3,4-O-Isopropyl­idene-2-C-methyl-d-arabinono-1,5-lactone

Punzo, F.; Watkin, D.J.; Jenkinson, S.F.; Fleet, G.W.J.

doi:10.1107/S1600536804032659

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 61| Part 1| January 2005| Pages o127-o129

https://doi.org/10.1107/S1600536804032659

3,4-O-Isopropylidene-2-C-methyl-D-arabinono-1,5-lactone

Francesco Punzo,^a ^*‡ David J. Watkin,^b Sarah F. Jenkinson ^c and George W. J. Fleet ^c

^aDipartimento di Scienze Chimiche, Facoltà di Farmacia, Università di Catania, Viale A. Doria 6, 95125, Catania, Italy, ^bDepartment of Chemical Crystallography, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, and ^cDepartment of Organic Chemistry, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, England
^*Correspondence e-mail: francesco.punzo@chemistry.oxford.ac.uk

(Received 23 November 2004; accepted 9 December 2004; online 18 December 2004)

The title δ-lactone, C₉H₁₄O₅, formed in high diastereoselectivity by the Kiliani reaction of a protected 1-deoxyketose, adopts a boat conformation in which an OH group occupies a flagpole position.

Comment

Although sugars provide the largest group of readily available chiral building blocks and bioactive scaffolds (Lichtenthaler & Peters, 2004 ), the potential of the Kiliani ascension of ketoses to provide readily available branched scaffolds has only just begun to be developed (Hotchkiss et al., 2004 ; Shallard-Brown et al., 2004 Cowley et al., 2004 ; van Ameijde et al., 2004 ). While the range of commercially available ketoses is restricted, 1-deoxyketoses may readily be generated by addition of organometallic reagents to sugar lactones. As an extension to the branching chemistry of ketoses, the protected 1-deoxyketose (1) was treated with sodium cyanide and gave a single diastereomeric product. The crystal structure reported in this paper firmly establishes that the lactone (2) was formed; none of the epimeric lactone (3) was isolated.

The δ-lactone (2) (Fig. 1) adopts a boat conformation. While there are several example of fused 3,4-ketals of δ-lactones that adopt boat conformations (Bruce et al., 1990 ; Bichard et al., 1991 ; Beacham et al., 1991 ), very few of them have a flagpole substituent (Wheatley et al., 1994 ); the hydroxy group at atom C1 is clearly in a very hindered position, being additionally attached to a tertiary C atom. Nonetheless, as usually expected for sugar derivatives, hydrogen bonding occurs between molecules (Fig. 2 and Table 2).

Figure 1
The molecular structure of (2), with displacement ellipsoids drawn at the 50% probability level. H-atom radii are arbitrary.

Figure 2
Partial packing diagram of (2), viewed down the b axis. Hydrogen bonds are shown as dotted lines.

Experimental

The sugar was crystallized by dissolving it in diethyl ether, adding a few drops of cyclohexane and allowing the slow competitive evaporation of the two solvents until crystals formed.

Crystal data

C₉H₁₄O₅
M_r = 202.21
Monoclinic, P2₁
a = 7.7315 (3) Å
b = 6.2859 (3) Å
c = 10.4209 (6) Å
β = 102.1024 (17)°
V = 495.19 (4) Å³
Z = 2
D_x = 1.356 Mg m⁻³
Mo Kα radiation
Cell parameters from 1264 reflections
θ = 5–30°
μ = 0.11 mm⁻¹
T = 190 K
Needle, colourless
0.90 × 0.20 × 0.20 mm

Data collection

Nonius KappaCCD diffractometer
ω scans
2579 measured reflections
1527 independent reflections
1448 reflections with I > 2σ(I)
R_int = 0.018
θ_max = 30.0°
h = −10 → 10
k = −8 → 8
l = −14 → 14

