3-Azido-3-deoxy-2,2′:5,6-di-O-iso­propyl­idene-2-C-hydro­xmethyl-d-gulono-1,4-lactone

Harding, C.C.; Shallard-Brown, H.; Watkin, D.J.; Soengas, R.; Fleet, G.W.J.

doi:10.1107/S1600536804029113

organic compounds

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ISSN: 2056-9890

Volume 60| Part 12| December 2004| Pages o2334-o2336

https://doi.org/10.1107/S1600536804029113

3-Azido-3-deoxy-2,2′:5,6-di-O-isopropylidene-2-C-hydroxmethyl-D-gulono-1,4-lactone

Christopher C. Harding,^a ^* Howard Shallard-Brown,^a David J. Watkin,^a Raquel Soengas ^b and George W. J. Fleet ^b

^aDepartment of Chemical Crystallography, Chemical Research Laboratory, Oxford University, Mansfield Road, Oxford OX1 3TA, England, and ^bDepartment of Organic Chemistry, Chemical Research Laboratory, Oxford University, Mansfield Road, Oxford OX1 3TA, England
^*Correspondence e-mail: christopher.harding@seh.ox.ac.uk

(Received 22 October 2004; accepted 10 November 2004; online 20 November 2004)

The title azidolactone, C₁₃H₁₉O₆N₃, formed by S_N2 displacement of the trifluoromethanesulfonate with sodium azide, is the first example of a branched β-sugar amino acid scaffold.

Comment

Gellman (Lai & Gellman, 2003 ; Hayen et al., 2004 ) and Seebach (Lelais & Seebach, 2003 ; Rueping et al., 2004 ) have pioneered studies on the exploitation of β-amino acids in their adoption of secondary structural features in short chains. Although sugar amino acids (SAA) have been extensively investigated as peptidomimetics and dipeptide isosteres (Schweizer, 2002 ; Chakraborty et al., 2004 ), there have been very few studies of β-SAAs (Jenkinson & Fleet, 2004 ; Johnson et al., 2004 ), even though some oxetane-derived β-SAAs exhibited novel helical structures (Barker et al., 2001 ). This paper reports the structure of the β-azidolactone, (4), which is a novel β-SAA scaffold containing a branched carbon chain.

D-Fructose may be readily converted into the diacetonide (2) (Hotchkiss et al., 2004 ); esterification of (2) with triflic anhydride gave the corresponding stable trifluoromethanesulfonate. Reaction of (3) with sodium azide in DMF gave an organic azide in good yield. The structure of this azide is fraught with uncertainties; the trifluoromethanesulfonate in (3) has two β-O atoms and the adjacent α-C atom is trisubstituted, so the efficiency of the S_N2 reaction is surprising. There is considerable ambiguity in the stereochemistry of the product, since there may well be neighbouring group participation by the O atom; it is also possible that some rearrangement that maintained the same connectivity of CH atoms may have occurred. However, X-ray crystallographic analysis of the product of the reaction showed that the anticipated inverted azide, (4), had indeed been produced.

Figure 1
The title molecule at 120 K, with displacement ellipsoids drawn at the 50% probability level. The large ellipsoids at atoms 07, C9 and C10 are discussed in the text. H atoms are shown as spheres of arbitrary radii.

Figure 2
The disordered fragment of the title molecule at 120 K, displayed as a `split atom' model. Even with firm anisotropic displacement parameter similarity restraints, the ellipsoids do not conform to any reasonable physical model.

Figure 3
F_o electron density map viewed perpendicular to the line through atoms O7a and O7b, computed excluding phasing information derived from these two partial atoms. There are no distinct lobes near the two atom positions proposed by the `split atom' refinement, suggesting that there still remains substantial dynamic disorder.

Figure 4
Packing diagram of the title compound, viewed along the b axis.

Experimental

The full preparative method is not available for publication as yet. The sample was crystallized from diethyl ether by inward diffusion of n-hexane to give lath-shaped colourless crystals.

