organic compounds
7-Azido-N,N-diethyl-4,5-O-isopropylidene-4-C-methyl-3,6-anhydro-7-deoxy-D-glycero-D-manno-heptonamide
aDepartment of Organic Chemistry, Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, England, bDepartamento de Bioquímica, Biología Molecular y Química Orgánica, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain, and cDepartment of Chemical Crystallography, Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, England
*Correspondence e-mail: sarah.jenkinson@chem.ox.ac.uk
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 was determined by the use of D-ribose as the starting material. The contains chains of molecules running parallel to the a axis, being linked by weak bifurcated O—H⋯(N,N) hydrogen bonds.
Related literature
For related literature see: Assiego et al. (2004); Pino-González et al. (2003, 2008); Valpuesta Fernández et al. (1990); Valpuesta et al. (1993); Görbitz (1999).
Experimental
Crystal data
|
Refinement
|
Data collection: COLLECT (Nonius, 2001); cell DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK; 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.
Supporting information
10.1107/S1600536808044279/lh2750sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536808044279/lh2750Isup2.hkl
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).
In the absence of significant
Friedel pairs were merged and the 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 σ(I).
was performed excluding the data for which I was less than 3The 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.
Data collection: COLLECT (Nonius, 2001).; cell
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).C15H26N4O5 | F(000) = 736 |
Mr = 342.40 | Dx = 1.232 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 2356 reflections |
a = 8.6440 (1) Å | θ = 5–27° |
b = 13.4195 (2) Å | µ = 0.09 mm−1 |
c = 15.9146 (3) Å | T = 150 K |
V = 1846.06 (5) Å3 | Plate, colourless |
Z = 4 | 0.60 × 0.60 × 0.40 mm |
Area diffractometer | 2077 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.077 |
ω scans | θmax = 27.5°, θmin = 5.1° |
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) | h = −11→11 |
Tmin = 0.82, Tmax = 0.96 | k = −17→17 |
23123 measured reflections | l = −20→20 |
2354 independent reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.049 | H-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 = 0.000268 |
1992 reflections | Δρmax = 0.24 e Å−3 |
217 parameters | Δρmin = −0.20 e Å−3 |
0 restraints |
C15H26N4O5 | V = 1846.06 (5) Å3 |
