2-Azido-2-de­oxy-3,4-O-isopropyl­idene-2-C-methyl-D-talono-1,5-lactone

The relative stereochemistry of the title compound, C₁₀H₁₅N₃O₅, was confirmed by the crystal structure determin­ation. The absolute configuration was determined from the use of D-lyxonolactone as the starting material. The six-membered ring adopts a boat conformation with the larger azide group, rather than the methyl group, in the bowsprit position. In the crystal structure, a bifurcated inter­molecular O—H...O/O—H...N hydrogen bond links mol­ecules into chains running parallel to the b axis.

Key indicators

• Single-crystal X-ray study
• T = 150 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.038
• wR factor = 0.087
• Data-to-parameter ratio = 10.0

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT910_ALERT_3_B Missing # of FCF Reflections Below Th(Min) .....         16

Alert level C
PLAT230_ALERT_2_C Hirshfeld Test Diff for    N7     --  N8      ..       5.62 su
PLAT913_ALERT_3_C Missing # of Very Strong Reflections in FCF ....         11

Alert level G
REFLT03_ALERT_4_G 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.
           From the CIF: _diffrn_reflns_theta_max           27.49
           From the CIF: _reflns_number_total               1647
           Count of symmetry unique reflns         1663
           Completeness (_total/calc)             99.04%
           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
PLAT960_ALERT_3_G Number of Intensities with I .LT. - 2*sig(I) ..           1
PLAT791_ALERT_4_G The Model has Chirality at C4      (Verify) ....          R
PLAT791_ALERT_4_G The Model has Chirality at C5      (Verify) ....          R
PLAT791_ALERT_4_G The Model has Chirality at C6      (Verify) ....          S
PLAT791_ALERT_4_G The Model has Chirality at C13     (Verify) ....          R
PLAT808_ALERT_5_G No Parsable SHELXL style Weighting Scheme Found           !
PLAT929_ALERT_4_G No Interpretable (SHELX) Weight Parameters found          ?

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   8 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   3 ALERT type 3 Indicator that the structure quality may be low
   6 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

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S1. Comment

Carbohydrates are a diverse set of chirons for the synthesis of complex amino acids and iminosugars (Lichtenthaler & Peters, 2004; Fechter et al., 1999; Fleet, 1989). 2-C-Methyl branched sugars constitute a class of rare sugars with chemotherapeutic potential (Rao et al., 2008; Jones et al., 2008; Booth et al., 2008) and can be used as building blocks in the synthesis of biologically active compounds (da Cruz et al., 2008; Hotchkiss, Kato et al., 2007; Soengas et al., 2005).

The azidolactone 3 (Fig. 1) would be a key intermediate for the synethsis of branched pyrrolidines, piperidines and prolines derived from D-lyxonolactone. Nucleophilic displacement of a triflate leaving group at the tertiary centre by azide was confirmed by X-ray crystallography to have proceeded with overall inversion of configuration (Booth et al. 2007; Hotchkiss, Jenkinson et al. 2007). The 6-membered lactone ring adopts a boat conformation, as is common with 3,4-O-isopropylidene-1,5-lactones (Baird et al., 1987; Bruce et al., 1990; Punzo et al., 2005), with the larger azide group, rather than the methyl, in the bowsprit position (Fig. 2). The absolute configuration was determined from the use of D-lyxonolactone as the starting material. As is common with these materials the azide is non linear [N7 - N8 - N9 = 172.4 (3) °] (Chesterton et al., 2006), with the anisotropic atomic displacement parameter of the central atom lowered with respect to its neighbours. The compound exists as hydrogen bonded chains of molecules running parallel to the b-axis (Fig. 3). The hydrogen bond is bifurcated. Only classical hydrogen bonding is considered.

