4,8-An­hydro-1,2,3,5-tetra­deoxy-D-allo-non-1-enitol

The crystal structure of 4,8-anhydro-1,2,3,5-tetra­deoxy-D-allo-non-1-enitol, C₉H₁₆O₄, is reported. The pyran ring adopts the ⁴C₇ chair conformation, in which the hydroxy­methyl group is oriented axially. This chair conformer can be viewed as inverted relative to those observed in the crystal structures of the majority of other C-glycosides reported to date, in which the hydroxy­methyl group is generally equatorial. The conformation about the hydroxy­methyl group bond is gauche-trans and the internal alkene C atom is oriented gauche to the ring O atom.

Key indicators

• Single-crystal X-ray study
• T = 193 K
• Mean [sigma](C-C) = 0.010 Å
• R factor = 0.063
• wR factor = 0.179
• Data-to-parameter ratio = 8.8

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT063_ALERT_3_A Crystal Probably too Large for Beam Size .......       1.25 mm

Author Response: ...Owing to the nature of the crystals (i.e. tendancy for the compound to grow as very long, thin needles), attempts were made to cleave several crystals in order to obtain shorter (approx. 0.50 mm in length) samples to use. However, they displayed a tendency to splay (fracture along the length of the crystal) upon cutting, rendering them useless for diffraction trials. Therefore, on the basis of the very low linear absorption coefficient, it was decided to proceed with data collection on an intact crystal, which ultimately has yielded useful results.

Alert level B
CRYSS02_ALERT_3_B  The value of _exptl_crystal_size_max is > 1.0
   Maximum crystal size given =   1.250

Alert level C
PLAT220_ALERT_2_C Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       3.44 Ratio
PLAT222_ALERT_3_C Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       3.45 Ratio
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...         10
PLAT417_ALERT_2_C Short Inter D-H..H-D       H9O    ..  H9O     ..       2.15 Ang.
PLAT417_ALERT_2_C Short Inter D-H..H-D       H9O    ..  H9O     ..       2.15 Ang.

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           26.41
           From the CIF: _reflns_number_total               1068
           Count of symmetry unique reflns         1074
           Completeness (_total/calc)             99.44%
           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

   1 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   5 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
   3 ALERT type 2 Indicator that the structure model may be wrong or deficient
   4 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: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 1997); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997b); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997b); molecular graphics: SHELXTL (Sheldrick, 1997a); software used to prepare material for publication: SHELXTL.

4,8-anhydro-1,2,3,5-tetradeoxy-D-allo-non-1-enitol

Crystal data

C9H16O4	Dx = 1.195 Mg m^−3
Mr = 188.22	Melting point: 368 K
Trigonal, P32	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 32	Cell parameters from 1272 reflections
a = 13.3072 (14) Å	θ = 3.1–25.8°
c = 5.1172 (11) Å	µ = 0.09 mm^−1
V = 784.8 (2) Å^3	T = 193 K
Z = 3	Needle, colourless
F(000) = 306	1.25 × 0.06 × 0.06 mm

Data collection

Bruker PLATFORM/SMART 1000 CCD area-detector diffractometer	1068 independent reflections
Radiation source: fine-focus sealed tube	797 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.079
Detector resolution: 8.192 pixels mm^-1	θmax = 26.4°, θmin = 1.8°
ω scans	h = −16→16
Absorption correction: integration (SHELXTL; Sheldrick, 1997a)	k = −14→16
Tmin = 0.946, Tmax = 0.996	l = −5→6
4402 measured 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)] = 0.063	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.179	H-atom parameters constrained
S = 1.14	w = 1/[σ^2(Fo^2) + (0.0659P)^2 + 0.4028P] where P = (Fo^2 + 2Fc^2)/3
1068 reflections	(Δ/σ)max < 0.001
121 parameters	Δρmax = 0.34 e Å^−3
1 restraint	Δρmin = −0.32 e Å^−3

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) 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.

