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Acta Cryst. (2009). E65, o263    [ doi:10.1107/S1600536808044279 ]

7-Azido-N,N-diethyl-4,5-O-isopropylidene-4-C-methyl-3,6-anhydro-7-deoxy-D-glycero-D-manno-heptonamide

S. F. Jenkinson, C. Wang, M.-S. Pino-González, G. W. J. Fleet and D. J. Watkin

Abstract top

The reaction of 5-azido-5-deoxy-2,3-O-isopropylidene-2-C-methyl-D-ribose with N,N-diethyl-2-(dimethylsulfuranylidene)acetamide gave the title compound, C15H26N4O5, as the major product arising from initial formation of an epoxide which was subsequently opened by intramolecular attack of the free 4-hydroxyl group. X-ray crystallography confirmed the relative stereochemistry of the title compound and the absolute configuration was determined by the use of D-ribose as the starting material. The crystal structure contains chains of molecules running parallel to the a axis, being linked by weak bifurcated O-H...(N,N) hydrogen bonds.

Comment top

The use of sulfur ylids in the stereoselective formation of epoxides and their subsequent regioselective opening has been utilized in the formation of iminosugars such as the seven-membered ring azepanes (Assiego et al., 2004), pipecolic acid derivatives (Pino-González et al.,2008) and piperidines (Pino-González et al., 2003). In order to extend this methodology the reaction of azido ribose derivative 1 with N,N-diethyl-2-(dimethylsulfuranylidene)acetamide was investigated.

Reaction of azido ribose derivative 1 with the sulfur ylid gave the title compound, furan 3, as the major product (Fig. 1). The product was confirmed, by both X-ray crystallography and the use of D-ribose as the starting material, to have the D-glycero-D-manno stereochemistry (Fig. 2) arising from initial attack of the ylid on the Si face of the aldehyde, as predicted from a Felkin-Ahn model (Valpuesta Fernández et al., 1990; Valpuesta et al., 1993), resulting in formation of epoxide 2, followed by intramolecular opening of the epoxide to give the title compound 3.

The compound was seen to adopt weakly (O—H···N) hydrogen bonded chains of molecules running parallel to the a-axis. The hydrogen bond is bifurcated (Fig. 3). Only classical hydrogen bonding has been considered.

Related literature top

For related literature see: Assiego et al. (2004); Pino-González et al. (2003, 2008); Valpuesta Fernández et al. (1990); Valpuesta et al. (1993).

For related literature, see: Görbitz (1999).

Experimental top

The title compound was recrystallized by vapour diffusion from a mixture of ethyl acetate and cyclohexane: m.p. 371–373 K; [α]D23 +16.4 (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.

The relatively large ratio of minimum to maximum corrections applied in the multiscan process (1:1.16) reflects changes in the illuminated volume of the crystal. 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 refinement was performed excluding the data for which I was less than 3σ(I).