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.031
wR(F²) = 0.078
S = 0.99
1527 reflections
127 parameters
H-atom parameters constrained
w = 1/[σ²(F²) + 0.04 + 0.06P], where P = [max(F_o²,0) + 2F_c²]/3
(Δ/σ)_max < 0.001
Δρ_max = 0.24 e Å⁻³
Δρ_min = −0.16 e Å⁻³

Table 1
Selected geometric parameters (Å, °)

C1—C2	1.5284 (18)
C1—C11	1.5318 (19)
C1—O13	1.4334 (15)
C1—C14	1.5237 (17)
C2—C3	1.5468 (18)
C2—O6	1.4261 (16)
C3—O4	1.4268 (16)
C3—C9	1.509 (2)
O4—C5	1.4312 (16)
C5—O6	1.4314 (16)
C5—C7	1.522 (2)
C5—C8	1.508 (2)
C9—O10	1.4581 (18)
O10—C11	1.3367 (16)
C11—O12	1.2124 (17)

C2—C1—C11	108.66 (10)
C2—C1—O13	106.76 (10)
C11—C1—O13	106.76 (11)
C2—C1—C14	111.22 (11)
C11—C1—C14	111.17 (12)
O13—C1—C14	112.04 (10)
C1—C2—C3	113.22 (11)
C1—C2—O6	107.54 (10)
C3—C2—O6	103.56 (10)
C2—C3—O4	104.50 (10)
C2—C3—C9	113.06 (11)
O4—C3—C9	109.33 (13)
C3—O4—C5	108.01 (10)
O4—C5—O6	103.66 (10)
O4—C5—C7	111.02 (13)
O6—C5—C7	110.14 (13)
O4—C5—C8	109.15 (13)
O6—C5—C8	108.63 (12)
C7—C5—C8	113.74 (14)
C5—O6—C2	106.26 (9)
C3—C9—O10	111.94 (11)
C9—O10—C11	119.10 (11)
C1—C11—O10	117.08 (12)
C1—C11—O12	124.42 (12)
O10—C11—O12	118.49 (13)

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O13—H3⋯O12ⁱ	0.94	1.87	2.8103 (14)	175
Symmetry code: (i) $[-x+1, y+{\script{1\over 2}}, -z+1]$ .

The multi-scan technique (Otwinowski & Minor, 1997 ) was used to correct for changes in the illuminated volume of the long needle crystal. In the absence of significant anomalous scattering effects, Friedel pairs were merged. The absolute configuration was assigned from the known configuration of the starting material in the synthesis. 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 = 0.97–1.01 Å and O—H = 0.94 Å), after which they were refined as riding, with U_iso(H) = 1.2U_eq(C) for those bonded to C atoms, and U_iso(H) = 0.05 Å² for the hydroxy group.

Data collection: COLLECT (Nonius, 1997 ); 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 I, global. DOI: https://doi.org/10.1107/S1600536804032659/cf6391sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536804032659/cf6391Isup2.hkl

Computing details top

Data collection: COLLECT (Nonius, 1997); 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.

3,4-O-Isoprpylidene-D-arabinono-1,5-lactone top

Crystal data top

C₉H₁₄O₅	F(000) = 216
M_r = 202.21	D_x = 1.356 Mg m⁻³
Monoclinic, P2₁	Mo Kα radiation, λ = 0.71073 Å
a = 7.7315 (3) Å	Cell parameters from 1264 reflections
b = 6.2859 (3) Å	θ = 5–30°
c = 10.4209 (6) Å	µ = 0.11 mm⁻¹
β = 102.1024 (17)°	T = 190 K
V = 495.19 (4) Å³	Needle, colourless
Z = 2	0.90 × 0.20 × 0.20 mm

Data collection top

Nonius KappaCCD diffractometer	R_int = 0.018
Graphite monochromator	θ_max = 30.0°, θ_min = 5.3°
ω scans	h = −10→10
2579 measured reflections	k = −8→8
1527 independent reflections	l = −14→14
1448 reflections with I > 2σ(I)

