(3S)-3-Benzyl­oxymethyl-1,4-dioxane-2,5-dione

Kooijman, H.; Leemhuis, M.; Nostrum, C.F. van; Hennink, W.E.; Spek, A.L.

doi:10.1107/S1600536805030564

(3S)-3-Benzyloxymethyl-1,4-dioxane-2,5-dione

H. Kooijman, M. Leemhuis, C. F. van Nostrum, W. E. Hennink and A. L. Spek

The lactide ring in the title compound, C₁₂H₁₂O₅, adopts a screw-boat conformation. C—H

O interactions link the molecules into a chain in the [100] direction.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805030564/bt6747sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536805030564/bt6747Isup2.hkl Contains datablock I

CCDC reference: 287487

checkCIF report

Key indicators

Single-crystal X-ray study
T = 150 K
Mean (C-C) = 0.006 Å
R factor = 0.043
wR factor = 0.102
Data-to-parameter ratio = 7.1

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT432_ALERT_2_B Short Inter X...Y Contact  O1     ..  C4      ..       2.87 Ang.

Alert level C
PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax .LT. 18) .....       7.13
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          6

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           25.29
           From the CIF: _reflns_number_total               1098
           Count of symmetry unique reflns         1104
           Completeness (_total/calc)             99.46%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         0
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present         no

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion

Comment top

The structure of the title compound, (I), was determined in the course of our investigations towards a better understanding of the regioselectivity observed in the ring-opening polymerization of various substituted (3S)-3-benzyloxymethyl-1,4-dioxane-2,5-dione derivatives (Leemhuis et al., 2005). Earlier, we reported the crystal structures of the 6(R)-methyl (Kooijman et al., 2005a) and the 6(S)-methyl derivatives (Kooijman et al., 2005b). The molecular structure of (I) is displayed in Fig. 1 and selected geometric parameters are given in Table 1.

The lactide ring has taken a somewhat deformed screw-boat conformation. The asymmetry parameter (Duax & Norton, 1975) ΔC₂(C2—O3) = 6.4 (5)°; all other asymmetry parameters have values of 18° or higher. The Cremer & Pople puckering parameters (Cremer & Pople, 1975) are θ = 77.1 (6)° and ϕ = 320.3 (6)°; the ideal values for the observed screw-boat conformation are θ = 67.5° and ϕ = 330°. The benzyloxymethyl substituent of the lactide ring occupies the axial position, as illustrated by the angle between the least-squares plane through the lactide ring and the C5—C6 bond, which amounts to 77.9 (3)°. In the 6(R)-methyl derivative, the benzyloxymethyl group also occupies the axial position [plane–bond angle is 67.20 (13)°]. The 6(S)-methyl derivative, however, has the benzyloxymethyl group in the equatorial position [plane–bond angle is 13.13 (13)°], most likely due to steric hindrance between the substituents of the lactide ring. The link between the two ring systems is not in an all-trans conformation, the torsion angles O4—C5—C6—O5 and O5—C7—C8—C9 have a -gauche conformation.

The packing displays short C—H···O contacts, geometric details of which are given in Table 2. These contacts join the molecules into an infinite chain in the [100] direction (see Fig. 2).

Experimental top

The synthesis of the title compound is described elsewhere (Leemhuis et al., 2003). Crystals were grown from a solution in methyl tert-butyl ether.

Computing details top

Data collection: COLLECT (Hooft, 1998); cell refinement: DENZO (Otwinowski & Minor, 1997); data reduction: DENZO; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: PLATON.

Figures top

	Fig. 1. Atomic displacement plot (Spek, 2003) of the title compound, showing the atom-numbering scheme. The displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. Short contacts C6—H6A···O1(x − 1, y, z) link the molecules into an infinite chain in the [100] direction.