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 arbitrary radius.
[Figure 3] Fig. 3. Packing diagram for the title compound projected along the b-axis. Hydrogen bonds are indicated by dotted lines.
7-Azido-N,N-diethyl-4,5-O-isopropylidene-4-C- methyl-3,6-anhydro-7-deoxy-D-glycero-D-manno-heptonamide top
Crystal data top
C15H26N4O5F(000) = 736
Mr = 342.40Dx = 1.232 Mg m−3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 2356 reflections
a = 8.6440 (1) Åθ = 5–27°
b = 13.4195 (2) ŵ = 0.09 mm−1
c = 15.9146 (3) ÅT = 150 K
V = 1846.06 (5) Å3Plate, colourless
Z = 40.60 × 0.60 × 0.40 mm
Data collection top
Area
diffractometer		2077 reflections with I > 2σ(I)
graphiteRint = 0.077
ω scansθmax = 27.5°, θmin = 5.1°
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)		h = −11→11
Tmin = 0.82, Tmax = 0.96k = −17→17
23123 measured reflectionsl = −20→20
2354 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)] = 0.049H-atom parameters constrained
wR(F2) = 0.129 Method = Modified Sheldrick w = 1/[σ2(F2) + (0.1P)2 + 0.29P],
where P = [max(Fo2,0) + 2Fc2]/3
S = 1.02(Δ/σ)max = 0.0003
1992 reflectionsΔρmax = 0.24 e Å−3
217 parametersΔρmin = −0.20 e Å−3
0 restraints
Crystal data top
C15H26N4O5V = 1846.06 (5) Å3
Mr = 342.40Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 8.6440 (1) ŵ = 0.09 mm−1
b = 13.4195 (2) ÅT = 150 K
c = 15.9146 (3) Å0.60 × 0.60 × 0.40 mm
Data collection top
Area
diffractometer		2354 independent reflections
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)		2077 reflections with I > 2σ(I)
Tmin = 0.82, Tmax = 0.96Rint = 0.077
23123 measured reflectionsθmax = 27.5°
Refinement top
R[F2 > 2σ(F2)] = 0.049H-atom parameters constrained
wR(F2) = 0.129Δρmax = 0.24 e Å−3
S = 1.02Δρmin = −0.20 e Å−3
1992 reflectionsAbsolute structure: ?
217 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.35653 (19)0.34433 (12)0.66423 (11)0.0350
C20.3014 (3)0.24404 (17)0.66153 (15)0.0332
C30.4224 (3)0.18015 (18)0.70965 (16)0.0371
O40.3791 (2)0.17151 (16)0.79595 (11)0.0446
C50.4967 (3)0.2129 (2)0.84827 (18)0.0489
O60.5741 (3)0.28402 (17)0.79711 (13)0.0567
C70.5654 (3)0.2496 (2)0.71213 (16)0.0414
C80.5218 (3)0.33863 (19)0.65738 (15)0.0359
C90.5726 (3)0.32292 (19)0.56645 (15)0.0369
N100.5219 (3)0.40493 (18)0.51111 (14)0.0432
N110.3807 (3)0.40751 (17)0.49594 (14)0.0432
N120.2579 (3)0.4190 (2)0.47516 (19)0.0629
C130.4212 (5)0.2678 (3)0.9201 (2)0.0714
C140.6054 (4)0.1311 (3)0.8787 (2)0.0650
C150.4486 (3)0.0783 (2)0.6708 (2)0.0472
C160.1375 (3)0.23817 (17)0.69753 (16)0.0343
O170.0763 (2)0.14313 (12)0.67786 (11)0.0401
C180.0305 (3)0.31779 (18)0.65939 (15)0.0334
O19−0.0340 (2)0.29828 (14)0.59206 (12)0.0424
N200.0093 (2)0.40342 (15)0.70067 (14)0.0364
C21−0.0987 (3)0.47788 (19)0.66655 (18)0.0407
C22−0.0208 (4)0.5595 (3)0.6178 (2)0.0626
C230.0809 (3)0.4266 (2)0.78247 (16)0.0430
C24−0.0166 (4)0.3904 (3)0.85556 (18)0.0562