Crystal data

C₁₃H₁₉N₃O₆
M_r = 313.31
Monoclinic, P2₁
a = 8.7755 (2) Å
b = 7.6452 (2) Å
c = 12.2232 (3) Å
β = 106.9659 (11)°
V = 784.37 (3) Å³
Z = 2
D_x = 1.326 Mg m⁻³
Mo Kα radiation
Cell parameters from 1734 reflections
θ = 5–27°
μ = 0.11 mm⁻¹
T = 120 K
Lath, colourless
0.30 × 0.20 × 0.10 mm

Data collection

Nonius KappaCCD diffractometer
ω scans
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997 ) T_min = 0.98, T_max = 0.99
3320 measured reflections
1869 independent reflections
1655 reflections with I > 2σ(I)
R_int = 0.015
θ_max = 27.5°
h = −11 → 11
k = −9 → 9
l = −15 → 15

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.045
wR(F²) = 0.109
S = 0.93
1866 reflections
200 parameters
H-atom parameters constrained
w = 1/[σ²(F) + (0.0522p)² + 0.571p], where p = [max(F_o²,0) + 2F_c²]/3
(Δ/σ)_max < 0.001
Δρ_max = 0.65 e Å⁻³
Δρ_min = −0.42 e Å⁻³
Extinction correction: Larson (1970 )
Extinction coefficient: 3.0 (5) × 10²

Table 1
Selected interatomic distances (Å)

O5—C6	1.433 (3)
C6—O7	1.370 (5)
C6—C9	1.503 (6)
C6—C10	1.486 (7)
O7—C8	1.384 (4)

An initial data set was collected at 190 K. This gave reasonable refinement [N_measured = 2766, R_int = 0.02, N_ref = 1748, R_w(2σ) = 0.081, R(2σ) = 0.034], though atoms O7, C9 and C10 had very elongated displacement ellipsoids. It was unclear whether the C6/O7/C9/C10 fragment should be modelled with large anisotropic displacement parameters (ADPs) or with `split atoms'. Refinement was continued with this fragment represented by `split atoms'. However, the ADPs could not be explained by a rational physical model. As with the unsplit model, the bond lengths deviated unacceptably from averages drawn by MOGUL (Bruno et al., 2004 ) from the Cambridge Structural Database (CSD; Version 5.25; Allen, 2002 ), even with the application of firm bond length similarity restraints.

In order to resolve this issue, data were recollected at 120 K. It is the result of this refinement that is reported in the CIF. Even at this temperature, the ADPs of the problematic group remained large, though not as large as in the 190 K data set. Both the large ADP and the `split atom' refinements continued to give unacceptable bond lengths and ellipsoids (see Fig. 2). Fig. 3, plotted with MCE (Hušák & Kratochvíl, 2003 ), shows the observed electron density perpendicular to the line connecting atoms O7a and O7b. The map is phased by all of the structure except these two atoms, which are included for illustrative purposes at the positions they refine to in the `split atom' model. There is a smooth transition in electron density between the two sites, with no evident build-up of density at either site.

One interpretation of these observations is that neither the split atom model nor the large ADP model really represents what is occurring in this structure. It is clearly something more complicated than simply having the envelope flap (O7/O7a) distributed over two sites on opposite sides of a plane through the other ring atoms. Of 29 structures in the CSD containing this moiety some clearly have the atom corresponding to O7 as the `flap', some have C6 as the flap, but there are also a number in which no four atoms form a convincing plane. It seems that, even in the solid state, there is a continuum between an O-flap and a C-flap geometry. The amount of material available was insufficient to enable low-temperature solid-state NMR measurements to be carried out.

For the large ADP model, all H atoms were seen in the difference electron density map (even those on the highly anisotropic C9 and C10). Their positions and U_iso(H) values were regularized by several cycles of refinement using slack restraints, after which the refinement was completed using `riding' constraints and all reflections with I > −3σ(I). Fig. 4 is a packing diagram showing an alternation of highly mobile and highly ordered groups lying in a plane at approximately c/2.

Data collection: COLLECT (Nonius, 1997–2001 ); cell refinement: 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

Crystal structure: contains datablocks global, 4. DOI: https://doi.org/10.1107/S1600536804029113/lh6302sup1.cif

Structure factors: contains datablock 4. DOI: https://doi.org/10.1107/S1600536804029113/lh63024sup2.hkl

Computing details top

Data collection: COLLECT (Nonius, 1997–2001); cell refinement: DENZO/SCALEPACK; data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: User-defined structure solution (reference?); 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.

