1-De­oxy-4-C-hydroxy­methyl-3,4-O-isopropyl­idene-β-l-ribulofuran­ose [(2R,3S,4S)-4-(hydroxy­meth­yl)-3,4-O-isopropyl­idene-2-methyl­tetra­hydro­furan-2,3,4-triol]

Best, D.; Jenkinson, S.F.; Booth, K.V.; Fleet, G.W.J.; Watkin, D.J.

doi:10.1107/S1600536807014134

1-Deoxy-4-C-hydroxymethyl-3,4-O-isopropylidene-β-L-ribulofuranose [(2R,3S,4S)-4-(hydroxymethyl)-3,4-O-isopropylidene-2-methyltetrahydrofuran-2,3,4-triol]

D. Best, S. F. Jenkinson, K. V. Booth, G. W. J. Fleet and D. J. Watkin

The stereochemistry of crystalline 1-deoxy-4-C-hydroxymethyl-3,4-O-isopropylidene-β-L-ribulofuranose, C₉H₁₆O₅, was unequivocally established by X-ray crystallographic analysis to be the β-anomer; the absolute configuration was determined by the use of D-ribose as a starting material.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807014134/lh2347sup1.cif Contains datablocks global, 3
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536807014134/lh23473sup2.hkl Contains datablock 3

CCDC reference: 647273

checkCIF report

Key indicators

Single-crystal X-ray study
T = 150 K
Mean (C-C) = 0.003 Å
R factor = 0.041
wR factor = 0.106
Data-to-parameter ratio = 10.4

checkCIF/PLATON results

No syntax errors found



Alert level B
ABSTM02_ALERT_3_B  The ratio of expected to reported Tmax/Tmin(RR') is < 0.75
            Tmin and Tmax reported:      0.690     0.990
            Tmin(prime) and Tmax expected:      0.946     0.989
            RR(prime) =      0.729
            Please check that your absorption correction is appropriate.
PLAT061_ALERT_3_B Tmax/Tmin Range Test RR' too Large .............       0.73

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           27.46
           From the CIF: _reflns_number_total               1315
           Count of symmetry unique reflns         1351
           Completeness (_total/calc)             97.34%
           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
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C1     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3     = .          S

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

   3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 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
   0 ALERT type 5 Informative message, check

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.

(2R,3S,4S)-4-(hydroxymethyl)-3,4-O-isopropylidene-2- methyltetrahydrofuran-2,3,4-triol top

Crystal data top

C₉H₁₆O₅	F(000) = 440
M_r = 204.22	D_x = 1.346 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 1245 reflections
a = 6.2405 (2) Å	θ = 5–27°
b = 10.8088 (3) Å	µ = 0.11 mm⁻¹
c = 14.9369 (6) Å	T = 150 K
V = 1007.53 (6) Å³	Plate, colourless
Z = 4	0.50 × 0.20 × 0.10 mm

Data collection top

Nonius KappaCCD diffractometer	1210 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.066
ω scans	θ_max = 27.5°, θ_min = 5.2°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −8→8
T_min = 0.69, T_max = 0.99	k = −13→13
7730 measured reflections	l = −18→18
1315 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)] = 0.041	H-atom parameters constrained
wR(F²) = 0.106	w = 1/[σ²(F²) + (0.08P)² + 0.46P], where P = [max(F_o²,0) + 2F_c²]/3
S = 0.84	(Δ/σ)_max = 0.000274
1315 reflections	Δρ_max = 0.27 e Å⁻³
127 parameters	Δρ_min = −0.27 e Å⁻³
0 restraints

