(2R,3S,4S,5R)-Meth­yl 5-cyano-2,3:4,5-di-O-isopropyl­idene-2,3,4,5-tetra­hydroxy­penta­noate

Glawar, A.; Mayes, B.A.; Watkin, D.; Fleet, G.W.J.

doi:10.1107/S1600536805023834

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 61| Part 8| August 2005| Pages o2727-o2729

https://doi.org/10.1107/S1600536805023834

(2R,3S,4S,5R)-Methyl 5-cyano-2,3:4,5-di-O-isopropylidene-2,3,4,5-tetrahydroxypentanoate

Andreas Glawar,^a Benjamin A. Mayes,^b David Watkin ^a ^* and George W. J. Fleet ^b

^aChemical Crystallography, Chemical Research Laboratory, University of Oxford, Oxford OX1 3TA, England, and ^bDepartment of Organic Chemistry, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, England
^*Correspondence e-mail: david.watkin@chem.ox.ac.uk

(Received 15 July 2005; accepted 25 July 2005; online 27 July 2005)

The title nitrile, C₁₃H₁₉NO₆, a formal oxidation product, was unexpectedly isolated during hydrogenation of an azide precursor in the presence of palladium black.

Comment

The azide group is synthetically important due to its ability to be reduced under a variety of conditions, thus permitting the controlled introduction of an amine functionality (Scriven & Turnbull, 1988 ). Further reagents for the reduction of azides to form amines and amides continue to be discovered (Fazio & Wong, 2003 ); ruthenium(III) has been shown to be an efficient promoter for the formation of amides from azides and thioacids (Shangguan et al., 2003 ). Although catalytic hydrogenation is a particularly useful method of azide reduction, often providing excellent yields whilst leaving other sensitive functionalities intact, surprising complications are still discovered; thus catalytic reduction of a series of bicyclic azides (RN₃) resulted in the formation of a number of azoamines (RN=N—NH₂) arising from simple addition of hydrogen to the terminal nitrogen of the azide (Beacham et al., 1998 ). When the azido ester (1) was hydrogenated in the presence of palladium black in 1,4-dioxan, the majority of the products were derived from the amino ester (2) (Mayes, Simon et al., 2004 ; Mayes, Stetz, Watterson et al., 2004 ; Mayes, Stetz, Ansell & Fleet, 2004 ). However, significant amounts of the nitrile (3) were also formed during the reduction; this is unexpected, since the formation of the nitrile appears to be a formal oxidation occurring under reducing conditions. Although previous examples of the catalytic decomposition of primary azides to nitriles have been reported (Hayashi et al., 1976 ; Kappe, 1990 ; Kotsuki et al., 1997 ), this is the first example of the formation of a nitrile being formed under hydrogenation conditions. The structure of the unexpected product (3), including the relative configuration at C-5 (atom C13) bearing the nitrile, was firmly established by X-ray crystallographic analysis (Fig. 1); the absolute configuration arises from the use of D-galactose as the original starting material.

The crystal structure of (3) is unexceptional, consisting of layers of molecules lying parallel to the ab plane (Fig. 2). One face of the layer is relatively flat and consists of nitrile and methyl groups facing an identical face of the next layer. The other face of the layer is pleated, with the methyl carboxylate groups of one layer interleaving with the corresponding groups on the adjacent face. There are no unexpectedly short O-methyl or N-methyl contacts.

Figure 1
The title compound with displacement ellipsoids drawn at the 50% probability level. The H atoms are shown as spheres of arbitary radius.

Figure 2
Packing diagram of (3), viewed along the b axis.

Experimental

The azide ester (1) was hydrogenated in the presence of palladium black in 1,4-dioxan (Mayes, Simon et al., 2004) and the title material crystallized from ethyl acetate/hexane.

