(3S,6S)-3-Benzyl­oxymeth­yl-6-meth­yl-1,4-dioxane-2,5-dione

The chiral centres in the dilactone moiety of the title compound, C₁₃H₁₄O₅, are in the configuration 3S,6S. The ring itself has a boat conformation. C—H...O inter­actions link the mol­ecules into a chain in the [010] direction.

Key indicators

• Single-crystal X-ray study
• T = 150 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.036
• wR factor = 0.095
• Data-to-parameter ratio = 9.7

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for         C7

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           27.45
           From the CIF: _reflns_number_total               1590
           Count of symmetry unique reflns         1592
           Completeness (_total/calc)             99.87%
           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
   0 ALERT level B = Potentially serious problem
   1 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
   0 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion

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Computing details

Data collection: COLLECT (Nonius, 1998); cell refinement: DENZO (Otwinowski & Minor, 1997); data reduction: DENZO; program(s) used to solve structure: SHELXS86 (Sheldrick, 1986); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: PLATON.

(3S,6S)-3-benzyloxymethyl-6-methyl-1,4-dioxane-2,5-dione

Crystal data

C13H14O5	F(000) = 264
Mr = 250.24	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	Dx = 1.309 Mg m^−3
Hall symbol: P 2yb	Mo Kα radiation, λ = 0.71073 Å
a = 8.944 (2) Å	Cell parameters from 171 reflections
b = 5.940 (1) Å	θ = 2.0–25.0°
c = 12.559 (3) Å	µ = 0.10 mm^−1
β = 107.905 (12)°	T = 150 K
V = 634.9 (2) Å^3	Plate, colourless
Z = 2	0.35 × 0.15 × 0.05 mm

Data collection

Nonius KappaCCD area-detector diffractometer	1430 reflections with I > 2σ(I)
Radiation source: Rotating Anode	Rint = 0.093
Graphite monochromator	θmax = 27.5°, θmin = 1.7°
Detector resolution: 18.4 pixels mm^-1	h = −11→11
φ scans, and ω scans with κ offset	k = −7→7
16869 measured reflections	l = −16→16
1590 independent reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.095	H-atom parameters constrained
S = 1.08	w = 1/[σ^2(Fo^2) + (0.0565P)^2 + 0.05P] where P = (Fo^2 + 2Fc^2)/3
1590 reflections	(Δ/σ)max < 0.001
164 parameters	Δρmax = 0.19 e Å^−3
1 restraint	Δρmin = −0.22 e Å^−3

Special details

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 F^{2 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 F}2, conventional R-factors R are based on F, with F set to zero for negative F^{2. The observed criterion of F}2 > σ(F^{2) is used only for calculating -R-factor-obs etc. and is not relevant to the choice of reflections for refinement. R-factors based on F}2 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 (Ų)