(3S)-3-benzyloxymethyl-1,4-dioxane-2,5-dione top

Crystal data top

C₁₂H₁₂O₅	F(000) = 248
M_r = 236.22	Quoted _cell_measurement_* data items refer to the initial cell determination. The cell parameters as reported in _cell_* are based on the complete data set.
Monoclinic, P2₁	D_x = 1.413 Mg m⁻³
Hall symbol: P 2yb	Mo Kα radiation, λ = 0.71073 Å
a = 6.925 (4) Å	Cell parameters from 219 reflections
b = 7.025 (4) Å	θ = 2.0–25.0°
c = 11.733 (8) Å	µ = 0.11 mm⁻¹
β = 103.44 (3)°	T = 150 K
V = 555.2 (6) Å³	Prism, colourless
Z = 2	0.15 × 0.05 × 0.05 mm

Data collection top

Nonius KappaCCD area-detector diffractometer	899 reflections with I > 2σ(I)
Radiation source: Rotating Anode	R_int = 0.087
Graphite monochromator	θ_max = 25.3°, θ_min = 1.8°
Detector resolution: 18.4 pixels mm^-1	h = −8→8
ϕ scans and ω scans with κ offset	k = −8→8
12280 measured reflections	l = −14→14
1098 independent reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.043	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.102	H-atom parameters constrained
S = 1.11	w = 1/[σ²(F_o²) + (0.0492P)² + 0.1P] where P = (F_o² + 2F_c²)/3
1098 reflections	(Δ/σ)_max < 0.001
154 parameters	Δρ_max = 0.19 e Å⁻³
1 restraint	Δρ_min = −0.17 e Å⁻³

Crystal data top

C₁₂H₁₂O₅	V = 555.2 (6) Å³
M_r = 236.22	Z = 2
Monoclinic, P2₁	Mo Kα radiation
a = 6.925 (4) Å	µ = 0.11 mm⁻¹
b = 7.025 (4) Å	T = 150 K
c = 11.733 (8) Å	0.15 × 0.05 × 0.05 mm
β = 103.44 (3)°

Data collection top

Nonius KappaCCD area-detector diffractometer	899 reflections with I > 2σ(I)
12280 measured reflections	R_int = 0.087
1098 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.043	1 restraint
wR(F²) = 0.102	H-atom parameters constrained
S = 1.11	Δρ_max = 0.19 e Å⁻³
1098 reflections	Δρ_min = −0.17 e Å⁻³
154 parameters

Special details top

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F² for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The observed criterion of F² > σ(F²) is used only for calculating -R-factor-obs etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.