Crystal data

C₁₃H₁₉NO₆
M_r = 285.30
Monoclinic, P 2₁
a = 10.4312 (3) Å
b = 5.4469 (1) Å
c = 13.0536 (5) Å
β = 93.4825 (10)°
V = 740.31 (4) Å³
Z = 2
D_x = 1.280 Mg m⁻³
Mo Kα radiation
Cell parameters from 1417 reflections
θ = 3–27°
μ = 0.10 mm⁻¹
T = 190 K
Block, colourless
0.80 × 0.50 × 0.30 mm

Data collection

Nonius KappaCCD diffractometer
ω scans
Absorption correction: multi-scan(DENZO/SCALEPACK; Otwinowski & Minor, 1997 )T_min = 0.87, T_max = 0.97
4978 measured reflections
1848 independent reflections
1848 reflections with I > −3σ(I)
R_int = 0.020
θ_max = 27.5°
h = −13 → 13
k = −6 → 7
l = −16 → 16

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.032
wR(F²) = 0.069
S = 0.99
1848 reflections
182 parameters
H-atom parameters constrained
w = 1/[σ²(F²) + (0.03P)² + 0.15P] where P = [max(F_o²,0) + 2F_c²]/3
(Δ/σ)_max < 0.001
Δρ_max = 0.18 e Å⁻³
Δρ_min = −0.15 e Å⁻³
Extinction correction: Larson (1970), equation 22
Extinction coefficient: 1.6 (3) × 10²

Table 1
Selected geometric parameters (Å, °)

C1—O2	1.456 (2)
O2—C3	1.3378 (18)
C3—O4	1.1996 (19)
C3—C5	1.521 (2)
C5—O6	1.4178 (18)
C5—C11	1.523 (2)
O6—C7	1.438 (2)
C7—C8	1.516 (2)
C7—C9	1.510 (2)
C7—O10	1.4461 (19)
O10—C11	1.4222 (18)
C11—C12	1.530 (2)
C12—C13	1.522 (2)
C12—O20	1.4235 (19)
C13—C14	1.490 (2)
C13—O16	1.420 (2)
C14—N15	1.136 (2)
O16—C17	1.443 (2)
C17—C18	1.513 (2)
C17—C19	1.510 (2)
C17—O20	1.439 (2)

C1—O2—C3	115.80 (12)
O2—C3—O4	123.87 (15)
O2—C3—C5	110.05 (12)
O4—C3—C5	126.05 (14)
C3—C5—O6	112.57 (12)
C3—C5—C11	113.63 (13)
O6—C5—C11	103.27 (12)
C5—O6—C7	109.03 (12)
O6—C7—C8	110.98 (15)
O6—C7—C9	108.91 (15)
C8—C7—C9	112.88 (15)
O6—C7—O10	105.41 (13)
C8—C7—O10	108.12 (13)
C9—C7—O10	110.29 (13)
C7—O10—C11	109.36 (12)
C5—C11—O10	103.10 (11)
C5—C11—C12	111.47 (12)
O10—C11—C12	110.98 (12)
C11—C12—C13	111.06 (12)
C11—C12—O20	110.43 (12)
C13—C12—O20	102.95 (11)
C12—C13—C14	112.31 (15)
C12—C13—O16	103.07 (13)
C14—C13—O16	111.41 (13)
C13—C14—N15	179.74 (19)
C13—O16—C17	107.76 (13)
O16—C17—C18	111.13 (16)
O16—C17—C19	108.22 (16)
C18—C17—C19	113.72 (16)
O16—C17—O20	104.95 (13)
C18—C17—O20	108.84 (14)
C19—C17—O20	109.61 (14)
C17—O20—C12	110.26 (12)

In the absence of significant anomalous scattering, Friedel pairs were merged, and the absolute configuration is arbitrarily assigned. The relatively large ratio of minimum to maximum corrections applied in the multiscan process (1:1.11) reflect changes in the illuminated volume of the crystal. The H atoms were all located in a difference map, but those attached to C 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 = 0.93–0.98 Å) and displacement parameters [U_iso(H) = 1.2–1.5U_eq(parent atom)], after which they were refined with riding constraints.