3-Azido-3-deoxy-2,2':5,6-di-O-isopropylidene-2-C-hydroxmethyl-D– gulono-1,4-lactone top

Crystal data top

C₁₃H₁₉N₃O₆	F(000) = 332
M_r = 313.31	D_x = 1.326 Mg m⁻³
Monoclinic, P2₁	Mo Kα radiation, λ = 0.71073 Å
a = 8.7755 (2) Å	Cell parameters from 1734 reflections
b = 7.6452 (2) Å	θ = 5–27°
c = 12.2232 (3) Å	µ = 0.11 mm⁻¹
β = 106.9659 (11)°	T = 120 K
V = 784.37 (3) Å³	Plate, colourless
Z = 2	0.30 × 0.20 × 0.10 mm

Data collection top

Nonius KappaCCD diffractometer	1655 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.015
ω scans	θ_max = 27.5°, θ_min = 5.2°
Absorption correction: multi-scan DENZO/SCALEPACK (Otwinowski & Minor, 1997)	h = −11→11
T_min = 0.98, T_max = 0.99	k = −9→9
3320 measured reflections	l = −15→15
1869 independent reflections

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.045	Method: SHELXL97 (Sheldrick, 1997); w = 1/[σ²(f) + (0.0522p)² + 0.571p], where p = [max(F₀²,0) + 2F_c²]/3
wR(F²) = 0.109	(Δ/σ)_max = 0.000326
S = 0.93	Δρ_max = 0.65 e Å⁻³
1866 reflections	Δρ_min = −0.42 e Å⁻³
200 parameters	Extinction correction: Larson 1970 Crystallographic Computing eq 22
1 restraint	Extinction coefficient: 300 (50)
Primary atom site location: structure-invariant direct methods