Mr = 342.40 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 8.6440 (1) Å | µ = 0.09 mm−1 |
b = 13.4195 (2) Å | T = 150 K |
c = 15.9146 (3) Å | 0.60 × 0.60 × 0.40 mm |
Area diffractometer | 2354 independent reflections |
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) | 2077 reflections with I > 2σ(I) |
Tmin = 0.82, Tmax = 0.96 | Rint = 0.077 |
23123 measured reflections |
R[F2 > 2σ(F2)] = 0.049 | 0 restraints |
wR(F2) = 0.129 | H-atom parameters constrained |
S = 1.02 | Δρmax = 0.24 e Å−3 |
1992 reflections | Δρmin = −0.20 e Å−3 |
217 parameters |
x | y | z | Uiso*/Ueq | ||
O1 | 0.35653 (19) | 0.34433 (12) | 0.66423 (11) | 0.0350 | |
C2 | 0.3014 (3) | 0.24404 (17) | 0.66153 (15) | 0.0332 | |
C3 | 0.4224 (3) | 0.18015 (18) | 0.70965 (16) | 0.0371 | |
O4 | 0.3791 (2) | 0.17151 (16) | 0.79595 (11) | 0.0446 | |
C5 | 0.4967 (3) | 0.2129 (2) | 0.84827 (18) | 0.0489 | |
O6 | 0.5741 (3) | 0.28402 (17) | 0.79711 (13) | 0.0567 | |
C7 | 0.5654 (3) | 0.2496 (2) | 0.71213 (16) | 0.0414 | |
C8 | 0.5218 (3) | 0.33863 (19) | 0.65738 (15) | 0.0359 | |
C9 | 0.5726 (3) | 0.32292 (19) | 0.56645 (15) | 0.0369 | |
N10 | 0.5219 (3) | 0.40493 (18) | 0.51111 (14) | 0.0432 | |
N11 | 0.3807 (3) | 0.40751 (17) | 0.49594 (14) | 0.0432 | |
N12 | 0.2579 (3) | 0.4190 (2) | 0.47516 (19) | 0.0629 | |
C13 | 0.4212 (5) | 0.2678 (3) | 0.9201 (2) | 0.0714 | |
C14 | 0.6054 (4) | 0.1311 (3) | 0.8787 (2) | 0.0650 | |
C15 | 0.4486 (3) | 0.0783 (2) | 0.6708 (2) | 0.0472 | |
C16 | 0.1375 (3) | 0.23817 (17) | 0.69753 (16) | 0.0343 | |
O17 | 0.0763 (2) | 0.14313 (12) | 0.67786 (11) | 0.0401 | |
C18 | 0.0305 (3) | 0.31779 (18) | 0.65939 (15) | 0.0334 | |
O19 | −0.0340 (2) | 0.29828 (14) | 0.59206 (12) | 0.0424 | |
N20 | 0.0093 (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 | |
C23 | 0.0809 (3) | 0.4266 (2) | 0.78247 (16) | 0.0430 | |
C24 | −0.0166 (4) | 0.3904 (3) | 0.85556 (18) | 0.0562 | |
H21 | 0.2943 | 0.2241 | 0.6020 | 0.0397* | |
H71 | 0.6551 | 0.2162 | 0.6930 | 0.0485* | |
H81 | 0.5759 | 0.3970 | 0.6784 | 0.0443* | |
H91 | 0.5284 | 0.2612 | 0.5394 | 0.0490* | |
H92 | 0.6863 | 0.3164 | 0.5677 | 0.0495* | |
H131 | 0.4998 | 0.2997 | 0.9504 | 0.1074* | |
H132 | 0.3617 | 0.2267 | 0.9575 | 0.1071* | |
H133 | 0.3543 | 0.3189 | 0.9005 | 0.1069* | |
H141 | 0.7116 | 0.1505 | 0.8701 | 0.1022* | |
H142 | 0.5918 | 0.1211 | 0.9387 | 0.1023* | |
H143 | 0.5851 | 0.0695 | 0.8476 | 0.1021* | |
H151 | 0.5319 | 0.0397 | 0.6952 | 0.0807* | |
H152 | 0.3501 | 0.0445 | 0.6815 | 0.0799* | |
H153 | 0.4686 | 0.0848 | 0.6104 | 0.0790* | |
H161 | 0.1438 | 0.2430 | 0.7599 | 0.0419* | |
H211 | −0.1602 | 0.4457 | 0.6266 | 0.0494* | |