Related literature

For carbohydrates as chirons, see: Lichtenthaler & Peters (2004); Fechter et al. (1999); Fleet (1989). For branched sugars and their use as chirons, see: Rao et al. (2008); Jones et al. (2008); Booth et al. (2008); Hotchkiss, Kato et al. (2007); da Cruz et al. (2008); Soengas et al. (2005). For the structures of similar sugars, see: Chesterton et al. (2006); Booth et al. (2007); Hotchkiss, Jenkinson et al. (2007); Baird et al. (1987); Bruce et al. (1990); Punzo et al. (2005). For the extinction correction, see: Larson (1970).

S2. Experimental

The title compound was recrystallised by slow evaporation from a mixture of diethyl ether and cyclohexane: m.p. 397-403 K, [α]_D²⁵ +112.4 (c, 1.145 in CHCl₃).

S3. Refinement

In the absence of significant anomalous scattering, Friedel pairs were merged and the absolute configuration was assigned from the use of D-lyonolactone as the starting material.

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 U_iso(H) (in the range 1.2–1.5 times U_eq of the parent atom), after which the positions were refined with riding constraints.

Computing details

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

	Fig. 1. Synthetic Scheme
	Fig. 2. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
	Fig. 3. Packing diagram for the title compound projected along the a-axis. Hydrogen bonds are shown by dotted lines.

2-Azido-2-deoxy-3,4-O-isopropylidene-2-C-methyl-D-talono-1,5-lactone

Crystal data

C10H15N3O5	F(000) = 544
Mr = 257.25	Dx = 1.377 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 1637 reflections
a = 5.9481 (3) Å	θ = 5–27°
b = 13.3427 (7) Å	µ = 0.11 mm^−1
c = 15.6351 (9) Å	T = 150 K
V = 1240.86 (12) Å^3	Plate, colourless
Z = 4	0.20 × 0.15 × 0.05 mm

Data collection

Nonius KappaCCD diffractometer	1170 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.077
ω scans	θmax = 27.5°, θmin = 5.2°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −7→7
Tmin = 0.89, Tmax = 0.99	k = −17→17
10775 measured reflections	l = −20→20
1647 independent 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)] = 0.038	Method = Modified Sheldrick w = 1/[σ^2(F^2) + ( 0.05P)^2 + 0.16P], where P = [max(Fo^2,0) + 2Fc^2]/3
wR(F^2) = 0.087	(Δ/σ)max = 0.000278
S = 0.88	Δρmax = 0.53 e Å^−3
1647 reflections	Δρmin = −0.45 e Å^−3
164 parameters	Extinction correction: Larson (1970), Equation 22
0 restraints	Extinction coefficient: 460 (60)
Primary atom site location: structure-invariant direct methods