Hydrogen atoms were refined with fixed C—H and O—H distances and with isotropic displacement parameters 20% greater than those for their attached atoms. The absolute structure could not be determined from the X-ray data (light atoms only), but was assigned on the basis of the established stereochemistry of the precursor compound. Friedel pairs were merged before the final least-squares refinement.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O6	0.1319 (4)	0.1165 (5)	0.2846 (10)	0.0576 (13)
H6O	0.1417	0.0870	0.1487	0.069*
O7	0.1696 (3)	0.0573 (3)	0.8012 (8)	0.0434 (11)
H7O	0.1109	−0.0008	0.7389	0.052*
O8	0.3794 (3)	0.2766 (3)	0.8755 (8)	0.0369 (10)
O9	0.5754 (3)	0.2429 (3)	0.7439 (9)	0.0394 (10)
H9O	0.6355	0.2678	0.6520	0.047*
C1	0.5098 (9)	0.6303 (7)	1.044 (3)	0.109 (4)
H1A	0.4771	0.6701	0.9555	0.131*
H1B	0.5788	0.6726	1.1430	0.131*
C2	0.4589 (7)	0.5154 (6)	1.0274 (18)	0.067 (2)
H2	0.4942	0.4787	1.1181	0.080*
C3	0.3529 (6)	0.4412 (5)	0.8809 (16)	0.0544 (18)
H3A	0.3352	0.4912	0.7696	0.065*
H3B	0.2883	0.4012	1.0067	0.065*
C4	0.3568 (5)	0.3509 (5)	0.7097 (13)	0.0427 (15)
H4	0.4216	0.3905	0.5813	0.051*
C5	0.2435 (5)	0.2817 (6)	0.5620 (13)	0.0464 (16)
H5A	0.1778	0.2519	0.6864	0.056*
H5B	0.2345	0.3329	0.4355	0.056*
C6	0.2407 (4)	0.1818 (5)	0.4188 (12)	0.0391 (14)
H6	0.3048	0.2131	0.2873	0.047*
C7	0.2588 (4)	0.1058 (4)	0.6078 (12)	0.0344 (13)
H7	0.2605	0.0417	0.5097	0.041*
C8	0.3742 (4)	0.1783 (4)	0.7483 (11)	0.0317 (12)
H8	0.3758	0.1279	0.8912	0.038*
C9	0.4781 (4)	0.2086 (5)	0.5799 (14)	0.0412 (14)
H9A	0.4641	0.1405	0.4743	0.049*
H9B	0.4922	0.2726	0.4594	0.049*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O6	0.037 (2)	0.104 (4)	0.040 (3)	0.041 (2)	−0.005 (2)	−0.018 (3)
O7	0.0290 (18)	0.039 (2)	0.038 (3)	−0.0014 (15)	0.0032 (17)	−0.0040 (18)
O8	0.0322 (17)	0.0313 (17)	0.039 (3)	0.0095 (15)	0.0044 (17)	−0.0039 (17)
O9	0.0254 (16)	0.043 (2)	0.047 (3)	0.0146 (15)	−0.0007 (16)	−0.0098 (19)
C1	0.094 (7)	0.055 (5)	0.174 (12)	0.033 (5)	−0.019 (7)	−0.032 (6)
C2	0.065 (4)	0.055 (4)	0.085 (7)	0.033 (3)	0.009 (4)	−0.004 (4)
C3	0.065 (4)	0.042 (3)	0.053 (5)	0.025 (3)	0.011 (3)	0.002 (3)
C4	0.050 (3)	0.038 (3)	0.042 (4)	0.024 (2)	0.015 (3)	0.009 (3)
C5	0.051 (3)	0.059 (3)	0.042 (4)	0.037 (3)	0.005 (3)	0.007 (3)
C6	0.030 (2)	0.060 (3)	0.030 (4)	0.024 (2)	0.005 (2)	0.000 (3)
C7	0.031 (2)	0.031 (2)	0.038 (4)	0.012 (2)	0.007 (2)	−0.008 (2)
C8	0.028 (2)	0.027 (2)	0.034 (4)	0.0086 (19)	0.001 (2)	−0.002 (2)
C9	0.030 (2)	0.041 (3)	0.050 (4)	0.016 (2)	−0.003 (3)	−0.008 (3)

Geometric parameters (Å, º)