H212 | −0.1637 | 0.5025 | 0.7098 | 0.0491* | |
H222 | −0.1025 | 0.5966 | 0.5865 | 0.1080* | |
H221 | 0.0567 | 0.5295 | 0.5787 | 0.1079* | |
H223 | 0.0279 | 0.6004 | 0.6627 | 0.1076* | |
H232 | 0.1785 | 0.3960 | 0.7850 | 0.0507* | |
H231 | 0.0915 | 0.4974 | 0.7838 | 0.0496* | |
H243 | 0.0323 | 0.4135 | 0.9063 | 0.0898* | |
H242 | −0.0188 | 0.3185 | 0.8585 | 0.0891* | |
H241 | −0.1201 | 0.4187 | 0.8522 | 0.0890* | |
H171 | 0.0318 | 0.1201 | 0.6319 | 0.0671* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0338 (8) | 0.0344 (8) | 0.0368 (8) | −0.0019 (7) | 0.0028 (7) | −0.0011 (7) |
C2 | 0.0358 (12) | 0.0336 (11) | 0.0303 (10) | −0.0013 (9) | −0.0010 (9) | −0.0023 (9) |
C3 | 0.0367 (12) | 0.0413 (12) | 0.0333 (11) | 0.0024 (10) | 0.0011 (10) | 0.0029 (10) |
O4 | 0.0404 (9) | 0.0598 (11) | 0.0336 (9) | 0.0000 (9) | −0.0027 (8) | 0.0075 (8) |
C5 | 0.0477 (15) | 0.0614 (17) | 0.0376 (12) | 0.0017 (13) | −0.0068 (12) | 0.0052 (12) |
O6 | 0.0642 (13) | 0.0683 (13) | 0.0375 (9) | −0.0153 (11) | −0.0124 (10) | 0.0036 (9) |
C7 | 0.0361 (12) | 0.0505 (14) | 0.0375 (12) | −0.0017 (12) | −0.0042 (10) | −0.0010 (11) |
C8 | 0.0316 (11) | 0.0403 (12) | 0.0358 (11) | −0.0059 (10) | 0.0019 (10) | −0.0031 (11) |
C9 | 0.0333 (11) | 0.0418 (12) | 0.0357 (11) | −0.0024 (10) | 0.0015 (10) | 0.0000 (10) |
N10 | 0.0422 (12) | 0.0454 (12) | 0.0421 (11) | −0.0054 (10) | 0.0024 (10) | 0.0055 (9) |
N11 | 0.0482 (14) | 0.0450 (12) | 0.0365 (10) | 0.0012 (10) | 0.0022 (10) | 0.0005 (9) |
N12 | 0.0513 (16) | 0.080 (2) | 0.0577 (15) | 0.0105 (15) | −0.0074 (13) | 0.0077 (15) |
C13 | 0.079 (2) | 0.092 (3) | 0.0433 (15) | 0.010 (2) | −0.0073 (17) | −0.0083 (16) |
C14 | 0.0592 (19) | 0.077 (2) | 0.0588 (18) | 0.0085 (17) | −0.0179 (17) | 0.0139 (17) |
C15 | 0.0442 (14) | 0.0386 (12) | 0.0586 (16) | 0.0043 (12) | 0.0040 (13) | 0.0010 (12) |
C16 | 0.0347 (12) | 0.0340 (11) | 0.0342 (10) | −0.0023 (10) | −0.0002 (10) | −0.0002 (10) |
O17 | 0.0411 (9) | 0.0356 (8) | 0.0437 (9) | −0.0075 (8) | −0.0057 (8) | 0.0017 (7) |
C18 | 0.0286 (10) | 0.0371 (11) | 0.0345 (11) | −0.0013 (9) | 0.0011 (9) | 0.0013 (9) |
O19 | 0.0397 (10) | 0.0462 (9) | 0.0413 (9) | 0.0055 (8) | −0.0070 (8) | −0.0070 (8) |
N20 | 0.0348 (10) | 0.0377 (10) | 0.0366 (9) | 0.0027 (8) | −0.0017 (8) | −0.0055 (8) |
C21 | 0.0356 (12) | 0.0413 (12) | 0.0451 (13) | 0.0055 (10) | −0.0023 (11) | −0.0043 (11) |
C22 | 0.063 (2) | 0.0606 (19) | 0.0639 (19) | 0.0157 (16) | 0.0146 (17) | 0.0167 (16) |
C23 | 0.0496 (15) | 0.0401 (12) | 0.0393 (13) | 0.0020 (12) | −0.0046 (12) | −0.0080 (11) |
