2C-Methyl-d-arabinono-1,4-lactone monohydrate

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

doi:10.1107/S1600536805000723

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 61| Part 2| February 2005| Pages o326-o327

https://doi.org/10.1107/S1600536805000723

2C-Methyl-D-arabinono-1,4-lactone monohydrate

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 10 December 2004; accepted 10 January 2005; online 22 January 2005)

The title compound, C₆H₁₀O₅·H₂O, formed by the hydrolysis of a δ-lactone, is shown unequivocally to be a γ-lactone. The diol has a trans configuration.

Comment

The potential of the Kiliani ascension of ketoses to provide readily available branched scaffolds has been recognized (Hotchkiss et al., 2004 ). A further class of branched carbohydrate building blocks may be available from the reaction of cyanide on 1-deoxyketoses, themselves prepared by addition of organometallic reagents to sugar lactones. The protected 1-deoxy-D-ribulose, (1), was treated with sodium cyanide and gave a single diastereomeric product, (2), the structure of which was established by X-ray crystallography (Punzo et al., 2005 ). During the isolation of (2), some loss of the protecting acetonide group afforded an unprotected lactone (3), which was eventually crystallized. NMR and other structural studies on (3) could not firmly determine the size of the lactone ring; X-ray crystallographic analysis established that (3) is a 1,4-lactone (Fig. 1). It is noteworthy that none of the epimeric ribonolactone, (4), was isolated during the course of the synthesis. As usually expected for sugar derivatives, hydrogen bonding (Table 2) occurs between molecules, and the water of crystallization is involved in this network (Fig. 2).

Figure 1
The asymmetric unit of (3

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

Figure 2
Packing diagram of (3

), viewed down the a axis. Hydrogen bonds are indicated by dashed lines.

Experimental

Compound (3) 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 clear colourless crystals formed. Water was used as solvent during the synthesis of the compound. Moreover the compound was exposed to air before and after crystallization.

Crystal data

C₆H₁₀O₅·H₂O
M_r = 180.16
Orthorhombic, P2₁2₁2₁
a = 8.1624 (3) Å
b = 8.5569 (3) Å
c = 11.6000 (5) Å
V = 810.20 (5) Å³
Z = 4
D_x = 1.477 Mg m⁻³
Mo Kα radiation
Cell parameters from 1300 reflections
θ = 5–30°
μ = 0.13 mm⁻¹
T = 120 K
Plate, colourless
0.30 × 0.20 × 0.04 mm

Data collection

Nonius KappaCCD diffractometer
ω scans
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997 ) T_min = 0.97, T_max = 0.99
2296 measured reflections
1361 independent reflections
1201 reflections with I > 2 σ(I)
R_int = 0.013
θ_max = 30.0°
h = −11 → 11
k = −11 → 12
l = −16 → 16

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.031
wR(F²) = 0.071
S = 0.98
1361 reflections
109 parameters
H-atom parameters constrained
w = 1/[σ²(F²) + 0.03 + 0.17P], where P = [max(F_o²,0) + 2F_c²]/3
(Δ/σ)_max < 0.001
Δρ_max = 0.23 e Å⁻³
Δρ_min = −0.24 e Å⁻³
Absolute structure: see text

Table 1
Selected bond lengths (Å)

C1—C2	1.537 (2)
C1—C5	1.528 (2)
C1—O10	1.4169 (17)
C1—C11	1.526 (2)
C2—C3	1.525 (2)
C2—O9	1.4167 (18)
C3—O4	1.4695 (18)
C3—C7	1.516 (2)
O4—C5	1.3363 (18)
C5—O6	1.2106 (17)
C7—O8	1.4261 (19)

Table 2
Hydrogen-bonding geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O10—H5⋯O12	0.92	1.81	2.7191 (16)	175
O8—H7⋯O6ⁱ	0.97	1.78	2.7235 (15)	163
O9—H9⋯O8ⁱ	0.96	1.76	2.7157 (15)	169
O12—H12⋯O9ⁱⁱ	0.94	2.01	2.9138 (16)	163
O12—H1⋯O10ⁱⁱⁱ	0.91	2.00	2.8613 (16)	157
Symmetry codes: (i) $[1-x,{\script{1\over 2}}+y,{\script{3\over 2}}-z]$ ; (ii) $[1-x,y-{\script{1\over 2}},{\script{3\over 2}}-z]$ ; (iii) $[x-{\script{1\over 2}},{\script{1\over 2}}-y,1-z]$ .

