2-C-Methyl-d-allono-1,4-lactone

Harding, C.C.; Watkin, D.J.; Sawyer, N.K.; Jenkinson, S.F.; Fleet, G.W.J.

doi:10.1107/S1600536805012328

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 61| Part 5| May 2005| Pages o1472-o1474

https://doi.org/10.1107/S1600536805012328

2-C-Methyl-D-allono-1,4-lactone

Christopher C. Harding,^a ^* David J. Watkin,^a Nicola K. Sawyer,^b Sarah F. Jenkinson ^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 15 March 2005; accepted 19 April 2005; online 27 April 2005)

The relative stereochemistry at the quaternary C atom in the title compound, C₇H₁₂O₆, a 1,4-lactone formed from a protected D-ribonolactone, is firmly established by X-ray crystallographic analysis.

Comment

The potential of the Kiliani ascension of ketoses to provide readily available branched scaffolds has been recognized (Harding et al., 2005 ; Hotchkiss et al., 2004 ; Shallard-Brown et al., 2004 ); such materials are likely to be of value as a new family of chirons. A further class of branched carbohydrate building blocks may be available from the reaction of cyanide with 1-deoxyketoses, themselves prepared by addition of organometallic reagents to sugar lactones.

For example, when such a sequence was performed on the acetonide of D-erythronolactone (1), 2-C-methyl-D-arabinonolactone (2) was formed (Punzo et al., 2005 ), in which the 2,3-diol unit is trans; none of the epimeric ribonolactone was isolated during the course of the synthesis. When a similar synthetic sequence was applied to the protected D-ribonolactone (3), the crystalline product (4) was isolated, in which the 2,3-diol unit is cis. There is no reliable spectroscopic technique to establish the relative stereochemistry in (4), so its relative configuration was unambiguously defined by X-ray crystallographic analysis; the absolute stereochemistry was defined by the use of D-ribonolactone as a starting material. The reactions are being studied further in order to understand the difference in the stereochemical outcome of the two sequences.

The crystal structure is made up of layers of strongly hydrogen-bonded molecules which lie in the ab plane. The layers are made up of columns of molecules along the b axis held together by a zigzag chain of hydrogen bonds, which are in turn tied together by a helical hydrogen-bonding network (Figs. 3 and 4).

Figure 1
The molecular structure of (4

), with displacement ellipsoids drawn at the 50% probability level.

Figure 2
Packing diagram for the title compound, viewed down the b axis. Dashed lines indicate hydrogen bonds.

Figure 3
Hydrogen bonding (dashed lines): the zigzag network, forming columns of molecules.

Figure 4
Hydrogen bonding (dashed lines): the helical network which links the columns of molecules together to form a sheet.

Experimental

Crystals of the title compound were obtained by evaporation of a solution in an ethyl acetate/cyclohexane mixture, yielding colourless crystals. The full synthetic procedure will be published separately (Jenkinson et al., 2005 ).

Crystal data

C₇H₁₂O₆
M_r = 192.17
Monoclinic, P2₁
a = 6.1521 (5) Å
b = 7.5495 (7) Å
c = 9.3055 (8) Å
β = 98.501 (5)°
V = 427.45 (6) Å³
Z = 2
D_x = 1.493 Mg m⁻³
Mo Kα radiation
Cell parameters from 1283 reflections
θ = 5–27°
μ = 0.13 mm⁻¹
T = 190 K
Block, colourless
0.20 × 0.10 × 0.10 mm

Data collection

Nonius KappaCCD diffractometer
ω scans
Absorption correction: none
2940 measured reflections
1025 independent reflections
905 reflections with I > 2σ(I)
R_int = 0.026
θ_max = 27.5°
h = −7 → 7
k = −9 → 8
l = −11 → 12

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.037
wR(F²) = 0.092
S = 1.05
1025 reflections
118 parameters
H-atom parameters constrained
w = 1/[σ²(F²) + (0.04P)²], where P = [max(F_o²,0) + 2F_c²]/3
(Δ/σ)_max < 0.001
Δρ_max = 0.27 e Å⁻³
Δρ_min = −0.22 e Å⁻³

Table 1
Hydrogen-bonding geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O12—H4⋯O7ⁱ	0.88	1.84	2.723 (2)	178
O11—H6⋯O6ⁱⁱ	0.96	1.73	2.681 (2)	175
O6—H8⋯O11ⁱⁱⁱ	0.83	1.95	2.778 (2)	174
O7—H14⋯O12ⁱⁱⁱ	0.96	1.84	2.791 (2)	175
Symmetry codes: (i) x,y-1,z; (ii) x-1,y,z; (iii) $[-x,{\script{1\over 2}}+y,-z]$ .