	x	y	z	Uiso*/Ueq
O1	0.10088 (16)	0.8720 (3)	0.49473 (13)	0.0394 (4)
O2	0.17629 (14)	0.5660 (2)	0.42788 (11)	0.0295 (4)
O3	0.38516 (14)	0.4808 (3)	0.63653 (11)	0.0352 (4)
O4	0.49645 (16)	0.2201 (3)	0.56162 (15)	0.0493 (5)
O5	0.10719 (15)	0.1972 (3)	0.27576 (12)	0.0408 (5)
C1	0.16669 (19)	0.6942 (3)	0.51299 (16)	0.0278 (5)
C2	0.2390 (2)	0.5973 (4)	0.62920 (16)	0.0317 (5)
C3	0.2768 (3)	0.7754 (5)	0.7185 (2)	0.0488 (8)
C4	0.3858 (2)	0.3403 (3)	0.55323 (17)	0.0332 (6)
C5	0.2362 (2)	0.3401 (3)	0.45473 (16)	0.0296 (5)
C6	0.2588 (2)	0.2377 (4)	0.35165 (19)	0.0423 (7)
C7	0.1158 (3)	0.0525 (6)	0.1882 (2)	0.0590 (9)
C8	−0.0492 (2)	−0.0090 (4)	0.12000 (18)	0.0399 (7)
C9	−0.1375 (3)	0.1285 (4)	0.0348 (2)	0.0494 (8)
C10	−0.2882 (3)	0.0672 (5)	−0.0275 (2)	0.0528 (8)
C11	−0.3519 (3)	−0.1313 (5)	−0.0051 (2)	0.0496 (7)
C12	−0.2647 (3)	−0.2686 (4)	0.0797 (2)	0.0492 (8)
C13	−0.1137 (3)	−0.2081 (4)	0.14164 (19)	0.0433 (7)
H2	0.16370	0.48740	0.64490	0.0380*
H3A	0.32420	0.70510	0.79170	0.0730*
H3B	0.18010	0.85350	0.71800	0.0730*
H3C	0.35080	0.88390	0.70390	0.0730*
H5	0.15530	0.24980	0.47590	0.0360*
H6A	0.31820	0.34170	0.31810	0.0510*
H6B	0.31820	0.09480	0.37040	0.0510*
H7A	0.17580	−0.08490	0.21960	0.0710*
H7B	0.16980	0.12940	0.14040	0.0710*
H9	−0.09420	0.26600	0.01900	0.0590*
H10	−0.34780	0.16240	−0.08600	0.0630*
H11	−0.45540	−0.17340	−0.04780	0.0600*
H12	−0.30850	−0.40540	0.09580	0.0590*
H13	−0.05400	−0.30440	0.19950	0.0520*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0307 (7)	0.0289 (7)	0.0591 (9)	0.0031 (6)	0.0146 (6)	0.0020 (7)
O2	0.0228 (6)	0.0317 (7)	0.0331 (7)	0.0011 (5)	0.0073 (5)	0.0029 (6)
O3	0.0207 (6)	0.0439 (8)	0.0360 (7)	0.0018 (6)	0.0013 (5)	0.0009 (7)
O4	0.0282 (7)	0.0456 (9)	0.0668 (10)	0.0121 (8)	0.0039 (6)	−0.0018 (9)
O5	0.0290 (7)	0.0487 (9)	0.0425 (8)	−0.0010 (7)	0.0078 (6)	−0.0155 (7)
C1	0.0172 (7)	0.0265 (9)	0.0400 (10)	−0.0037 (7)	0.0093 (6)	−0.0006 (8)
C2	0.0224 (8)	0.0383 (10)	0.0348 (10)	−0.0023 (8)	0.0093 (7)	−0.0011 (9)
C3	0.0375 (11)	0.0643 (16)	0.0439 (12)	−0.0059 (11)	0.0115 (9)	−0.0166 (12)
C4	0.0211 (8)	0.0306 (10)	0.0447 (11)	0.0008 (8)	0.0054 (7)	0.0037 (9)
C5	0.0190 (8)	0.0287 (9)	0.0391 (10)	0.0008 (8)	0.0060 (7)	−0.0031 (8)
C6	0.0237 (9)	0.0499 (14)	0.0530 (13)	−0.0003 (9)	0.0115 (8)	−0.0166 (11)
C7	0.0389 (12)	0.079 (2)	0.0666 (16)	−0.0163 (13)	0.0271 (11)	−0.0393 (16)
C8	0.0370 (11)	0.0471 (12)	0.0403 (11)	−0.0067 (10)	0.0190 (9)	−0.0161 (10)
C9	0.0608 (14)	0.0401 (12)	0.0576 (14)	−0.0066 (11)	0.0336 (12)	−0.0005 (11)
C10	0.0577 (14)	0.0572 (15)	0.0423 (12)	0.0117 (13)	0.0138 (10)	0.0108 (12)
C11	0.0419 (12)	0.0564 (14)	0.0432 (12)	−0.0031 (12)	0.0022 (10)	−0.0055 (12)
C12	0.0463 (12)	0.0404 (13)	0.0563 (14)	−0.0093 (12)	0.0091 (10)	0.0001 (11)
C13	0.0391 (11)	0.0473 (13)	0.0401 (12)	0.0009 (10)	0.0073 (9)	0.0026 (10)

Geometric parameters (Å, º)

