473*0.358 (10)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0408 (6)0.0341 (6)0.0477 (7)0.0235 (5)−0.0023 (5)0.0055 (5)
C20.0319 (7)0.0255 (7)0.0436 (8)0.0150 (6)−0.0009 (6)0.0042 (6)
C30.0331 (8)0.0254 (7)0.0461 (9)0.0149 (6)−0.0014 (6)0.0017 (6)
O40.0358 (6)0.0264 (6)0.0545 (7)0.0084 (5)0.0071 (5)−0.0027 (5)
C50.0368 (8)0.0246 (7)0.0493 (9)0.0088 (6)−0.0017 (7)−0.0007 (6)
O60.0444 (7)0.0234 (5)0.0493 (7)0.0117 (5)−0.0005 (5)0.0004 (5)
C70.0401 (8)0.0251 (7)0.0449 (9)0.0156 (6)−0.0042 (7)0.0014 (6)
C90.0454 (9)0.0324 (8)0.0518 (10)0.0251 (7)0.0036 (8)0.0077 (7)
O100.0522 (8)0.0543 (8)0.0632 (8)0.0390 (7)0.0123 (7)0.0181 (7)
C140.0670 (13)0.0407 (10)0.0523 (12)0.0254 (10)−0.0002 (10)0.0048 (8)
C150.0359 (9)0.0534 (12)0.0609 (13)0.0125 (9)−0.0035 (9)−0.0009 (9)
C160.0341 (8)0.0311 (7)0.0438 (9)0.0133 (7)−0.0011 (6)0.0024 (6)
O170.0318 (6)0.0271 (5)0.0606 (8)0.0100 (5)0.0033 (5)−0.0025 (5)
C180.0361 (8)0.0287 (8)0.0475 (9)0.0086 (7)0.0026 (7)0.0017 (7)
O190.0317 (6)0.0391 (7)0.0562 (8)0.0100 (5)0.0028 (5)0.0012 (6)
C200.0368 (9)0.0405 (9)0.0573 (11)0.0150 (8)−0.0072 (8)−0.0021 (8)
C210.0641 (13)0.0517 (12)0.0538 (11)0.0239 (11)−0.0022 (10)0.0072 (9)
C220.0556 (12)0.0312 (9)0.0533 (11)0.0099 (8)0.0038 (9)−0.0034 (8)
C800.0489 (10)0.0299 (8)0.0448 (9)0.0226 (7)−0.0012 (7)−0.0005 (6)
N1100.064 (4)0.033 (3)0.043 (3)0.026 (3)0.004 (3)−0.0027 (19)
N1200.049 (2)0.0377 (17)0.049 (2)0.0148 (14)0.0016 (15)−0.0079 (14)
N1300.104 (4)0.063 (2)0.052 (2)0.021 (2)−0.0091 (19)−0.0184 (15)
C810.0489 (10)0.0299 (8)0.0448 (9)0.0226 (7)−0.0012 (7)−0.0005 (6)
N1110.072 (7)0.034 (4)0.060 (6)0.013 (4)0.032 (4)0.001 (3)
N1210.053 (4)0.045 (3)0.052 (4)0.022 (3)0.000 (3)0.002 (3)
N1310.112 (7)0.094 (6)0.050 (4)0.033 (5)0.009 (4)−0.010 (3)
Geometric parameters (Å, °) top
O1—C21.4261 (18)C15—H1520.966
O1—C91.419 (2)C15—H1530.985
C2—C31.524 (2)C15—H1510.963
C2—C161.515 (2)C16—O171.431 (2)
C2—H210.991C16—C201.520 (2)
C3—O41.431 (2)C16—H1610.968
C3—C71.538 (2)O17—C181.452 (2)
C3—H310.986C18—O191.419 (2)
O4—C51.4309 (19)C18—C211.508 (3)
C5—O61.436 (2)C18—C221.511 (3)
C5—C141.505 (3)O19—C201.430 (2)
C5—C151.511 (3)C20—H2010.983
O6—C71.434 (2)C20—H2020.978
C7—H710.986C21—H2120.971
C7—C801.515 (3)C21—H2130.974
C7—H710.986C21—H2110.962
C7—C811.515 (3)C22—H2220.969
C9—O101.398 (2)C22—H2230.974
C9—H910.982C22—H2210.971
C9—C801.534 (3)C80—N1101.491 (8)
C9—O101.398 (2)C80—H8010.971
C9—H910.982N110—N1201.221 (8)
C9—C811.534 (3)N120—N1301.123 (6)
O10—H1010.838C81—N1111.477 (19)
C14—H1410.974C81—H8110.975
C14—H1420.971N111—N1211.201 (16)