In the absence of significant anomalous scattering, Friedel pairs were merged. The absolute configuration was assigned since the starting material was D-erythronolactone with known absolute configuration. H atoms were located in difference density maps. 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 = 0.91–0.97 Å), after which they were refined as riding, with U_iso(H) = 1.2U_eq(C) and U_iso(H) = 0.05 Å² for those bonded to the O atoms.

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 global, 3. DOI: https://doi.org/10.1107/S1600536805000723/ob6460sup1.cif

Structure factors: contains datablock 3. DOI: https://doi.org/10.1107/S1600536805000723/ob64603sup2.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.

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

Crystal data top

C₆H₁₀O₅·H₂O	D_x = 1.477 Mg m⁻³
M_r = 180.16	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 1300 reflections
a = 8.1624 (3) Å	θ = 5–30°
b = 8.5569 (3) Å	µ = 0.13 mm⁻¹
c = 11.6000 (5) Å	T = 120 K
V = 810.20 (5) Å³	Plate, colourless
Z = 4	0.30 × 0.20 × 0.04 mm
F(000) = 384

Data collection top

Nonius KappaCCD diffractometer	1201 reflections with I > 2u(I)
Graphite monochromator	R_int = 0.013
ω scans	θ_max = 30.0°, θ_min = 5.3°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −11→11
T_min = 0.97, T_max = 0.99	k = −11→12
2296 measured reflections	l = −16→16
1361 independent reflections

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) = 0.071	w = 1/[σ²(F²) + 0.03 + 0.17P], where P = [max(F_o²,0) + 2F_c²]/3
S = 0.98	(Δ/σ)_max = 0.000246
1361 reflections	Δρ_max = 0.23 e Å⁻³
109 parameters	Δρ_min = −0.24 e Å⁻³
0 restraints	Absolute structure: see text

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

	x	y	z	U_iso*/U_eq
C1	0.77461 (19)	0.14456 (17)	0.69407 (12)	0.0165
C2	0.64570 (18)	0.21334 (16)	0.77623 (13)	0.0168
C3	0.63386 (19)	0.08861 (18)	0.86979 (13)	0.0181
O4	0.66325 (13)	−0.05809 (12)	0.80726 (9)	0.0179
C5	0.73681 (18)	−0.02955 (17)	0.70652 (13)	0.0165
O6	0.76709 (13)	−0.13251 (12)	0.63819 (9)	0.0197
C7	0.4700 (2)	0.0739 (2)	0.93035 (13)	0.0213
O8	0.33569 (13)	0.06498 (13)	0.85204 (10)	0.0220
O9	0.68542 (15)	0.35975 (12)	0.82592 (9)	0.0220
O10	0.76159 (13)	0.19458 (12)	0.57800 (8)	0.0194
C11	0.95038 (18)	0.1741 (2)	0.73335 (14)	0.0230
O12	0.47338 (14)	0.06611 (15)	0.50844 (10)	0.0282
H21	0.5406	0.2174	0.7354	0.0207*
H31	0.7252	0.1002	0.9253	0.0238*
H71	0.4532	0.1665	0.9824	0.0260*
H72	0.4727	−0.0243	0.9782	0.0260*
H111	1.0219	0.1159	0.6815	0.0286*
H112	0.9699	0.2875	0.7284	0.0286*
H113	0.9610	0.1360	0.8114	0.0286*
H5	0.6643	0.1552	0.5515	0.0500*
H7	0.2885	0.1680	0.8411	0.0500*
H9	0.6767	0.4424	0.7698	0.0500*
H12	0.4229	−0.0145	0.5497	0.0500*
H1	0.3899	0.1193	0.4735	0.0500*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0184 (7)	0.0167 (6)	0.0144 (6)	−0.0014 (6)	−0.0008 (6)	0.0019 (6)
C2	0.0178 (7)	0.0151 (6)	0.0175 (6)	−0.0019 (6)	0.0000 (6)	−0.0012 (6)
C3	0.0218 (7)	0.0172 (7)	0.0153 (7)	0.0006 (6)	−0.0013 (6)	−0.0010 (6)
O4	0.0221 (5)	0.0148 (5)	0.0169 (5)	0.0015 (4)	0.0016 (4)	0.0004 (4)
C5	0.0129 (6)	0.0182 (7)	0.0184 (7)	0.0009 (6)	−0.0036 (6)	0.0017 (5)
O6	0.0227 (5)	0.0167 (5)	0.0198 (5)	0.0013 (5)	0.0001 (5)	−0.0019 (4)
C7	0.0232 (7)	0.0222 (7)	0.0185 (7)	−0.0007 (7)	0.0014 (6)	0.0007 (7)
O8	0.0203 (5)	0.0186 (5)	0.0270 (6)	0.0006 (5)	−0.0003 (5)	−0.0015 (5)
O9	0.0304 (6)	0.0151 (5)	0.0205 (5)	−0.0022 (5)	0.0002 (5)	−0.0031 (4)
O10	0.0236 (5)	0.0196 (5)	0.0150 (5)	−0.0026 (5)	−0.0009 (4)	0.0019 (4)
C11	0.0190 (7)	0.0258 (8)	0.0242 (8)	−0.0028 (7)	−0.0033 (6)	0.0003 (7)
O12	0.0221 (5)	0.0318 (6)	0.0307 (6)	−0.0026 (6)	−0.0065 (5)	0.0094 (6)