O1—C1	1.196 (3)	C11—C12	1.377 (4)
O2—C1	1.337 (2)	C12—C13	1.383 (4)
O2—C5	1.446 (2)	C2—H2	1.0000
O3—C2	1.457 (2)	C3—H3A	0.9800
O3—C4	1.340 (2)	C3—H3B	0.9800
O4—C4	1.198 (2)	C3—H3C	0.9800
O5—C6	1.418 (3)	C5—H5	1.0000
O5—C7	1.416 (3)	C6—H6A	0.9900
C1—C2	1.516 (3)	C6—H6B	0.9900
C2—C3	1.503 (3)	C7—H7A	0.9900
C4—C5	1.518 (3)	C7—H7B	0.9900
C5—C6	1.499 (3)	C9—H9	0.9500
C7—C8	1.506 (3)	C10—H10	0.9500
C8—C9	1.384 (3)	C11—H11	0.9500
C8—C13	1.379 (3)	C12—H12	0.9500
C9—C10	1.383 (4)	C13—H13	0.9500
C10—C11	1.376 (4)
O1···C5^i	3.134 (3)	C7···H9^viii	3.0700
O1···C6^i	3.392 (3)	C8···H9^viii	2.8000
O1···O2^ii	3.146 (2)	C11···H7B^viii	3.0400
O1···C1^ii	3.043 (3)	C13···H2^iv	3.0800
O1···C2^ii	3.247 (3)	H2···C5	2.8000
O1···C5^ii	3.272 (3)	H2···H5	2.5300
O2···O5	2.847 (2)	H2···O1^iv	2.5700
O2···O3	2.757 (2)	H2···C13^ii	3.0800
O2···O4^iii	3.031 (2)	H3A···H11^ix	2.4500
O2···O1^iv	3.146 (2)	H3B···O1	2.6700
O3···O2	2.757 (2)	H3B···O5^ii	2.7600
O4···C4^v	3.035 (3)	H3C···O1	2.8800
O4···O2^v	3.031 (2)	H5···O1^vi	2.3200
O4···C5^v	3.340 (3)	H5···C2	2.7600
O5···O2	2.847 (2)	H5···H2	2.5300
O1···H2^ii	2.5700	H5···O1^iv	2.5400
O1···H5^ii	2.5400	H5···C1^iv	2.9400
O1···H3B	2.6700	H6A···H7B	2.5500
O1···H3C	2.8800	H6B···O4	2.5500
O1···H5^i	2.3200	H6B···H7A	2.2100
O3···H6B^iii	2.7700	H6B···O3^v	2.7700
O4···H6B	2.5500	H6B···O4^v	2.7500
O4···H6B^iii	2.7500	H6B···C4^v	2.9400
O5···H3B^iv	2.7600	H7A···H6B	2.2100
C1···O1^iv	3.043 (3)	H7A···H13	2.3800
C2···O1^iv	3.247 (3)	H7B···H6A	2.5500
C4···O4^iii	3.035 (3)	H7B···H9	2.5200
C5···O1^vi	3.134 (3)	H7B···C11^x	3.0400
C5···O4^iii	3.340 (3)	H9···H7B	2.5200
C5···O1^iv	3.272 (3)	H9···C7^x	3.0700
C6···O1^vi	3.392 (3)	H9···C8^x	2.8000
C1···H5^ii	2.9400	H11···H3A^xi	2.4500
C2···H5	2.7600	H11···H12^xii	2.5600
C3···H12^vii	2.9500	H12···C3^xiii	2.9500
C4···H6B^iii	2.9400	H12···H11^xiv	2.5600
C5···H2	2.8000	H13···H7A	2.3800
C1—O2—C5	116.91 (14)	C2—C3—H3B	109.00
C2—O3—C4	117.76 (15)	C2—C3—H3C	109.00
C6—O5—C7	110.84 (17)	H3A—C3—H3B	110.00
O1—C1—O2	119.90 (18)	H3A—C3—H3C	109.00
O1—C1—C2	123.97 (18)	H3B—C3—H3C	109.00
O2—C1—C2	116.12 (16)	O2—C5—H5	108.00