Refinement top

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)] = 0.031	H-atom parameters constrained
wR(F²) = 0.078	w = 1/[σ²(F²) + 0.04 + 0.06P], where P = (max(F_o²,0) + 2F_c²)/3
S = 0.99	(Δ/σ)_max = 0.000343
1527 reflections	Δρ_max = 0.24 e Å⁻³
127 parameters	Δρ_min = −0.16 e Å⁻³
1 restraint

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

	x	y	z	U_iso*/U_eq
C1	0.38045 (16)	0.7432 (2)	0.63155 (12)	0.0190
C2	0.28987 (16)	0.8696 (2)	0.72414 (13)	0.0206
C3	0.09390 (16)	0.8070 (2)	0.71356 (13)	0.0221
O4	0.08151 (12)	0.7559 (2)	0.84474 (9)	0.0292
C5	0.23824 (17)	0.8319 (3)	0.93106 (13)	0.0254
O6	0.37167 (12)	0.81163 (18)	0.85511 (9)	0.0231
C7	0.2183 (2)	1.0639 (3)	0.96718 (18)	0.0372
C8	0.2838 (2)	0.6857 (3)	1.04806 (15)	0.0382
C9	0.03922 (18)	0.6164 (3)	0.62648 (15)	0.0269
O10	0.17525 (13)	0.45193 (18)	0.64662 (11)	0.0274
C11	0.34223 (18)	0.5063 (2)	0.64601 (13)	0.0207
O12	0.45221 (14)	0.36653 (18)	0.65495 (10)	0.0273
O13	0.29608 (12)	0.80258 (19)	0.50056 (9)	0.0261
C14	0.57875 (16)	0.7863 (3)	0.65965 (13)	0.0244
H21	0.3019	1.0247	0.7105	0.0248*
H31	0.0179	0.9270	0.6816	0.0280*
H71	0.3345	1.1210	1.0175	0.0488*
H72	0.1220	1.0707	1.0178	0.0488*
H73	0.1804	1.1428	0.8838	0.0488*
H81	0.3965	0.7308	1.1071	0.0479*
H82	0.1833	0.7025	1.0914	0.0479*
H83	0.2915	0.5387	1.0159	0.0479*
H91	−0.0661	0.5480	0.6502	0.0333*
H92	0.0135	0.6646	0.5337	0.0333*
H141	0.6340	0.7072	0.5946	0.0310*
H142	0.5908	0.9419	0.6521	0.0310*
H143	0.6324	0.7393	0.7493	0.0310*
H3	0.3800	0.8152	0.4478	0.0500*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0200 (5)	0.0201 (6)	0.0178 (6)	0.0008 (5)	0.0061 (4)	0.0015 (4)
C2	0.0211 (5)	0.0193 (6)	0.0222 (6)	0.0010 (5)	0.0062 (4)	0.0002 (5)
C3	0.0193 (5)	0.0257 (6)	0.0218 (6)	0.0004 (5)	0.0057 (4)	−0.0008 (5)
O4	0.0230 (4)	0.0451 (7)	0.0214 (5)	−0.0088 (5)	0.0086 (4)	−0.0016 (5)
C5	0.0200 (5)	0.0368 (9)	0.0204 (6)	−0.0006 (6)	0.0068 (4)	−0.0051 (6)
O6	0.0194 (4)	0.0302 (5)	0.0205 (4)	0.0011 (4)	0.0063 (3)	−0.0042 (4)
C7	0.0321 (7)	0.0436 (10)	0.0381 (9)	0.0032 (7)	0.0127 (7)	−0.0163 (8)
C8	0.0360 (7)	0.0563 (11)	0.0230 (7)	0.0015 (8)	0.0075 (6)	0.0031 (7)
C9	0.0201 (5)	0.0299 (7)	0.0297 (7)	−0.0024 (6)	0.0029 (5)	−0.0053 (6)
O10	0.0261 (5)	0.0216 (5)	0.0355 (5)	−0.0041 (4)	0.0089 (4)	−0.0027 (4)
C11	0.0252 (6)	0.0219 (6)	0.0162 (5)	0.0010 (5)	0.0071 (4)	−0.0002 (5)
O12	0.0356 (5)	0.0228 (5)	0.0265 (5)	0.0061 (4)	0.0134 (4)	0.0020 (4)
O13	0.0256 (4)	0.0331 (5)	0.0205 (4)	0.0043 (5)	0.0069 (3)	0.0080 (4)
C14	0.0204 (5)	0.0275 (7)	0.0269 (6)	0.0003 (6)	0.0084 (5)	0.0015 (6)