Data collection: COLLECT (Nonius, 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 3, global. DOI: https://doi.org/10.1107/S1600536805023834/cf6447sup1.cif

Structure factors: contains datablock 3. DOI: https://doi.org/10.1107/S1600536805023834/cf64473sup2.hkl

Computing details top

Data collection: COLLECT (Nonius, 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.

(2R,3S,4S,5R)-Methyl 5-cyano-2,3:4,5-di-O-isopropylidene-2,3,4,5- tetrahydroxypentanoate top

Crystal data top

C₁₃H₁₉NO₆	F(000) = 304
M_r = 285.30	D_x = 1.280 Mg m⁻³
Monoclinic, P2₁	Mo Kα radiation, λ = 0.71073 Å
a = 10.4312 (3) Å	Cell parameters from 1417 reflections
b = 5.4469 (1) Å	θ = 3–27°
c = 13.0536 (5) Å	µ = 0.10 mm⁻¹
β = 93.4825 (10)°	T = 190 K
V = 740.31 (4) Å³	Block, colourless
Z = 2	0.80 × 0.50 × 0.30 mm

Data collection top

Nonius KappaCCD diffractometer	1848 reflections with I > −3σ(I)
Graphite monochromator	R_int = 0.020
ω scans	θ_max = 27.5°, θ_min = 4.7°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −13→13
T_min = 0.87, T_max = 0.97	k = −6→7
4978 measured reflections	l = −16→16
1848 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)] = 0.032	w = 1/[σ²(F²) + ( 0.03P)² + 0.15P] where P = [max(F_o²,0) + 2F_c²]/3
wR(F²) = 0.069	(Δ/σ)_max = 0.000365
S = 0.99	Δρ_max = 0.18 e Å⁻³
1848 reflections	Δρ_min = −0.15 e Å⁻³
182 parameters	Extinction correction: Larson 1970 Crystallographic Computing eq 22
1 restraint	Extinction coefficient: 160 (30)
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	0.65764 (17)	0.6699 (5)	1.04143 (13)	0.0426
O2	0.71146 (10)	0.6530 (3)	0.94132 (9)	0.0372
C3	0.62621 (14)	0.6379 (3)	0.86076 (12)	0.0272
O4	0.51203 (10)	0.6423 (3)	0.86742 (9)	0.0389
C5	0.69562 (14)	0.6225 (3)	0.76183 (11)	0.0250
O6	0.61174 (11)	0.5653 (2)	0.67559 (9)	0.0284
C7	0.61457 (16)	0.3048 (3)	0.65796 (13)	0.0275
C8	0.49552 (15)	0.1822 (4)	0.69526 (14)	0.0354
C9	0.63211 (18)	0.2588 (4)	0.54558 (13)	0.0396
O10	0.72462 (10)	0.2156 (2)	0.71971 (9)	0.0296
C11	0.79554 (14)	0.4185 (3)	0.76192 (12)	0.0240
C12	0.90623 (14)	0.4853 (3)	0.69547 (12)	0.0249
C13	1.00643 (15)	0.2819 (3)	0.69727 (13)	0.0289
C14	1.07823 (16)	0.2771 (4)	0.60205 (14)	0.0384
N15	1.13337 (18)	0.2738 (4)	0.52965 (14)	0.0613
O16	1.08841 (12)	0.3413 (2)	0.78462 (9)	0.0320