O3—C2—C1	110.49 (15)	C4—C5—H5	108.00
O3—C2—C3	107.20 (17)	C6—C5—H5	108.00
C1—C2—C3	112.50 (19)	O5—C6—H6A	110.00
O3—C4—O4	120.28 (19)	O5—C6—H6B	110.00
O3—C4—C5	115.01 (16)	C5—C6—H6A	110.00
O4—C4—C5	124.65 (18)	C5—C6—H6B	110.00
O2—C5—C4	111.11 (14)	H6A—C6—H6B	108.00
O2—C5—C6	108.29 (16)	O5—C7—H7A	110.00
C4—C5—C6	112.65 (16)	O5—C7—H7B	110.00
O5—C6—C5	107.12 (16)	C8—C7—H7A	110.00
O5—C7—C8	108.1 (2)	C8—C7—H7B	110.00
C7—C8—C9	121.5 (2)	H7A—C7—H7B	108.00
C7—C8—C13	119.5 (2)	C8—C9—H9	120.00
C9—C8—C13	119.0 (2)	C10—C9—H9	120.00
C8—C9—C10	120.5 (2)	C9—C10—H10	120.00
C9—C10—C11	120.2 (2)	C11—C10—H10	120.00
C10—C11—C12	119.6 (2)	C10—C11—H11	120.00
C11—C12—C13	120.3 (2)	C12—C11—H11	120.00
C8—C13—C12	120.5 (2)	C11—C12—H12	120.00
O3—C2—H2	109.00	C13—C12—H12	120.00
C1—C2—H2	109.00	C8—C13—H13	120.00
C3—C2—H2	109.00	C12—C13—H13	120.00
C2—C3—H3A	109.00
C5—O2—C1—O1	−171.03 (17)	O4—C4—C5—O2	−142.10 (19)
C5—O2—C1—C2	7.5 (2)	O4—C4—C5—C6	−20.4 (3)
C1—O2—C5—C4	−47.9 (2)	O3—C4—C5—C6	162.66 (17)
C1—O2—C5—C6	−172.09 (15)	C4—C5—C6—O5	166.08 (16)
C4—O3—C2—C1	−46.1 (2)	O2—C5—C6—O5	−70.6 (2)
C4—O3—C2—C3	−168.96 (18)	O5—C7—C8—C9	84.7 (3)
C2—O3—C4—O4	−170.84 (19)	O5—C7—C8—C13	−96.1 (3)
C2—O3—C4—C5	6.3 (2)	C7—C8—C9—C10	179.3 (2)
C7—O5—C6—C5	−165.8 (2)	C9—C8—C13—C12	−0.5 (4)
C6—O5—C7—C8	172.4 (2)	C13—C8—C9—C10	0.1 (4)
O1—C1—C2—O3	−142.3 (2)	C7—C8—C13—C12	−179.7 (2)
O2—C1—C2—C3	159.02 (18)	C8—C9—C10—C11	0.1 (4)
O1—C1—C2—C3	−22.6 (3)	C9—C10—C11—C12	0.0 (4)
O2—C1—C2—O3	39.3 (2)	C10—C11—C12—C13	−0.3 (4)
O3—C4—C5—O2	41.0 (2)	C11—C12—C13—C8	0.6 (4)

Symmetry codes: (i) x, y+1, z; (ii) −x, y+1/2, −z+1; (iii) −x+1, y+1/2, −z+1; (iv) −x, y−1/2, −z+1; (v) −x+1, y−1/2, −z+1; (vi) x, y−1, z; (vii) −x, y+3/2, −z+1; (viii) −x, y−1/2, −z; (ix) x+1, y+1, z+1; (x) −x, y+1/2, −z; (xi) x−1, y−1, z−1; (xii) −x−1, y+1/2, −z; (xiii) −x, y−3/2, −z+1; (xiv) −x−1, y−1/2, −z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···O1^iv	1.00	2.57	3.247 (3)	125
C5—H5···O1^vi	1.00	2.32	3.134 (3)	137
C5—H5···O1^iv	1.00	2.54	3.272 (3)	130

Symmetry codes: (iv) −x, y−1/2, −z+1; (vi) x, y−1, z.