Geometric parameters (Å, º) top

C1—C2	1.5284 (18)	C7—H72	0.999
C1—C11	1.5318 (19)	C7—H73	0.990
C1—O13	1.4334 (15)	C8—H81	0.997
C1—C14	1.5237 (17)	C8—H82	0.983
C2—C3	1.5468 (18)	C8—H83	0.989
C2—O6	1.4261 (16)	C9—O10	1.4581 (18)
C2—H21	0.992	C9—H91	0.996
C3—O4	1.4268 (16)	C9—H92	0.993
C3—C9	1.509 (2)	O10—C11	1.3367 (16)
C3—H31	0.971	C11—O12	1.2124 (17)
O4—C5	1.4312 (16)	O13—H3	0.938
C5—O6	1.4314 (16)	C14—H141	1.006
C5—C7	1.522 (2)	C14—H142	0.987
C5—C8	1.508 (2)	C14—H143	0.985
C7—H71	1.007

C2—C1—C11	108.66 (10)	H71—C7—H72	113.1
C2—C1—O13	106.76 (10)	C5—C7—H73	106.8
C11—C1—O13	106.76 (11)	H71—C7—H73	110.2
C2—C1—C14	111.22 (11)	H72—C7—H73	109.0
C11—C1—C14	111.17 (12)	C5—C8—H81	110.5
O13—C1—C14	112.04 (10)	C5—C8—H82	103.5
C1—C2—C3	113.22 (11)	H81—C8—H82	111.0
C1—C2—O6	107.54 (10)	C5—C8—H83	108.4
C3—C2—O6	103.56 (10)	H81—C8—H83	111.6
C1—C2—H21	110.6	H82—C8—H83	111.5
C3—C2—H21	111.1	C3—C9—O10	111.94 (11)
O6—C2—H21	110.6	C3—C9—H91	109.5
C2—C3—O4	104.50 (10)	O10—C9—H91	105.1
C2—C3—C9	113.06 (11)	C3—C9—H92	108.5
O4—C3—C9	109.33 (13)	O10—C9—H92	110.3
C2—C3—H31	109.9	H91—C9—H92	111.5
O4—C3—H31	110.2	C9—O10—C11	119.10 (11)
C9—C3—H31	109.7	C1—C11—O10	117.08 (12)
C3—O4—C5	108.01 (10)	C1—C11—O12	124.42 (12)
O4—C5—O6	103.66 (10)	O10—C11—O12	118.49 (13)
O4—C5—C7	111.02 (13)	C1—O13—H3	110.4
O6—C5—C7	110.14 (13)	C1—C14—H141	109.6
O4—C5—C8	109.15 (13)	C1—C14—H142	105.6
O6—C5—C8	108.63 (12)	H141—C14—H142	112.1
C7—C5—C8	113.74 (14)	C1—C14—H143	109.6
C5—O6—C2	106.26 (9)	H141—C14—H143	109.7
C5—C7—H71	110.2	H142—C14—H143	110.2
C5—C7—H72	107.3

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O13—H3···O12ⁱ	0.94	1.87	2.8103 (14)	175

Symmetry code: (i) −x+1, y+1/2, −z+1.

Footnotes

‡Visiting Scientist at the Department of Chemical Crystallography, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, England.

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