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.4977 (3)	0.87439 (12)	0.79200 (10)	0.0276
C2	0.5736 (5)	0.85325 (19)	0.87769 (16)	0.0297
O3	0.7326 (3)	0.77432 (13)	0.86551 (10)	0.0334
C4	0.8307 (4)	0.78267 (17)	0.78210 (15)	0.0258
C5	0.6901 (4)	0.86484 (17)	0.73767 (14)	0.0250
C6	0.6110 (4)	0.83522 (18)	0.64929 (15)	0.0247
N7	0.4436 (4)	0.91275 (16)	0.62475 (14)	0.0317
N8	0.3742 (4)	0.90581 (16)	0.55031 (15)	0.0313
N9	0.2976 (4)	0.90888 (18)	0.48383 (15)	0.0443
C10	0.4914 (4)	0.73333 (18)	0.65603 (15)	0.0243
O11	0.3123 (3)	0.71606 (13)	0.62348 (11)	0.0323
O12	0.5913 (3)	0.66364 (12)	0.70449 (11)	0.0256
C13	0.8169 (4)	0.68186 (17)	0.73740 (16)	0.0250
C14	0.8716 (5)	0.59403 (17)	0.79413 (17)	0.0309
O15	0.8866 (3)	0.50433 (11)	0.74599 (11)	0.0351
C16	0.8056 (4)	0.83600 (19)	0.58502 (16)	0.0303
C17	0.6857 (5)	0.9437 (2)	0.91665 (18)	0.0385
C18	0.3762 (5)	0.8142 (2)	0.92680 (19)	0.0459
H41	0.9905	0.8032	0.7872	0.0311*
H51	0.7740	0.9284	0.7350	0.0310*
H131	0.9235	0.6813	0.6888	0.0288*
H141	1.0180	0.6075	0.8209	0.0398*
H142	0.7552	0.5873	0.8388	0.0391*
H161	0.7461	0.8167	0.5292	0.0461*
H162	0.8707	0.9027	0.5818	0.0463*
H163	0.9219	0.7893	0.6024	0.0460*
H172	0.7391	0.9258	0.9730	0.0598*
H171	0.5743	0.9972	0.9206	0.0603*
H173	0.8113	0.9635	0.8797	0.0603*
H182	0.4260	0.7957	0.9845	0.0690*
H181	0.2604	0.8655	0.9297	0.0694*
H183	0.3174	0.7559	0.8975	0.0688*
H151	0.7591	0.4778	0.7453	0.0532*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0272 (9)	0.0348 (9)	0.0207 (8)	0.0036 (8)	−0.0008 (8)	0.0009 (7)
C2	0.0358 (14)	0.0323 (13)	0.0209 (12)	0.0025 (12)	−0.0027 (11)	−0.0011 (12)
O3	0.0480 (11)	0.0305 (9)	0.0217 (9)	0.0089 (9)	−0.0031 (8)	0.0004 (8)
C4	0.0254 (13)	0.0278 (12)	0.0241 (13)	−0.0041 (11)	−0.0031 (10)	0.0007 (11)
C5	0.0249 (12)	0.0250 (12)	0.0252 (12)	0.0006 (10)	−0.0006 (11)	0.0016 (11)
C6	0.0253 (12)	0.0255 (12)	0.0233 (13)	0.0057 (11)	−0.0011 (11)	0.0031 (10)
N7	0.0361 (12)	0.0337 (11)	0.0253 (11)	0.0090 (10)	−0.0035 (10)	−0.0003 (10)
N8	0.0309 (12)	0.0300 (11)	0.0330 (13)	0.0066 (10)	0.0013 (11)	0.0030 (11)
N9	0.0446 (14)	0.0544 (16)	0.0340 (14)	0.0089 (13)	−0.0105 (12)	0.0052 (12)
C10	0.0210 (12)	0.0297 (13)	0.0221 (11)	0.0039 (11)	0.0023 (11)	−0.0047 (11)
O11	0.0255 (9)	0.0391 (10)	0.0322 (10)	−0.0029 (9)	−0.0047 (8)	−0.0022 (9)
O12	0.0228 (8)	0.0246 (8)	0.0293 (9)	−0.0005 (7)	−0.0023 (7)	0.0012 (8)
C13	0.0192 (11)	0.0267 (12)	0.0292 (14)	0.0008 (10)	−0.0021 (11)	0.0020 (11)
C14	0.0327 (14)	0.0247 (12)	0.0351 (14)	0.0018 (12)	−0.0044 (12)	0.0045 (12)
O15	0.0297 (9)	0.0248 (9)	0.0509 (12)	0.0035 (8)	0.0037 (9)	0.0003 (9)
C16	0.0318 (13)	0.0317 (13)	0.0274 (13)	0.0010 (12)	0.0036 (11)	0.0049 (11)
C17	0.0484 (17)	0.0374 (15)	0.0297 (14)	0.0015 (14)	−0.0060 (14)	−0.0059 (12)
C18	0.0446 (17)	0.063 (2)	0.0300 (16)	−0.0052 (15)	0.0033 (13)	0.0041 (15)

Geometric parameters (Å, º)