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

	x	y	z	U_iso*/U_eq
O1	0.2154 (4)	0.2620 (5)	0.5602 (2)	0.0658 (10)
O2	−0.1082 (3)	0.3022 (4)	0.5193 (2)	0.0548 (9)
O3	−0.0721 (3)	0.5943 (4)	0.6849 (2)	0.0477 (8)
O4	−0.3966 (3)	0.6193 (4)	0.6488 (2)	0.0518 (9)
O5	−0.1340 (3)	0.1770 (4)	0.7395 (2)	0.0532 (9)
C1	0.0746 (5)	0.3390 (6)	0.5835 (3)	0.0487 (12)
C2	0.0993 (5)	0.4821 (6)	0.6801 (3)	0.0460 (11)
C4	−0.2542 (5)	0.5320 (5)	0.6357 (3)	0.0469 (12)
C5	−0.2757 (5)	0.3459 (6)	0.5689 (3)	0.0533 (13)
C6	−0.3069 (5)	0.1841 (6)	0.6473 (4)	0.0592 (13)
C7	−0.1362 (5)	0.0292 (5)	0.8232 (4)	0.0562 (14)
C8	0.0742 (5)	−0.0144 (5)	0.8858 (3)	0.0463 (11)
C9	0.2064 (5)	−0.0757 (5)	0.8208 (3)	0.0469 (12)
C10	0.3972 (5)	−0.1295 (5)	0.8764 (4)	0.0513 (12)
C11	0.4575 (6)	−0.1222 (6)	0.9968 (4)	0.0570 (14)
C12	0.3313 (7)	−0.0590 (6)	1.0611 (4)	0.0624 (16)
C13	0.1376 (6)	−0.0052 (6)	1.0059 (3)	0.0591 (16)
H2A	0.14260	0.41410	0.75560	0.0550*
H2B	0.20770	0.57000	0.67310	0.0550*
H5	−0.39640	0.35520	0.50310	0.0640*
H6A	−0.42570	0.20750	0.67860	0.0710*
H6B	−0.32510	0.06260	0.60330	0.0710*
H7A	−0.20020	−0.08620	0.78290	0.0680*
H7B	−0.21280	0.07100	0.88020	0.0680*
H9	0.16560	−0.08070	0.73780	0.0560*
H10	0.48690	−0.17150	0.83150	0.0610*
H11	0.58790	−0.16150	1.03480	0.0680*
H12	0.37450	−0.05130	1.14400	0.0740*
H13	0.04950	0.03780	1.05150	0.0710*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0425 (15)	0.080 (2)	0.0730 (18)	0.0098 (14)	0.0097 (13)	−0.0190 (16)
O2	0.0353 (13)	0.0676 (18)	0.0574 (15)	0.0040 (12)	0.0023 (11)	−0.0176 (14)
O3	0.0410 (13)	0.0442 (13)	0.0546 (15)	0.0025 (10)	0.0043 (11)	−0.0053 (12)
O4	0.0455 (14)	0.0510 (15)	0.0584 (16)	0.0100 (13)	0.0110 (12)	0.0010 (13)
O5	0.0370 (13)	0.0410 (14)	0.0788 (18)	−0.0046 (11)	0.0077 (12)	0.0011 (14)
C1	0.039 (2)	0.054 (2)	0.051 (2)	0.0021 (18)	0.0062 (16)	−0.0047 (19)
C2	0.0412 (18)	0.047 (2)	0.048 (2)	−0.0016 (16)	0.0070 (15)	0.0008 (18)
C4	0.042 (2)	0.047 (2)	0.050 (2)	0.0060 (17)	0.0073 (16)	0.0016 (17)
C5	0.0317 (18)	0.064 (3)	0.059 (2)	0.0050 (18)	0.0001 (16)	−0.014 (2)
C6	0.0304 (18)	0.052 (2)	0.090 (3)	−0.0009 (18)	0.0034 (19)	−0.018 (2)
C7	0.049 (2)	0.037 (2)	0.089 (3)	−0.0028 (17)	0.029 (2)	0.001 (2)
C8	0.049 (2)	0.0312 (18)	0.063 (2)	−0.0074 (16)	0.0218 (17)	0.0017 (18)
C9	0.044 (2)	0.040 (2)	0.057 (2)	−0.0031 (16)	0.0123 (17)	−0.0017 (18)
C10	0.044 (2)	0.043 (2)	0.068 (2)	−0.0039 (17)	0.0153 (17)	−0.0047 (19)
C11	0.059 (3)	0.045 (2)	0.063 (2)	−0.0072 (19)	0.006 (2)	0.000 (2)
C12	0.078 (3)	0.053 (3)	0.054 (2)	−0.009 (2)	0.011 (2)	0.005 (2)
C13	0.080 (3)	0.042 (2)	0.067 (3)	−0.007 (2)	0.041 (2)	−0.002 (2)

Geometric parameters (Å, º) top

O1—C1	1.201 (5)	C10—C11	1.378 (7)
O2—C1	1.339 (4)	C11—C12	1.355 (7)
O2—C5	1.446 (4)	C12—C13	1.399 (6)
O3—C2	1.437 (5)	C2—H2A	0.9900
O3—C4	1.333 (4)	C2—H2B	0.9900
O4—C4	1.201 (4)	C5—H5	1.0000
O5—C6	1.416 (5)	C6—H6A	0.9900
O5—C7	1.432 (5)	C6—H6B	0.9900
C1—C2	1.495 (5)	C7—H7A	0.9900
C4—C5	1.514 (5)	C7—H7B	0.9900
C5—C6	1.509 (6)	C9—H9	0.9500
C7—C8	1.503 (5)	C10—H10	0.9500
C8—C9	1.389 (5)	C11—H11	0.9500
C8—C13	1.377 (5)	C12—H12	0.9500
C9—C10	1.383 (5)	C13—H13	0.9500