C17	1.09141 (16)	0.6051 (3)	0.79421 (13)	0.0291
C18	1.20660 (15)	0.7121 (4)	0.74499 (14)	0.0371
C19	1.0856 (2)	0.6692 (5)	0.90635 (14)	0.0486
O20	0.97635 (10)	0.6886 (2)	0.73847 (9)	0.0317
H11	0.7301	0.6879	1.0916	0.0619*
H12	0.6097	0.5201	1.0535	0.0644*
H13	0.6005	0.8096	1.0434	0.0632*
H51	0.7344	0.7826	0.7521	0.0275*
H81	0.5034	0.0085	0.6846	0.0524*
H82	0.4877	0.2168	0.7692	0.0517*
H83	0.4225	0.2499	0.6549	0.0524*
H91	0.6504	0.0870	0.5351	0.0585*
H92	0.7051	0.3564	0.5250	0.0583*
H93	0.5536	0.3026	0.5039	0.0582*
H111	0.8278	0.3770	0.8310	0.0273*
H121	0.8747	0.5279	0.6267	0.0290*
H131	0.9680	0.1242	0.7065	0.0337*
H181	1.2034	0.8935	0.7523	0.0530*
H182	1.2828	0.6540	0.7793	0.0551*
H183	1.2058	0.6714	0.6734	0.0540*
H191	1.0804	0.8469	0.9130	0.0725*
H192	1.1623	0.6100	0.9426	0.0726*
H193	1.0081	0.5924	0.9306	0.0724*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0387 (9)	0.0557 (12)	0.0331 (8)	0.0046 (10)	0.0010 (7)	−0.0069 (10)
O2	0.0275 (5)	0.0516 (8)	0.0322 (6)	0.0015 (6)	−0.0013 (4)	−0.0073 (6)
C3	0.0267 (7)	0.0211 (8)	0.0336 (8)	0.0008 (7)	0.0005 (6)	−0.0007 (7)
O4	0.0250 (5)	0.0508 (8)	0.0408 (6)	0.0015 (6)	0.0026 (5)	−0.0050 (7)
C5	0.0230 (7)	0.0199 (8)	0.0318 (8)	−0.0001 (6)	−0.0009 (6)	0.0025 (7)
O6	0.0312 (6)	0.0210 (6)	0.0322 (6)	0.0029 (5)	−0.0045 (5)	0.0017 (5)
C7	0.0261 (8)	0.0215 (8)	0.0346 (8)	0.0015 (6)	−0.0016 (6)	0.0014 (7)
C8	0.0285 (7)	0.0304 (9)	0.0473 (10)	−0.0042 (8)	0.0022 (7)	−0.0009 (8)
C9	0.0445 (10)	0.0384 (10)	0.0357 (9)	−0.0002 (9)	0.0008 (7)	−0.0034 (8)
O10	0.0265 (5)	0.0184 (6)	0.0431 (6)	−0.0008 (5)	−0.0050 (5)	0.0031 (5)
C11	0.0243 (7)	0.0188 (7)	0.0288 (7)	−0.0002 (6)	0.0000 (6)	0.0030 (6)
C12	0.0251 (7)	0.0200 (8)	0.0296 (7)	0.0011 (6)	0.0018 (6)	0.0025 (6)
C13	0.0248 (7)	0.0244 (8)	0.0376 (8)	0.0005 (7)	0.0014 (6)	−0.0035 (7)
C14	0.0315 (8)	0.0381 (11)	0.0455 (10)	−0.0015 (8)	0.0024 (7)	−0.0165 (9)
N15	0.0566 (10)	0.0740 (15)	0.0553 (11)	−0.0094 (11)	0.0200 (9)	−0.0304 (11)
O16	0.0331 (6)	0.0235 (6)	0.0385 (7)	0.0049 (5)	−0.0052 (5)	0.0002 (5)
C17	0.0284 (8)	0.0234 (8)	0.0352 (8)	0.0021 (6)	−0.0006 (7)	−0.0018 (7)
C18	0.0252 (7)	0.0365 (10)	0.0491 (10)	−0.0020 (8)	−0.0008 (7)	−0.0053 (8)
C19	0.0621 (12)	0.0453 (12)	0.0385 (10)	−0.0004 (11)	0.0035 (9)	−0.0087 (10)
O20	0.0234 (5)	0.0189 (6)	0.0525 (7)	0.0002 (5)	0.0003 (5)	0.0012 (5)