O6—C6	1.437 (7)	C3—H3B	0.9900
O6—H6O	0.8400	C4—C5	1.518 (9)
O7—C7	1.427 (6)	C4—H4	1.0000
O7—H7O	0.8400	C5—C6	1.502 (9)
O8—C8	1.431 (6)	C5—H5A	0.9900
O8—C4	1.444 (7)	C5—H5B	0.9900
O9—C9	1.413 (7)	C6—C7	1.503 (8)
O9—H9O	0.8400	C6—H6	1.0000
C1—C2	1.330 (10)	C7—C8	1.525 (7)
C1—H1A	0.9500	C7—H7	1.0000
C1—H1B	0.9500	C8—C9	1.503 (8)
C2—C3	1.461 (11)	C8—H8	1.0000
C2—H2	0.9500	C9—H9A	0.9900
C3—C4	1.509 (9)	C9—H9B	0.9900
C3—H3A	0.9900
C6—O6—H6O	109.5	C4—C5—H5B	109.4
C7—O7—H7O	109.5	H5A—C5—H5B	108.0
C8—O8—C4	115.3 (4)	O6—C6—C5	109.9 (4)
C9—O9—H9O	109.5	O6—C6—C7	110.6 (5)
C2—C1—H1A	120.0	C5—C6—C7	109.9 (5)
C2—C1—H1B	120.0	O6—C6—H6	108.8
H1A—C1—H1B	120.0	C5—C6—H6	108.8
C1—C2—C3	125.0 (9)	C7—C6—H6	108.8
C1—C2—H2	117.5	O7—C7—C6	112.0 (4)
C3—C2—H2	117.5	O7—C7—C8	107.8 (5)
C2—C3—C4	115.5 (6)	C6—C7—C8	109.1 (4)
C2—C3—H3A	108.4	O7—C7—H7	109.3
C4—C3—H3A	108.4	C6—C7—H7	109.3
C2—C3—H3B	108.4	C8—C7—H7	109.3
C4—C3—H3B	108.4	O8—C8—C9	113.5 (4)
H3A—C3—H3B	107.5	O8—C8—C7	111.5 (4)
O8—C4—C3	107.8 (5)	C9—C8—C7	113.6 (4)
O8—C4—C5	111.1 (4)	O8—C8—H8	105.9
C3—C4—C5	110.7 (5)	C9—C8—H8	105.9
O8—C4—H4	109.0	C7—C8—H8	105.9
C3—C4—H4	109.0	O9—C9—C8	108.5 (5)
C5—C4—H4	109.0	O9—C9—H9A	110.0
C6—C5—C4	111.0 (4)	C8—C9—H9A	110.0
C6—C5—H5A	109.4	O9—C9—H9B	110.0
C4—C5—H5A	109.4	C8—C9—H9B	110.0
C6—C5—H5B	109.4	H9A—C9—H9B	108.4
C1—C2—C3—C4	133.0 (10)	O6—C6—C7—C8	−179.4 (4)
C8—O8—C4—C3	173.9 (4)	C5—C6—C7—C8	−57.9 (5)
C8—O8—C4—C5	52.4 (6)	C4—O8—C8—C9	75.2 (6)
C2—C3—C4—O8	59.8 (7)	C4—O8—C8—C7	−54.5 (5)
C2—C3—C4—C5	−178.4 (6)	O7—C7—C8—O8	−65.7 (5)
O8—C4—C5—C6	−52.8 (7)	C6—C7—C8—O8	56.1 (5)
C3—C4—C5—C6	−172.6 (5)	O7—C7—C8—C9	164.6 (4)
C4—C5—C6—O6	179.0 (5)	C6—C7—C8—C9	−73.6 (5)
C4—C5—C6—C7	57.0 (6)	O8—C8—C9—O9	69.1 (6)
O6—C6—C7—O7	−60.2 (6)	C7—C8—C9—O9	−162.2 (4)
C5—C6—C7—O7	61.4 (6)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O6—H6O···O7^i	0.84	1.90	2.718 (6)	165
O7—H7O···O6^ii	0.84	1.82	2.661 (5)	177
O9—H9O···O9^iii	0.84	1.87	2.701 (5)	170

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