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

	x	y	z	U_iso*/U_eq
C1	0.4665 (4)	0.74459 (18)	0.67571 (12)	0.0180
C2	0.5277 (4)	0.60607 (18)	0.68257 (13)	0.0190
C3	0.6693 (4)	0.5833 (2)	0.60104 (14)	0.0212
O4	0.7697 (2)	0.69873 (13)	0.58458 (9)	0.0220
C5	0.6151 (4)	0.79423 (19)	0.60212 (14)	0.0213
O6	0.5229 (3)	0.55251 (15)	0.53238 (9)	0.0266
C7	0.8450 (4)	0.4880 (2)	0.61209 (15)	0.0294
O8	0.6530 (3)	0.59994 (14)	0.76291 (9)	0.0222
C9	0.5781 (4)	0.69651 (19)	0.82087 (13)	0.0226
O10	0.5235 (3)	0.79561 (12)	0.76172 (9)	0.0210
C11	0.3864 (4)	0.6512 (2)	0.87373 (15)	0.0286
C12	0.7615 (4)	0.7381 (2)	0.87942 (15)	0.0323
C13	0.2320 (4)	0.7688 (2)	0.65531 (14)	0.0223
O14	0.1938 (3)	0.89698 (14)	0.63582 (10)	0.0264
H21	0.4078	0.5501	0.6842	0.0197*
H51	0.6816	0.8700	0.6206	0.0242*
H52	0.5301	0.8109	0.5501	0.0245*
H71	0.9168	0.4750	0.5561	0.0443*
H72	0.9529	0.5161	0.6535	0.0434*
H73	0.7893	0.4091	0.6316	0.0446*
H111	0.3425	0.7168	0.9127	0.0414*
H112	0.4397	0.5800	0.9060	0.0407*
H113	0.2763	0.6283	0.8313	0.0417*
H121	0.7204	0.8077	0.9152	0.0463*
H122	0.8003	0.6730	0.9227	0.0462*
H123	0.8950	0.7577	0.8453	0.0458*
H131	0.1463	0.7449	0.7073	0.0259*
H132	0.1832	0.7195	0.6031	0.0267*
H13	0.2537	0.9371	0.6774	0.0395*
H7	0.6052	0.5557	0.4890	0.0394*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0228 (10)	0.0161 (9)	0.0152 (9)	−0.0002 (8)	−0.0028 (8)	−0.0014 (7)
C2	0.0207 (10)	0.0193 (9)	0.0169 (9)	−0.0022 (8)	−0.0014 (8)	−0.0003 (7)
C3	0.0248 (11)	0.0209 (10)	0.0179 (9)	−0.0023 (9)	0.0016 (8)	−0.0011 (7)
O4	0.0223 (7)	0.0208 (7)	0.0230 (7)	−0.0021 (6)	0.0033 (6)	0.0011 (5)
C5	0.0254 (10)	0.0188 (10)	0.0196 (9)	0.0001 (9)	0.0012 (9)	0.0011 (7)
O6	0.0313 (8)	0.0324 (8)	0.0160 (6)	−0.0075 (7)	0.0009 (7)	−0.0041 (6)
C7	0.0337 (12)	0.0245 (11)	0.0299 (11)	0.0059 (10)	0.0077 (10)	0.0000 (9)
O8	0.0291 (8)	0.0218 (7)	0.0157 (6)	0.0060 (7)	−0.0034 (6)	−0.0017 (5)
C9	0.0314 (12)	0.0208 (10)	0.0156 (9)	0.0050 (9)	−0.0028 (8)	−0.0010 (8)
O10	0.0315 (8)	0.0180 (7)	0.0134 (6)	0.0005 (6)	−0.0038 (6)	−0.0017 (5)
C11	0.0377 (13)	0.0269 (11)	0.0213 (10)	0.0038 (10)	0.0058 (10)	0.0032 (8)
C12	0.0392 (13)	0.0329 (12)	0.0248 (10)	0.0015 (11)	−0.0131 (10)	−0.0036 (9)
C13	0.0233 (10)	0.0228 (10)	0.0207 (9)	0.0019 (9)	−0.0010 (8)	−0.0011 (8)
O14	0.0336 (9)	0.0233 (7)	0.0223 (7)	0.0065 (7)	−0.0091 (7)	−0.0031 (6)