H210.29430.22410.60200.0397*
H710.65510.21620.69300.0485*
H810.57590.39700.67840.0443*
H910.52840.26120.53940.0490*
H920.68630.31640.56770.0495*
H1310.49980.29970.95040.1074*
H1320.36170.22670.95750.1071*
H1330.35430.31890.90050.1069*
H1410.71160.15050.87010.1022*
H1420.59180.12110.93870.1023*
H1430.58510.06950.84760.1021*
H1510.53190.03970.69520.0807*
H1520.35010.04450.68150.0799*
H1530.46860.08480.61040.0790*
H1610.14380.24300.75990.0419*
H211−0.16020.44570.62660.0494*
H212−0.16370.50250.70980.0491*
H222−0.10250.59660.58650.1080*
H2210.05670.52950.57870.1079*
H2230.02790.60040.66270.1076*
H2320.17850.39600.78500.0507*
H2310.09150.49740.78380.0496*
H2430.03230.41350.90630.0898*
H242−0.01880.31850.85850.0891*
H241−0.12010.41870.85220.0890*
H1710.03180.12010.63190.0671*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0338 (8)0.0344 (8)0.0368 (8)−0.0019 (7)0.0028 (7)−0.0011 (7)
C20.0358 (12)0.0336 (11)0.0303 (10)−0.0013 (9)−0.0010 (9)−0.0023 (9)
C30.0367 (12)0.0413 (12)0.0333 (11)0.0024 (10)0.0011 (10)0.0029 (10)
O40.0404 (9)0.0598 (11)0.0336 (9)0.0000 (9)−0.0027 (8)0.0075 (8)
C50.0477 (15)0.0614 (17)0.0376 (12)0.0017 (13)−0.0068 (12)0.0052 (12)
O60.0642 (13)0.0683 (13)0.0375 (9)−0.0153 (11)−0.0124 (10)0.0036 (9)
C70.0361 (12)0.0505 (14)0.0375 (12)−0.0017 (12)−0.0042 (10)−0.0010 (11)
C80.0316 (11)0.0403 (12)0.0358 (11)−0.0059 (10)0.0019 (10)−0.0031 (11)
C90.0333 (11)0.0418 (12)0.0357 (11)−0.0024 (10)0.0015 (10)0.0000 (10)
N100.0422 (12)0.0454 (12)0.0421 (11)−0.0054 (10)0.0024 (10)0.0055 (9)
N110.0482 (14)0.0450 (12)0.0365 (10)0.0012 (10)0.0022 (10)0.0005 (9)
N120.0513 (16)0.080 (2)0.0577 (15)0.0105 (15)−0.0074 (13)0.0077 (15)
C130.079 (2)0.092 (3)0.0433 (15)0.010 (2)−0.0073 (17)−0.0083 (16)
C140.0592 (19)0.077 (2)0.0588 (18)0.0085 (17)−0.0179 (17)0.0139 (17)
C150.0442 (14)0.0386 (12)0.0586 (16)0.0043 (12)0.0040 (13)0.0010 (12)
C160.0347 (12)0.0340 (11)0.0342 (10)−0.0023 (10)−0.0002 (10)−0.0002 (10)
O170.0411 (9)0.0356 (8)0.0437 (9)−0.0075 (8)−0.0057 (8)0.0017 (7)
C180.0286 (10)0.0371 (11)0.0345 (11)−0.0013 (9)0.0011 (9)0.0013 (9)
O190.0397 (10)0.0462 (9)0.0413 (9)0.0055 (8)−0.0070 (8)−0.0070 (8)
N200.0348 (10)0.0377 (10)0.0366 (9)0.0027 (8)−0.0017 (8)−0.0055 (8)
C210.0356 (12)0.0413 (12)0.0451 (13)0.0055 (10)−0.0023 (11)−0.0043 (11)
C220.063 (2)0.0606 (19)0.0639 (19)0.0157 (16)0.0146 (17)0.0167 (16)
C230.0496 (15)0.0401 (12)0.0393 (13)0.0020 (12)−0.0046 (12)−0.0080 (11)
C240.070 (2)0.0591 (17)0.0393 (13)0.0089 (16)0.0069 (14)−0.0047 (13)
Geometric parameters (Å, °) top
O1—C21.429 (3)C14—H1420.972
O1—C81.435 (3)C14—H1430.979
C2—C31.554 (3)C15—H1510.968
C2—C161.530 (3)C15—H1520.979
C2—H210.986C15—H1530.982
C3—O41.428 (3)C16—O171.415 (3)
C3—C71.548 (4)C16—C181.538 (3)
C3—C151.517 (4)C16—H1610.997
O4—C51.427 (4)O17—H1710.882
C5—O61.422 (4)C18—O191.236 (3)
C5—C131.509 (5)C18—N201.336 (3)
C5—C141.524 (4)N20—C211.471 (3)