C24 | 0.070 (2) | 0.0591 (17) | 0.0393 (13) | 0.0089 (16) | 0.0069 (14) | −0.0047 (13) |
O1—C2 | 1.429 (3) | C14—H142 | 0.972 |
O1—C8 | 1.435 (3) | C14—H143 | 0.979 |
C2—C3 | 1.554 (3) | C15—H151 | 0.968 |
C2—C16 | 1.530 (3) | C15—H152 | 0.979 |
C2—H21 | 0.986 | C15—H153 | 0.982 |
C3—O4 | 1.428 (3) | C16—O17 | 1.415 (3) |
C3—C7 | 1.548 (4) | C16—C18 | 1.538 (3) |
C3—C15 | 1.517 (4) | C16—H161 | 0.997 |
O4—C5 | 1.427 (4) | O17—H171 | 0.882 |
C5—O6 | 1.422 (4) | C18—O19 | 1.236 (3) |
C5—C13 | 1.509 (5) | C18—N20 | 1.336 (3) |
C5—C14 | 1.524 (4) | N20—C21 | 1.471 (3) |
O6—C7 | 1.431 (3) | N20—C23 | 1.475 (3) |
C7—C8 | 1.526 (4) | C21—C22 | 1.501 (4) |
C7—H71 | 0.946 | C21—H211 | 0.934 |
C8—C9 | 1.527 (3) | C21—H212 | 0.947 |
C8—H81 | 0.972 | C22—H222 | 0.998 |
C9—N10 | 1.476 (3) | C22—H221 | 0.999 |
C9—H91 | 1.009 | C22—H223 | 0.994 |
C9—H92 | 0.987 | C23—C24 | 1.516 (4) |
N10—N11 | 1.245 (4) | C23—H232 | 0.940 |
N11—N12 | 1.122 (4) | C23—H231 | 0.955 |
C13—H131 | 0.936 | C24—H243 | 0.962 |
C13—H132 | 0.960 | C24—H242 | 0.967 |
C13—H133 | 0.950 | C24—H241 | 0.973 |
C14—H141 | 0.964 | ||
C2—O1—C8 | 106.25 (18) | C5—C14—H142 | 109.8 |
O1—C2—C3 | 106.27 (19) | H141—C14—H142 | 107.0 |
O1—C2—C16 | 110.26 (19) | C5—C14—H143 | 109.7 |
C3—C2—C16 | 114.23 (19) | H141—C14—H143 | 109.0 |
O1—C2—H21 | 107.7 | H142—C14—H143 | 111.0 |
C3—C2—H21 | 111.4 | C3—C15—H151 | 115.5 |
C16—C2—H21 | 106.8 | C3—C15—H152 | 102.5 |
C2—C3—O4 | 110.0 (2) | H151—C15—H152 | 109.3 |
C2—C3—C7 | 102.59 (19) | C3—C15—H153 | 110.2 |
O4—C3—C7 | 103.5 (2) | H151—C15—H153 | 108.0 |
C2—C3—C15 | 113.4 (2) | H152—C15—H153 | 111.4 |
O4—C3—C15 | 110.9 (2) | C2—C16—O17 | 108.00 (19) |
C7—C3—C15 | 115.7 (2) | C2—C16—C18 | 111.91 (19) |
C3—O4—C5 | 110.1 (2) | O17—C16—C18 | 108.32 (19) |
O4—C5—O6 | 105.2 (2) | C2—C16—H161 | 108.6 |
O4—C5—C13 | 108.9 (3) | O17—C16—H161 | 107.5 |
O6—C5—C13 | 108.1 (3) | C18—C16—H161 | 112.4 |
O4—C5—C14 | 110.1 (3) | C16—O17—H171 | 131.5 |
O6—C5—C14 | 112.1 (3) | C16—C18—O19 | 117.8 (2) |
C13—C5—C14 | 112.2 (3) | C16—C18—N20 | 119.1 (2) |
C5—O6—C7 | 107.4 (2) | O19—C18—N20 | 123.1 (2) |
C3—C7—O6 | 105.1 (2) | C18—N20—C21 | 119.3 (2) |
C3—C7—C8 | 105.0 (2) | C18—N20—C23 | 123.9 (2) |
O6—C7—C8 | 107.4 (2) | C21—N20—C23 | 116.7 (2) |
C3—C7—H71 | 111.2 | N20—C21—C22 | 113.7 (2) |
O6—C7—H71 | 114.5 | N20—C21—H211 | 107.4 |
C8—C7—H71 | 112.9 | C22—C21—H211 | 104.0 |
C7—C8—O1 | 104.13 (19) | N20—C21—H212 | 110.2 |
C7—C8—C9 | 111.2 (2) | C22—C21—H212 | 112.8 |
O1—C8—C9 | 111.5 (2) | H211—C21—H212 | 108.5 |
C7—C8—H81 | 108.4 | C21—C22—H222 | 107.7 |