C14—H1430.982N121—N1311.179 (13)
C2—O1—C9113.04 (12)C5—C15—H153111.3
O1—C2—C3108.58 (13)H152—C15—H153108.8
O1—C2—C16106.97 (13)C5—C15—H151110.7
C3—C2—C16113.98 (14)H152—C15—H151108.9
O1—C2—H21109.4H153—C15—H151108.8
C3—C2—H21108.7C2—C16—O17109.54 (13)
C16—C2—H21109.2C2—C16—C20111.86 (16)
C2—C3—O4109.97 (14)O17—C16—C20103.32 (14)
C2—C3—C7109.94 (14)C2—C16—H161109.8
O4—C3—C7104.67 (12)O17—C16—H161110.2
C2—C3—H31109.7C20—C16—H161111.9
O4—C3—H31110.6C16—O17—C18108.78 (13)
C7—C3—H31111.8O17—C18—O19105.35 (14)
C3—O4—C5110.27 (13)O17—C18—C21109.73 (16)
O4—C5—O6104.70 (14)O19—C18—C21108.44 (17)
O4—C5—C14109.19 (15)O17—C18—C22108.82 (15)
O6—C5—C14107.89 (15)O19—C18—C22111.41 (16)
O4—C5—C15109.94 (15)C21—C18—C22112.81 (17)
O6—C5—C15110.88 (16)C18—O19—C20106.42 (14)
C14—C5—C15113.82 (17)C16—C20—O19102.19 (15)
C5—O6—C7107.99 (12)C16—C20—H201110.8
C3—C7—O6103.40 (13)O19—C20—H201110.7
C3—C7—H71111.3C16—C20—H202112.1
O6—C7—H71110.5O19—C20—H202111.9
C3—C7—C80111.47 (14)H201—C20—H202109.0
O6—C7—C80109.47 (13)C18—C21—H212108.5
H71—C7—C80110.5C18—C21—H213109.9
C3—C7—O6103.40 (13)H212—C21—H213108.2
C3—C7—H71111.3C18—C21—H211110.0
O6—C7—H71110.5H212—C21—H211109.8
C3—C7—C81111.47 (14)H213—C21—H211110.3
O6—C7—C81109.47 (13)C18—C22—H222109.1
H71—C7—C81110.5C18—C22—H223109.8
O1—C9—O10110.79 (15)H222—C22—H223110.3
O1—C9—H91107.3C18—C22—H221109.1
O10—C9—H91109.7H222—C22—H221108.8
O1—C9—C80111.36 (13)H223—C22—H221109.8
O10—C9—C80107.23 (15)C9—C80—C7111.64 (15)
H91—C9—C80110.5C9—C80—N110106.6 (3)
O1—C9—O10110.79 (15)C7—C80—N110114.6 (3)
O1—C9—H91107.3C9—C80—H801108.4
O10—C9—H91109.7C7—C80—H801107.6
O1—C9—C81111.36 (13)N110—C80—H801107.8
O10—C9—C81107.23 (15)C80—N110—N120116.4 (6)
H91—C9—C81110.5N110—N120—N130173.3 (6)
C9—O10—H101106.7C9—C81—C7111.64 (15)
C5—C14—H141110.3C9—C81—N111108.6 (8)
C5—C14—H142108.7C7—C81—N111100.5 (5)
H141—C14—H142109.5C9—C81—H811111.2
C5—C14—H143108.9C7—C81—H811110.2
H141—C14—H143109.4N111—C81—H811114.3
H142—C14—H143110.1C81—N111—N121110.6 (11)
C5—C15—H152108.4N111—N121—N131172.0 (13)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
C15—H153···O10i0.992.513.361 (3)145
O10—H101···O6ii0.841.932.761 (3)171
C80—H801···O4iii0.972.363.296 (3)161
C81—H801···O4iii0.972.363.296 (3)161
C80—H811···O4iii0.972.343.296 (3)166
C81—H811···O4iii0.972.343.296 (3)166
Symmetry codes: (i) −x+y+2/3, −x+4/3, z+1/3; (ii) −x+y+1, −x+1, z; (iii) −y+4/3, x−y+2/3, z−1/3.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O10—H101···O6i0.841.932.761 (3)171
Symmetry codes: (i) −x+y+1, −x+1, z.
references
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