All H atoms were observed in a difference electron density map and were refined using slack restraints to optimize their geometry [C—H = 0.98 Å, O—H = 0.82 Å, with U_iso(H) = 1.2U_eq(C) or 1.5U_eq(O)], then made to ride on their parent atoms. In the absence of significant anomalous scattering effects, Friedel pairs were merged. The absolute configuration is known from the synthesis.

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 4, global. DOI: https://doi.org/10.1107/S1600536805012328/cf6418sup1.cif

Structure factors: contains datablock 4. DOI: https://doi.org/10.1107/S1600536805012328/cf64184sup2.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.

2-C-Methyl-D-allono-1,4-lactone top

Crystal data top

C₇H₁₂O₆	F(000) = 204
M_r = 192.17	D_x = 1.493 Mg m⁻³
Monoclinic, P2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 1283 reflections
a = 6.1521 (5) Å	θ = 5–27°
b = 7.5495 (7) Å	µ = 0.13 mm⁻¹
c = 9.3055 (8) Å	T = 190 K
β = 98.501 (5)°	Block, colourless
V = 427.45 (6) Å³	0.20 × 0.10 × 0.10 mm
Z = 2

Data collection top

Nonius KappaCCD diffractometer	R_int = 0.026
Graphite monochromator	θ_max = 27.5°, θ_min = 5.2°
ω scans	h = −7→7
2940 measured reflections	k = −9→8
1025 independent reflections	l = −11→12
905 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)] = 0.037	H-atom parameters constrained
wR(F²) = 0.092	w = 1/[σ²(F²) + (0.04P)²], where P = [max(F_o²,0) + 2F_c²]/3
S = 1.05	(Δ/σ)_max = 0.000076
1025 reflections	Δρ_max = 0.27 e Å⁻³
118 parameters	Δρ_min = −0.22 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	−0.0984 (3)	0.3222 (3)	0.2531 (2)	0.0320
C2	−0.1385 (4)	0.5174 (3)	0.2177 (2)	0.0296
C3	0.0955 (3)	0.5864 (3)	0.2218 (2)	0.0290
C4	0.1288 (3)	0.7823 (3)	0.2541 (2)	0.0304
C5	0.3673 (3)	0.8415 (3)	0.2636 (3)	0.0357
O6	0.4517 (2)	0.8076 (2)	0.13170 (17)	0.0386
O7	−0.0091 (3)	0.8810 (2)	0.14479 (17)	0.0312
O8	0.2203 (2)	0.4860 (2)	0.34013 (17)	0.0345
C9	0.1124 (3)	0.3352 (3)	0.3624 (2)	0.0324
O10	0.1853 (3)	0.2291 (3)	0.45428 (18)	0.0440
O11	−0.2766 (2)	0.5436 (2)	0.08380 (15)	0.0339
O12	−0.0337 (3)	0.2406 (2)	0.12701 (17)	0.0373
C13	−0.2852 (4)	0.2248 (4)	0.3069 (3)	0.0449
H21	−0.1993	0.5739	0.2957	0.0336*
H31	0.1497	0.5606	0.1295	0.0337*
H41	0.0760	0.8081	0.3461	0.0353*
H51	0.3799	0.9682	0.2861	0.0430*
H52	0.4571	0.7735	0.3426	0.0409*
H131	−0.2364	0.1024	0.3341	0.0549*
H132	−0.3180	0.2916	0.3959	0.0531*
H133	−0.4211	0.2216	0.2324	0.0543*
H4	−0.0218	0.1243	0.1329	0.0585*
H6	−0.3733	0.6401	0.0949	0.0487*
H8	0.3924	0.8804	0.0718	0.0768*
H14	0.0116	0.8276	0.0546	0.0746*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0369 (11)	0.0294 (12)	0.0292 (10)	−0.0010 (10)	0.0033 (8)	0.0017 (10)
C2	0.0316 (10)	0.0281 (13)	0.0281 (10)	−0.0016 (9)	0.0013 (8)	−0.0015 (9)
C3	0.0320 (11)	0.0250 (12)	0.0296 (10)	0.0002 (9)	0.0030 (8)	0.0013 (9)
C4	0.0349 (11)	0.0269 (12)	0.0290 (10)	−0.0001 (9)	0.0031 (8)	0.0004 (8)
C5	0.0342 (11)	0.0322 (12)	0.0394 (11)	−0.0033 (10)	0.0015 (9)	−0.0013 (10)
O6	0.0329 (8)	0.0388 (10)	0.0449 (9)	0.0061 (8)	0.0085 (7)	0.0091 (8)
O7	0.0344 (7)	0.0237 (8)	0.0345 (8)	0.0016 (6)	0.0020 (6)	0.0003 (7)
O8	0.0342 (8)	0.0295 (9)	0.0381 (8)	0.0004 (7)	−0.0006 (7)	0.0044 (7)
C9	0.0351 (11)	0.0317 (12)	0.0305 (11)	0.0008 (10)	0.0055 (8)	0.0029 (9)
O10	0.0488 (9)	0.0425 (11)	0.0396 (9)	0.0022 (9)	0.0025 (7)	0.0134 (8)
O11	0.0378 (8)	0.0290 (9)	0.0324 (7)	0.0044 (7)	−0.0036 (6)	−0.0028 (7)
O12	0.0527 (10)	0.0240 (8)	0.0354 (9)	0.0027 (8)	0.0070 (7)	−0.0009 (7)
C13	0.0451 (13)	0.0413 (15)	0.0475 (14)	−0.0076 (12)	0.0043 (11)	0.0082 (12)