O6—C71.431 (3)N20—C231.475 (3)
C7—C81.526 (4)C21—C221.501 (4)
C7—H710.946C21—H2110.934
C8—C91.527 (3)C21—H2120.947
C8—H810.972C22—H2220.998
C9—N101.476 (3)C22—H2210.999
C9—H911.009C22—H2230.994
C9—H920.987C23—C241.516 (4)
N10—N111.245 (4)C23—H2320.940
N11—N121.122 (4)C23—H2310.955
C13—H1310.936C24—H2430.962
C13—H1320.960C24—H2420.967
C13—H1330.950C24—H2410.973
C14—H1410.964
C2—O1—C8106.25 (18)C5—C14—H142109.8
O1—C2—C3106.27 (19)H141—C14—H142107.0
O1—C2—C16110.26 (19)C5—C14—H143109.7
C3—C2—C16114.23 (19)H141—C14—H143109.0
O1—C2—H21107.7H142—C14—H143111.0
C3—C2—H21111.4C3—C15—H151115.5
C16—C2—H21106.8C3—C15—H152102.5
C2—C3—O4110.0 (2)H151—C15—H152109.3
C2—C3—C7102.59 (19)C3—C15—H153110.2
O4—C3—C7103.5 (2)H151—C15—H153108.0
C2—C3—C15113.4 (2)H152—C15—H153111.4
O4—C3—C15110.9 (2)C2—C16—O17108.00 (19)
C7—C3—C15115.7 (2)C2—C16—C18111.91 (19)
C3—O4—C5110.1 (2)O17—C16—C18108.32 (19)
O4—C5—O6105.2 (2)C2—C16—H161108.6
O4—C5—C13108.9 (3)O17—C16—H161107.5
O6—C5—C13108.1 (3)C18—C16—H161112.4
O4—C5—C14110.1 (3)C16—O17—H171131.5
O6—C5—C14112.1 (3)C16—C18—O19117.8 (2)
C13—C5—C14112.2 (3)C16—C18—N20119.1 (2)
C5—O6—C7107.4 (2)O19—C18—N20123.1 (2)
C3—C7—O6105.1 (2)C18—N20—C21119.3 (2)
C3—C7—C8105.0 (2)C18—N20—C23123.9 (2)
O6—C7—C8107.4 (2)C21—N20—C23116.7 (2)
C3—C7—H71111.2N20—C21—C22113.7 (2)
O6—C7—H71114.5N20—C21—H211107.4
C8—C7—H71112.9C22—C21—H211104.0
C7—C8—O1104.13 (19)N20—C21—H212110.2
C7—C8—C9111.2 (2)C22—C21—H212112.8
O1—C8—C9111.5 (2)H211—C21—H212108.5
C7—C8—H81108.4C21—C22—H222107.7
O1—C8—H81114.2C21—C22—H221109.2
C9—C8—H81107.4H222—C22—H221111.3
C8—C9—N10112.2 (2)C21—C22—H223102.8
C8—C9—H91114.2H222—C22—H223112.6
N10—C9—H91104.2H221—C22—H223112.7
C8—C9—H92106.3N20—C23—C24112.1 (2)
N10—C9—H92112.0N20—C23—H232108.8
H91—C9—H92108.2C24—C23—H232109.1
C9—N10—N11115.3 (2)N20—C23—H231105.7
N10—N11—N12171.3 (3)C24—C23—H231110.8
C5—C13—H131107.4H232—C23—H231110.3
C5—C13—H132114.9C23—C24—H243107.2
H131—C13—H132109.5C23—C24—H242111.6
C5—C13—H133111.5H243—C24—H242106.8
H131—C13—H133106.3C23—C24—H241110.1
H132—C13—H133107.0H243—C24—H241109.0
C5—C14—H141110.3H242—C24—H241112.0
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
C9—H91···O19i1.012.303.140 (4)140
C9—H92···O19ii0.992.463.441 (4)172
C23—H232···O10.942.563.231 (4)129
C23—H231···O17iii0.952.513.269 (4)136
O17—H171···N10iv0.882.303.112 (4)152
O17—H171···N11iv0.882.453.313 (4)167
Symmetry codes: (i) x+1/2, −y+1/2, −z+1; (ii) x+1, y, z; (iii) −x, y+1/2, −z+3/2; (iv) x−1/2, −y+1/2, −z+1.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O17—H171···N10i0.882.303.112 (4)152
O17—H171···N11i0.882.453.313 (4)167
Symmetry codes: (i) x−1/2, −y+1/2, −z+1.
Acknowledgements top

MSPG is grateful to Junta de Andalucia for a grant. The authors thank the Oxford University Crystallography Service for use of the instruments.

references
References top

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