O1···C6ⁱ	3.274 (5)	C7···C12^vi	3.590 (6)
O1···C4ⁱⁱ	2.873 (5)	C9···C2^x	3.515 (6)
O1···O3ⁱⁱ	3.052 (4)	C9···O3^x	3.195 (5)
O1···O4ⁱⁱ	3.166 (4)	C10···C12^xi	3.541 (6)
O1···C5ⁱⁱ	3.363 (6)	C11···C12^xi	3.533 (7)
O2···C2ⁱⁱ	3.256 (5)	C11···C11^xii	3.559 (6)
O2···O3	2.797 (4)	C11···C11^xi	3.559 (6)
O2···O5	2.774 (4)	C12···C10^xii	3.541 (6)
O3···O1ⁱⁱⁱ	3.052 (4)	C12···C11^xii	3.533 (7)
O3···C9^iv	3.195 (5)	C12···C7^xiii	3.590 (6)
O3···O2	2.797 (4)	C4···H12^vi	2.9500
O3···O5	3.052 (4)	C7···H10^viii	2.9900
O4···C5^v	3.393 (5)	C9···H2B^x	3.0300
O4···O1ⁱⁱⁱ	3.166 (4)	C10···H7Bⁱ	3.0400
O5···O3	3.052 (4)	C12···H7B^xiii	2.8600
O5···C2	2.866 (5)	H2A···O5	2.5100
O5···C1	2.822 (5)	H2B···O4ⁱ	2.8400
O5···O2	2.774 (4)	H2B···C9^iv	3.0300
O1···H6Aⁱ	2.5800	H2B···O2ⁱⁱⁱ	2.7400
O2···H2Bⁱⁱ	2.7400	H5···O4^ix	2.6100
O3···H9^iv	2.8000	H5···H6B^v	2.5100
O3···H7A^iv	2.7600	H6A···O1^viii	2.5800
O4···H5^v	2.6100	H6B···H7A	2.3300
O4···H12^vi	2.6800	H6B···H5^ix	2.5100
O4···H7A^iv	2.7600	H7A···O3^x	2.7600
O4···H10^vii	2.8700	H7A···O4^x	2.7600
O4···H2B^viii	2.8400	H7A···H6B	2.3300
O5···H2A	2.5100	H7A···H10^viii	2.4400
O5···H9	2.7600	H7B···C10^viii	3.0400
C1···O5	2.822 (5)	H7B···H13	2.3900
C2···O5	2.866 (5)	H7B···C12^vi	2.8600
C2···C6	3.455 (6)	H9···O3^x	2.8000
C2···C9^iv	3.515 (6)	H9···O5	2.7600
C2···O2ⁱⁱⁱ	3.256 (5)	H10···O4^xiv	2.8700
C4···O1ⁱⁱⁱ	2.873 (5)	H10···C7ⁱ	2.9900
C5···O1ⁱⁱⁱ	3.363 (6)	H10···H7Aⁱ	2.4400
C5···O4^ix	3.393 (5)	H12···O4^xiii	2.6800
C6···O1^viii	3.274 (5)	H12···C4^xiii	2.9500
C6···C2	3.455 (6)	H13···H7B	2.3900

C1—O2—C5	118.3 (3)	C1—C2—H2B	108.00
C2—O3—C4	120.7 (3)	H2A—C2—H2B	107.00
C6—O5—C7	114.1 (3)	O2—C5—H5	108.00
O1—C1—O2	119.8 (3)	C4—C5—H5	108.00
O1—C1—C2	121.3 (3)	C6—C5—H5	108.00
O2—C1—C2	118.9 (3)	O5—C6—H6A	111.00
O3—C2—C1	116.7 (3)	O5—C6—H6B	111.00
O3—C4—O4	120.0 (3)	C5—C6—H6A	111.00
O3—C4—C5	118.5 (3)	C5—C6—H6B	111.00
O4—C4—C5	121.5 (3)	H6A—C6—H6B	109.00
O2—C5—C4	113.6 (3)	O5—C7—H7A	110.00
O2—C5—C6	109.1 (3)	O5—C7—H7B	110.00
C4—C5—C6	110.2 (3)	C8—C7—H7A	110.00
O5—C6—C5	106.1 (3)	C8—C7—H7B	110.00
O5—C7—C8	108.6 (3)	H7A—C7—H7B	108.00
C7—C8—C9	118.9 (3)	C8—C9—H9	120.00
C7—C8—C13	122.2 (3)	C10—C9—H9	120.00
C9—C8—C13	118.9 (3)	C9—C10—H10	120.00
C8—C9—C10	120.3 (3)	C11—C10—H10	120.00
C9—C10—C11	120.1 (4)	C10—C11—H11	120.00
C10—C11—C12	120.1 (4)	C12—C11—H11	120.00
C11—C12—C13	120.3 (4)	C11—C12—H12	120.00
C8—C13—C12	120.3 (4)	C13—C12—H12	120.00
O3—C2—H2A	108.00	C8—C13—H13	120.00
O3—C2—H2B	108.00	C12—C13—H13	120.00
C1—C2—H2A	108.00