O1—C8—H81 | 114.2 | C21—C22—H221 | 109.2 |
C9—C8—H81 | 107.4 | H222—C22—H221 | 111.3 |
C8—C9—N10 | 112.2 (2) | C21—C22—H223 | 102.8 |
C8—C9—H91 | 114.2 | H222—C22—H223 | 112.6 |
N10—C9—H91 | 104.2 | H221—C22—H223 | 112.7 |
C8—C9—H92 | 106.3 | N20—C23—C24 | 112.1 (2) |
N10—C9—H92 | 112.0 | N20—C23—H232 | 108.8 |
H91—C9—H92 | 108.2 | C24—C23—H232 | 109.1 |
C9—N10—N11 | 115.3 (2) | N20—C23—H231 | 105.7 |
N10—N11—N12 | 171.3 (3) | C24—C23—H231 | 110.8 |
C5—C13—H131 | 107.4 | H232—C23—H231 | 110.3 |
C5—C13—H132 | 114.9 | C23—C24—H243 | 107.2 |
H131—C13—H132 | 109.5 | C23—C24—H242 | 111.6 |
C5—C13—H133 | 111.5 | H243—C24—H242 | 106.8 |
H131—C13—H133 | 106.3 | C23—C24—H241 | 110.1 |
H132—C13—H133 | 107.0 | H243—C24—H241 | 109.0 |
C5—C14—H141 | 110.3 | H242—C24—H241 | 112.0 |
D—H···A | D—H | H···A | D···A | D—H···A |
C9—H91···O19i | 1.01 | 2.30 | 3.140 (4) | 140 |
C9—H92···O19ii | 0.99 | 2.46 | 3.441 (4) | 172 |
C23—H232···O1 | 0.94 | 2.56 | 3.231 (4) | 129 |
C23—H231···O17iii | 0.95 | 2.51 | 3.269 (4) | 136 |
O17—H171···N10iv | 0.88 | 2.30 | 3.112 (4) | 152 |
O17—H171···N11iv | 0.88 | 2.45 | 3.313 (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. |
Experimental details
Crystal data | |
Chemical formula | C15H26N4O5 |
Mr | 342.40 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 150 |
a, b, c (Å) | 8.6440 (1), 13.4195 (2), 15.9146 (3) |
V (Å3) | 1846.06 (5) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.60 × 0.60 × 0.40 |
Data collection | |
Diffractometer | Area diffractometer |
Absorption correction | Multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) |
Tmin, Tmax | 0.82, 0.96 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 23123, 2354, 2077 |
Rint | 0.077 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.049, 0.129, 1.02 |
No. of reflections | 1992 |
No. of parameters | 217 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.24, −0.20 |
Computer programs: COLLECT (Nonius, 2001)., DENZO/SCALEPACK (Otwinowski & Minor, 1997), SIR92 (Altomare et al., 1994), CRYSTALS (Betteridge et al., 2003), CAMERON (Watkin et al., 1996).
D—H···A | D—H | H···A | D···A | D—H···A |
O17—H171···N10i | 0.88 | 2.30 | 3.112 (4) | 152 |
O17—H171···N11i | 0.88 | 2.45 | 3.313 (4) | 167 |
Symmetry code: (i) x−1/2, −y+1/2, −z+1. |
Acknowledgements
MSPG is grateful to Junta de Andalucia for a grant. The authors thank the Oxford University Crystallography Service for use of the instruments.
References
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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.