Geometric parameters (Å, º) top

C1—O2	1.456 (2)	O10—C11	1.4222 (18)
C1—H11	0.975	C11—C12	1.530 (2)
C1—H12	0.975	C11—H111	0.970
C1—H13	0.968	C12—C13	1.522 (2)
O2—C3	1.3378 (18)	C12—O20	1.4235 (19)
C3—O4	1.1996 (19)	C12—H121	0.965
C3—C5	1.521 (2)	C13—C14	1.490 (2)
C5—O6	1.4178 (18)	C13—O16	1.420 (2)
C5—C11	1.523 (2)	C13—H131	0.958
C5—H51	0.973	C14—N15	1.136 (2)
O6—C7	1.438 (2)	O16—C17	1.443 (2)
C7—C8	1.516 (2)	C17—C18	1.513 (2)
C7—C9	1.510 (2)	C17—C19	1.510 (2)
C7—O10	1.4461 (19)	C17—O20	1.439 (2)
C8—H81	0.961	C18—H181	0.993
C8—H82	0.992	C18—H182	0.943
C8—H83	0.972	C18—H183	0.960
C9—H91	0.966	C19—H191	0.974
C9—H92	0.980	C19—H192	0.960
C9—H93	0.985	C19—H193	0.980

O2—C1—H11	106.5	O10—C11—C12	110.98 (12)
O2—C1—H12	108.7	C5—C11—H111	111.7
H11—C1—H12	111.2	O10—C11—H111	108.8
O2—C1—H13	110.2	C12—C11—H111	110.6
H11—C1—H13	110.9	C11—C12—C13	111.06 (12)
H12—C1—H13	109.3	C11—C12—O20	110.43 (12)
C1—O2—C3	115.80 (12)	C13—C12—O20	102.95 (11)
O2—C3—O4	123.87 (15)	C11—C12—H121	111.0
O2—C3—C5	110.05 (12)	C13—C12—H121	112.6
O4—C3—C5	126.05 (14)	O20—C12—H121	108.5
C3—C5—O6	112.57 (12)	C12—C13—C14	112.31 (15)
C3—C5—C11	113.63 (13)	C12—C13—O16	103.07 (13)
O6—C5—C11	103.27 (12)	C14—C13—O16	111.41 (13)
C3—C5—H51	106.5	C12—C13—H131	111.2
O6—C5—H51	109.5	C14—C13—H131	108.9
C11—C5—H51	111.3	O16—C13—H131	109.8
C5—O6—C7	109.03 (12)	C13—C14—N15	179.74 (19)
O6—C7—C8	110.98 (15)	C13—O16—C17	107.76 (13)
O6—C7—C9	108.91 (15)	O16—C17—C18	111.13 (16)
C8—C7—C9	112.88 (15)	O16—C17—C19	108.22 (16)
O6—C7—O10	105.41 (13)	C18—C17—C19	113.72 (16)
C8—C7—O10	108.12 (13)	O16—C17—O20	104.95 (13)
C9—C7—O10	110.29 (13)	C18—C17—O20	108.84 (14)
C7—C8—H81	107.9	C19—C17—O20	109.61 (14)
C7—C8—H82	110.2	C17—C18—H181	108.1
H81—C8—H82	110.0	C17—C18—H182	109.7
C7—C8—H83	106.8	H181—C18—H182	108.7
H81—C8—H83	111.5	C17—C18—H183	111.3
H82—C8—H83	110.3	H181—C18—H183	109.0
C7—C9—H91	109.5	H182—C18—H183	110.0
C7—C9—H92	108.5	C17—C19—H191	108.8
H91—C9—H92	108.9	C17—C19—H192	108.5
C7—C9—H93	110.5	H191—C19—H192	109.9
H91—C9—H93	108.8	C17—C19—H193	107.3
H92—C9—H93	110.6	H191—C19—H193	110.1
C7—O10—C11	109.36 (12)	H192—C19—H193	112.1
C5—C11—O10	103.10 (11)	C17—O20—C12	110.26 (12)
C5—C11—C12	111.47 (12)

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