Geometric parameters (Å, º) top

C1—C2	1.537 (2)	C7—O8	1.4261 (19)
C1—C5	1.528 (2)	C7—H71	1.006
C1—O10	1.4169 (17)	C7—H72	1.007
C1—C11	1.526 (2)	O8—H7	0.970
C2—C3	1.525 (2)	O9—H9	0.964
C2—O9	1.4167 (18)	O10—H5	0.916
C2—H21	0.980	C11—H111	0.975
C3—O4	1.4695 (18)	C11—H112	0.985
C3—C7	1.516 (2)	C11—H113	0.967
C3—H31	0.990	O12—H12	0.935
O4—C5	1.3363 (18)	O12—H1	0.914
C5—O6	1.2106 (17)

C2—C1—C5	100.17 (12)	C1—C5—O4	110.58 (12)
C2—C1—O10	114.98 (12)	C1—C5—O6	127.33 (14)
C5—C1—O10	111.66 (12)	O4—C5—O6	122.09 (13)
C2—C1—C11	113.27 (12)	C3—C7—O8	112.81 (12)
C5—C1—C11	108.84 (13)	C3—C7—H71	109.5
O10—C1—C11	107.71 (12)	O8—C7—H71	108.6
C1—C2—C3	102.51 (12)	C3—C7—H72	107.8
C1—C2—O9	115.74 (12)	O8—C7—H72	108.8
C3—C2—O9	110.11 (12)	H71—C7—H72	109.3
C1—C2—H21	108.3	C7—O8—H7	109.9
C3—C2—H21	108.2	C2—O9—H9	110.9
O9—C2—H21	111.4	C1—O10—H5	105.8
C2—C3—O4	103.66 (11)	C1—C11—H111	107.1
C2—C3—C7	116.35 (13)	C1—C11—H112	107.3
O4—C3—C7	107.56 (12)	H111—C11—H112	111.8
C2—C3—H31	110.2	C1—C11—H113	107.9
O4—C3—H31	106.5	H111—C11—H113	110.6
C7—C3—H31	111.8	H112—C11—H113	111.9
C3—O4—C5	110.42 (11)	H12—O12—H1	105.4

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O10—H5···O12	0.92	1.81	2.7191 (16)	175
O8—H7···O6ⁱ	0.97	1.78	2.7235 (15)	163
O9—H9···O8ⁱ	0.96	1.76	2.7157 (15)	169
O12—H12···O9ⁱⁱ	0.94	2.01	2.9138 (16)	163
O12—H1···O10ⁱⁱⁱ	0.91	2.00	2.8613 (16)	157

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

Footnotes

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

References

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