Geometric parameters (Å, º) top

C1—C2	1.522 (3)	C5—O6	1.425 (3)
C1—C9	1.528 (3)	C5—H51	0.980
C1—O12	1.432 (3)	C5—H52	0.994
C1—C13	1.511 (4)	O6—H8	0.828
C2—C3	1.526 (3)	O7—H14	0.956
C2—O11	1.415 (2)	O8—C9	1.349 (3)
C2—H21	0.964	C9—O10	1.208 (3)
C3—C4	1.517 (3)	O11—H6	0.956
C3—O8	1.459 (2)	O12—H4	0.882
C3—H31	0.986	C13—H131	0.993
C4—C5	1.524 (3)	C13—H132	1.015
C4—O7	1.433 (3)	C13—H133	1.004
C4—H41	0.979

C2—C1—C9	100.2 (2)	C5—C4—H41	109.4
C2—C1—O12	107.2 (2)	O7—C4—H41	106.2
C9—C1—O12	105.2 (2)	C4—C5—O6	111.6 (2)
C2—C1—C13	115.8 (2)	C4—C5—H51	110.1
C9—C1—C13	115.0 (2)	O6—C5—H51	109.4
O12—C1—C13	112.3 (2)	C4—C5—H52	108.4
C1—C2—C3	101.7 (2)	O6—C5—H52	108.1
C1—C2—O11	112.5 (2)	H51—C5—H52	109.2
C3—C2—O11	114.6 (2)	C5—O6—H8	106.3
C1—C2—H21	109.5	C4—O7—H14	105.2
C3—C2—H21	107.5	C3—O8—C9	109.8 (2)
O11—C2—H21	110.6	C1—C9—O8	109.9 (2)
C2—C3—C4	115.9 (2)	C1—C9—O10	128.2 (2)
C2—C3—O8	103.3 (2)	O8—C9—O10	121.9 (2)
C4—C3—O8	108.5 (2)	C2—O11—H6	108.3
C2—C3—H31	110.5	C1—O12—H4	114.0
C4—C3—H31	108.2	C1—C13—H131	108.7
O8—C3—H31	110.3	C1—C13—H132	106.3
C3—C4—C5	113.5 (2)	H131—C13—H132	110.1
C3—C4—O7	108.5 (2)	C1—C13—H133	112.3
C5—C4—O7	110.6 (2)	H131—C13—H133	110.1
C3—C4—H41	108.4	H132—C13—H133	109.2

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O12—H4···O7ⁱ	0.88	1.84	2.723 (2)	178
O11—H6···O6ⁱⁱ	0.96	1.73	2.681 (2)	175
O6—H8···O11ⁱⁱⁱ	0.83	1.95	2.778 (2)	174
O7—H14···O12ⁱⁱⁱ	0.96	1.84	2.791 (2)	175

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

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