O1—C2	1.442 (3)	C10—O12	1.338 (3)
O1—C5	1.431 (3)	O12—C13	1.458 (3)
C2—O3	1.428 (3)	C13—C14	1.505 (3)
C2—C17	1.508 (4)	C13—H131	0.989
C2—C18	1.496 (4)	C14—O15	1.417 (3)
O3—C4	1.433 (3)	C14—H141	0.983
C4—C5	1.544 (3)	C14—H142	0.987
C4—C13	1.518 (3)	O15—H151	0.837
C4—H41	0.993	C16—H161	0.977
C5—C6	1.512 (3)	C16—H162	0.972
C5—H51	0.985	C16—H163	0.969
C6—N7	1.486 (3)	C17—H172	0.967
C6—C10	1.538 (3)	C17—H171	0.976
C6—C16	1.533 (3)	C17—H173	0.981
N7—N8	1.238 (3)	C18—H182	0.981
N8—N9	1.136 (3)	C18—H181	0.972
C10—O11	1.203 (3)	C18—H183	0.969
C2—O1—C5	106.47 (18)	C4—C13—O12	111.08 (19)
O1—C2—O3	103.17 (18)	C4—C13—C14	114.0 (2)
O1—C2—C17	110.9 (2)	O12—C13—C14	106.09 (19)
O3—C2—C17	110.6 (2)	C4—C13—H131	109.0
O1—C2—C18	107.4 (2)	O12—C13—H131	108.6
O3—C2—C18	109.4 (2)	C14—C13—H131	108.0
C17—C2—C18	114.7 (2)	C13—C14—O15	111.0 (2)
C2—O3—C4	109.49 (17)	C13—C14—H141	107.5
O3—C4—C5	104.14 (19)	O15—C14—H141	109.0
O3—C4—C13	109.17 (18)	C13—C14—H142	109.6
C5—C4—C13	113.14 (19)	O15—C14—H142	110.1
O3—C4—H41	109.8	H141—C14—H142	109.7
C5—C4—H41	111.0	C14—O15—H151	107.9
C13—C4—H41	109.5	C6—C16—H161	108.1
C4—C5—O1	103.26 (17)	C6—C16—H162	110.0
C4—C5—C6	113.20 (19)	H161—C16—H162	109.8
O1—C5—C6	108.46 (18)	C6—C16—H163	110.5
C4—C5—H51	110.9	H161—C16—H163	109.9
O1—C5—H51	110.7	H162—C16—H163	108.6
C6—C5—H51	110.1	C2—C17—H172	108.4
C5—C6—N7	105.21 (19)	C2—C17—H171	108.1
C5—C6—C10	108.20 (19)	H172—C17—H171	110.3
N7—C6—C10	108.84 (18)	C2—C17—H173	108.3
C5—C6—C16	111.2 (2)	H172—C17—H173	110.7
N7—C6—C16	109.39 (19)	H171—C17—H173	111.0
C10—C6—C16	113.6 (2)	C2—C18—H182	108.8
C6—N7—N8	114.5 (2)	C2—C18—H181	109.6
N7—N8—N9	172.4 (3)	H182—C18—H181	110.4
C6—C10—O11	123.4 (2)	C2—C18—H183	108.6
C6—C10—O12	116.6 (2)	H182—C18—H183	110.0
O11—C10—O12	120.0 (2)	H181—C18—H183	109.4
C10—O12—C13	119.50 (19)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C5—H51···O15^i	0.99	2.28	3.141 (4)	146
C13—H131···O11^ii	0.99	2.57	3.473 (4)	152
C16—H161···O11^iii	0.98	2.46	3.333 (4)	149
C16—H163···O11^ii	0.97	2.54	3.465 (4)	159
O15—H151···O1^iv	0.84	2.14	2.930 (4)	157
O15—H151···N7^iv	0.84	2.52	3.072 (4)	125

Symmetry codes: (i) −x+2, y+1/2, −z+3/2; (ii) x+1, y, z; (iii) x+1/2, −y+3/2, −z+1; (iv) −x+1, y−1/2, −z+3/2.