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
C1	0.8173 (3)	0.1205 (4)	0.8704 (2)	0.0207
C2	0.8728 (3)	0.0356 (4)	0.9895 (2)	0.0197
C3	0.7808 (3)	0.1387 (4)	1.0574 (2)	0.0214
C4	0.8684 (3)	0.1553 (4)	1.1835 (2)	0.0253
O5	0.8788 (3)	−0.0165 (3)	1.22982 (16)	0.0306
C6	0.8328 (4)	−0.0098 (5)	1.3330 (3)	0.0349
O7	0.7463 (5)	0.1409 (5)	1.3271 (3)	0.0777
C8	0.7788 (4)	0.2612 (4)	1.2524 (3)	0.0345
C9	0.9801 (6)	0.0021 (9)	1.4333 (3)	0.0762
C10	0.7390 (8)	−0.1702 (9)	1.3373 (5)	0.0891
O11	0.7642 (2)	0.3122 (3)	1.00698 (16)	0.0251
C12	0.7805 (3)	0.3076 (4)	0.8996 (2)	0.0234
O13	0.7649 (3)	0.4350 (3)	0.84141 (18)	0.0315
N14	0.8584 (3)	−0.1555 (3)	0.9887 (2)	0.0219
N15	0.7245 (3)	−0.2124 (4)	0.9845 (2)	0.0267
N16	0.6106 (4)	−0.2828 (4)	0.9831 (3)	0.0454
O17	0.6748 (2)	0.0412 (3)	0.80306 (15)	0.0223
C18	0.6968 (3)	−0.0131 (4)	0.6948 (2)	0.0246
O19	0.8643 (2)	−0.0228 (3)	0.71573 (16)	0.0250
C20	0.9322 (3)	0.1103 (4)	0.7966 (2)	0.0252
C21	0.6301 (4)	−0.1943 (5)	0.6674 (3)	0.0338
C22	0.6235 (4)	0.1233 (5)	0.6046 (3)	0.0408
H21	0.9848	0.0640	1.0229	0.0240*
H31	0.6712	0.0884	1.0445	0.0251*
H41	0.9753	0.2039	1.1948	0.0304*
H81	0.8497	0.3528	1.2967	0.0438*
H82	0.6789	0.3123	1.2055	0.0432*
H91	0.9408	0.0093	1.5009	0.0912*
H92	1.0438	−0.1057	1.4370	0.0913*
H93	1.0444	0.1073	1.4251	0.0920*
H101	0.7105	−0.1659	1.4094	0.1170*
H102	0.8053	−0.2750	1.3328	0.1173*
H103	0.6413	−0.1563	1.2703	0.1167*
H201	1.0400	0.0778	0.8411	0.0321*
H202	0.9326	0.2218	0.7573	0.0317*
H211	0.6543	−0.2349	0.5979	0.0399*
H212	0.6785	−0.2742	0.7300	0.0403*
H213	0.5151	−0.1924	0.6528	0.0409*
H221	0.6405	0.1021	0.5300	0.0487*
H222	0.6603	0.2431	0.6279	0.0489*
H223	0.5076	0.1206	0.5922	0.0491*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0206 (13)	0.0191 (13)	0.0222 (12)	−0.0012 (11)	0.0061 (10)	−0.0002 (11)
C2	0.0206 (13)	0.0182 (13)	0.0199 (12)	−0.0019 (11)	0.0051 (10)	−0.0009 (10)
C3	0.0215 (13)	0.0186 (15)	0.0256 (13)	0.0009 (11)	0.0090 (10)	−0.0002 (11)
C4	0.0289 (15)	0.0252 (16)	0.0223 (12)	−0.0017 (12)	0.0084 (11)	−0.0032 (12)
O5	0.0445 (12)	0.0282 (11)	0.0235 (9)	0.0034 (10)	0.0166 (9)	0.0017 (9)
C6	0.0495 (19)	0.0342 (17)	0.0279 (14)	−0.0014 (17)	0.0220 (13)	0.0011 (14)
O7	0.118 (3)	0.069 (2)	0.080 (2)	0.051 (2)	0.082 (2)	0.0350 (19)
C8	0.0481 (19)	0.0326 (18)	0.0262 (14)	0.0028 (15)	0.0161 (14)	−0.0044 (13)
C9	0.086 (3)	0.109 (5)	0.0317 (18)	0.019 (4)	0.013 (2)	−0.001 (3)
C10	0.120 (5)	0.089 (5)	0.080 (4)	−0.047 (4)	0.064 (4)	−0.009 (3)
O11	0.0307 (11)	0.0208 (11)	0.0253 (9)	0.0038 (9)	0.0106 (8)	−0.0001 (8)
C12	0.0244 (14)	0.0229 (15)	0.0225 (12)	−0.0005 (12)	0.0063 (10)	−0.0013 (12)
O13	0.0395 (12)	0.0238 (11)	0.0315 (11)	0.0066 (10)	0.0106 (9)	0.0059 (9)
N14	0.0187 (12)	0.0206 (12)	0.0266 (11)	−0.0017 (10)	0.0069 (9)	−0.0019 (10)
N15	0.0279 (13)	0.0217 (12)	0.0320 (13)	0.0018 (11)	0.0109 (10)	−0.0010 (10)
N16	0.0334 (15)	0.0299 (16)	0.078 (2)	−0.0116 (13)	0.0236 (15)	−0.0071 (16)
O17	0.0209 (9)	0.0272 (11)	0.0189 (8)	−0.0018 (8)	0.0057 (7)	−0.0032 (8)
C18	0.0245 (13)	0.0301 (15)	0.0186 (11)	0.0025 (13)	0.0053 (10)	−0.0021 (12)
O19	0.0254 (10)	0.0270 (11)	0.0236 (9)	0.0018 (9)	0.0089 (7)	−0.0026 (8)
C20	0.0287 (14)	0.0239 (14)	0.0259 (13)	−0.0041 (13)	0.0125 (11)	−0.0043 (12)
C21	0.0341 (16)	0.0377 (19)	0.0289 (14)	−0.0073 (15)	0.0084 (12)	−0.0114 (14)
C22	0.0436 (18)	0.054 (2)	0.0262 (14)	0.0194 (18)	0.0116 (13)	0.0104 (15)