C5—O2—C1—O1	160.7 (4)	O4—C4—C5—O2	155.3 (3)
C5—O2—C1—C2	−21.8 (5)	O2—C5—C6—O5	63.5 (4)
C1—O2—C5—C4	40.4 (4)	C4—C5—C6—O5	−61.9 (4)
C1—O2—C5—C6	−83.0 (4)	O5—C7—C8—C13	123.8 (4)
C4—O3—C2—C1	22.9 (5)	O5—C7—C8—C9	−59.7 (4)
C2—O3—C4—O4	173.7 (3)	C7—C8—C9—C10	−175.6 (3)
C2—O3—C4—C5	−3.4 (5)	C13—C8—C9—C10	1.1 (5)
C7—O5—C6—C5	−179.6 (3)	C7—C8—C13—C12	175.8 (4)
C6—O5—C7—C8	158.0 (3)	C9—C8—C13—C12	−0.7 (6)
O1—C1—C2—O3	167.3 (3)	C8—C9—C10—C11	−0.1 (6)
O2—C1—C2—O3	−10.2 (5)	C9—C10—C11—C12	−1.2 (6)
O3—C4—C5—O2	−27.7 (4)	C10—C11—C12—C13	1.6 (6)
O4—C4—C5—C6	−81.9 (4)	C11—C12—C13—C8	−0.6 (6)
O3—C4—C5—C6	95.1 (4)

Symmetry codes: (i) x+1, y, z; (ii) −x, y−1/2, −z+1; (iii) −x, y+1/2, −z+1; (iv) x, y+1, z; (v) −x−1, y+1/2, −z+1; (vi) −x, y+1/2, −z+2; (vii) x−1, y+1, z; (viii) x−1, y, z; (ix) −x−1, y−1/2, −z+1; (x) x, y−1, z; (xi) −x+1, y−1/2, −z+2; (xii) −x+1, y+1/2, −z+2; (xiii) −x, y−1/2, −z+2; (xiv) x+1, y−1, z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2A···O5	0.99	2.51	2.866 (5)	101
C6—H6A···O1^viii	0.99	2.58	3.274 (5)	127

Symmetry code: (viii) x−1, y, z.

Experimental details

Crystal data
Chemical formula	C₁₂H₁₂O₅
M_r	236.22
Crystal system, space group	Monoclinic, P2₁
Temperature (K)	150
a, b, c (Å)	6.925 (4), 7.025 (4), 11.733 (8)
β (°)	103.44 (3)
V (Å³)	555.2 (6)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.15 × 0.05 × 0.05

Data collection
Diffractometer	Nonius KappaCCD area-detector diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	12280, 1098, 899
R_int	0.087
(sin θ/λ)_max (Å⁻¹)	0.601

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.043, 0.102, 1.11
No. of reflections	1098
No. of parameters	154
No. of restraints	1
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.19, −0.17

Computer programs: COLLECT (Hooft, 1998), DENZO (Otwinowski & Minor, 1997), DENZO, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003), PLATON.

Selected geometric parameters (Å, º) top

O2—C1	1.339 (4)	O3—C2	1.437 (5)
O2—C5	1.446 (4)	O3—C4	1.333 (4)

C1—O2—C5	118.3 (3)	C2—O3—C4	120.7 (3)

C7—O5—C6—C5	−179.6 (3)	C4—C5—C6—O5	−61.9 (4)
C6—O5—C7—C8	158.0 (3)	O5—C7—C8—C9	−59.7 (4)