Geometric parameters (Å, º) top

C1—C2	1.549 (3)	C7—H73	0.966
C1—C5	1.535 (3)	O8—C9	1.434 (2)
C1—O10	1.443 (2)	C9—O10	1.430 (2)
C1—C13	1.518 (3)	C9—C11	1.515 (3)
C2—C3	1.525 (3)	C9—C12	1.509 (3)
C2—O8	1.434 (2)	C11—H111	0.957
C2—H21	0.963	C11—H112	0.967
C3—O4	1.418 (3)	C11—H113	0.967
C3—O6	1.413 (3)	C12—H121	0.959
C3—C7	1.513 (3)	C12—H122	0.985
O4—C5	1.437 (3)	C12—H123	1.000
C5—H51	0.959	C13—O14	1.436 (3)
C5—H52	0.958	C13—H131	0.978
O6—H7	0.827	C13—H132	0.992
C7—H71	0.959	O14—H13	0.845
C7—H72	0.964

C2—C1—C5	103.68 (16)	H71—C7—H73	107.5
C2—C1—O10	104.47 (15)	H72—C7—H73	109.7
C5—C1—O10	110.81 (16)	C2—O8—C9	107.09 (15)
C2—C1—C13	114.68 (17)	O8—C9—O10	104.47 (14)
C5—C1—C13	112.24 (16)	O8—C9—C11	109.66 (18)
O10—C1—C13	110.53 (18)	O10—C9—C11	112.11 (18)
C1—C2—C3	104.25 (16)	O8—C9—C12	108.63 (19)
C1—C2—O8	103.56 (15)	O10—C9—C12	108.42 (18)
C3—C2—O8	110.17 (16)	C11—C9—C12	113.15 (18)
C1—C2—H21	114.7	C1—O10—C9	108.83 (14)
C3—C2—H21	111.7	C9—C11—H111	107.7
O8—C2—H21	111.9	C9—C11—H112	104.2
C2—C3—O4	104.63 (16)	H111—C11—H112	112.6
C2—C3—O6	104.05 (16)	C9—C11—H113	107.6
O4—C3—O6	111.52 (17)	H111—C11—H113	112.6
C2—C3—C7	116.28 (18)	H112—C11—H113	111.6
O4—C3—C7	107.34 (18)	C9—C12—H121	110.8
O6—C3—C7	112.78 (18)	C9—C12—H122	110.7
C3—O4—C5	107.71 (15)	H121—C12—H122	105.1
C1—C5—O4	106.56 (16)	C9—C12—H123	113.5
C1—C5—H51	110.7	H121—C12—H123	109.9
O4—C5—H51	112.1	H122—C12—H123	106.4
C1—C5—H52	108.2	C1—C13—O14	111.55 (18)
O4—C5—H52	111.0	C1—C13—H131	108.8
H51—C5—H52	108.2	O14—C13—H131	109.0
C3—O6—H7	99.1	C1—C13—H132	111.2
C3—C7—H71	110.1	O14—C13—H132	107.9
C3—C7—H72	111.2	H131—C13—H132	108.3
H71—C7—H72	106.2	C13—O14—H13	105.8
C3—C7—H73	111.9

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O14—H13···O8ⁱ	0.85	2.06	2.831 (2)	152
O6—H7···O14ⁱⁱ	0.83	2.01	2.783 (2)	155

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

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1-De­oxy-4-C-hydroxy­methyl-3,4-O-isopropyl­idene-β-L-ribulofuran­ose [(2R,3S,4S)-4-(hydroxy­meth­yl)-3,4-O-isopropyl­idene-2-methyl­tetra­hydro­furan-2,3,4-triol]

Supporting information

Key indicators

checkCIF/PLATON results

1-Deoxy-4-C-hydroxymethyl-3,4-O-isopropylidene-β-L-ribulofuranose [(2R,3S,4S)-4-(hydroxymethyl)-3,4-O-isopropylidene-2-methyltetrahydrofuran-2,3,4-triol]