Geometric parameters (Å, º) top

C1—C2	1.538 (4)	C9—H93	1.004
C1—C12	1.531 (4)	C10—H101	0.984
C1—O17	1.417 (3)	C10—H102	1.001
C1—C20	1.539 (3)	C10—H103	1.004
C2—C3	1.533 (4)	O11—C12	1.362 (3)
C2—N14	1.466 (4)	C12—O13	1.190 (4)
C2—H21	0.973	N14—N15	1.240 (3)
C3—C4	1.514 (4)	N15—N16	1.131 (4)
C3—O11	1.452 (3)	O17—C18	1.452 (3)
C3—H31	1.005	C18—O19	1.419 (3)
C4—O5	1.423 (4)	C18—C21	1.504 (5)
C4—C8	1.538 (4)	C18—C22	1.518 (4)
C4—H41	0.981	O19—C20	1.422 (3)
O5—C6	1.433 (3)	C20—H201	0.976
C6—O7	1.370 (5)	C20—H202	0.979
C6—C9	1.503 (6)	C21—H211	0.984
C6—C10	1.486 (7)	C21—H212	0.974
O7—C8	1.384 (4)	C21—H213	0.973
C8—H81	0.987	C22—H221	0.980
C8—H82	0.979	C22—H222	0.985
C9—H91	0.985	C22—H223	0.984
C9—H92	0.989

C2—C1—C12	101.8 (2)	C6—C9—H93	109.937
C2—C1—O17	110.6 (2)	H91—C9—H93	112.584
C12—C1—O17	109.0 (2)	H92—C9—H93	110.192
C2—C1—C20	116.9 (2)	C6—C10—H101	107.044
C12—C1—C20	113.8 (2)	C6—C10—H102	108.749
O17—C1—C20	104.8 (2)	H101—C10—H102	112.303
C1—C2—C3	102.9 (2)	C6—C10—H103	103.516
C1—C2—N14	114.3 (2)	H101—C10—H103	110.346
C3—C2—N14	117.3 (2)	H102—C10—H103	114.253
C1—C2—H21	107.763	C3—O11—C12	111.1 (2)
C3—C2—H21	106.585	C1—C12—O11	109.7 (2)
N14—C2—H21	107.444	C1—C12—O13	128.4 (2)
C2—C3—C4	113.8 (2)	O11—C12—O13	121.9 (3)
C2—C3—O11	104.1 (2)	C2—N14—N15	115.4 (2)
C4—C3—O11	108.3 (2)	N14—N15—N16	172.0 (3)
C2—C3—H31	110.457	C1—O17—C18	108.8 (2)
C4—C3—H31	111.708	O17—C18—O19	104.9 (2)
O11—C3—H31	108.048	O17—C18—C21	108.6 (2)
C3—C4—O5	106.4 (2)	O19—C18—C21	107.9 (2)
C3—C4—C8	114.4 (2)	O17—C18—C22	109.0 (2)
O5—C4—C8	104.6 (2)	O19—C18—C22	111.4 (2)
C3—C4—H41	110.832	C21—C18—C22	114.6 (3)
O5—C4—H41	110.245	C18—O19—C20	106.8 (2)
C8—C4—H41	110.109	C1—C20—O19	103.3 (2)
C4—O5—C6	108.4 (2)	C1—C20—H201	112.385
O5—C6—O7	106.2 (3)	O19—C20—H201	110.314
O5—C6—C9	108.9 (3)	C1—C20—H202	109.886
O7—C6—C9	108.9 (4)	O19—C20—H202	110.026
O5—C6—C10	107.6 (3)	H201—C20—H202	110.659
O7—C6—C10	113.0 (4)	C18—C21—H211	108.339
C9—C6—C10	112.0 (4)	C18—C21—H212	110.490
C6—O7—C8	112.1 (2)	H211—C21—H212	109.050
C4—C8—O7	104.4 (3)	C18—C21—H213	110.056
C4—C8—H81	109.437	H211—C21—H213	108.699
O7—C8—H81	109.119	H212—C21—H213	110.158
C4—C8—H82	113.777	C18—C22—H221	114.558
O7—C8—H82	109.278	C18—C22—H222	113.225
H81—C8—H82	110.606	H221—C22—H222	107.285
C6—C9—H91	105.028	C18—C22—H223	107.279
C6—C9—H92	109.043	H221—C22—H223	106.580
H91—C9—H92	109.895	H222—C22—H223	107.508

Acknowledgements

Financial support (to RS) provided through the European Community's Human Potential Programme under contract HPRN-CT-2002-00173 is gratefully acknowledged.

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