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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 66| Part 6| June 2010| Page o1315
https://doi.org/10.1107/S1600536810016612

6-De­­oxy-6-fluoro-D-galactose

Sarah F. Jenkinson,a* Daniel Best,a Ken Izumori,b Francis X. Wilson,c Alexander C. Weymouth-Wilson,d George W. J. Fleeta and Amber L. Thompsone

aDepartment of Organic Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, England, bRare Sugar Research Centre, Kagawa University, 2393 Miki-cho, Kita-gun, Kagawa 761-0795, Japan, cSummit PLC, 91 Milton Park, Abingdon, Oxon OX14 4RY, England, dDextra Laboratories Ltd, Science and Technology Centre, Whiteknights Road, Reading RG6 6BZ, England, and eDepartment of Chemical Crystallography, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, England
*Correspondence e-mail: sarah.jenkinson@chem.ox.ac.uk

(Received 23 April 2010; accepted 6 May 2010; online 12 May 2010)

The crystal structure unequivocally confirms the relative stereochemistry of the title compound, C6H11FO5. The absolute stereochemistry was determined by the use of D-galactose as the starting material. The compound exists as a three-dimensional O—H⋯O hydrogen-bonded network with each mol­ecule acting as a donor and acceptor for four hydrogen bonds.

Related literature

For literature relating to the biotechnological inter­conversion of carbohydrates (Izumoring), see: Granström et al. (2004[Granström, T. B., Takata, G., Tokuda, M. & Izumori, K. J. (2004). J. Biosci. Bioeng. 97, 89-94.]); Izumori (2006[Izumori, K. J. (2006). J. Biotechnol. 124, 717-722.]); Jones et al. (2008[Jones, N. A., Rao, D., Yoshihara, A., Gullapalli, P., Morimoto, K., Takata, G., Hunter, S. J., Wormald, M. R., Dwek, R. A., Izumori, K. & Fleet, G. W. J. (2008). Tetrahedron Asymmetry, 16, 1904-1918.]); Rao et al. (2009[Rao, D., Best, D., Yoshihara, A., Gullapalli, P., Morimoto, K., Wormald, M. R., Wilson, F. X., Izumori, K. & Fleet, G. W. J. (2009). Tetrahedron Lett. 50, 3559-3563.]); Jenkinson et al. (2009[Jenkinson, S. F., Booth, K. V., Newberry, S., Fleet, G. W. J., Izumori, K., Morimoto, K., Nash, R. J., Jones, L., Watkin, D. J. & Thompson, A. L. (2009). Acta Cryst. E65, o1755-o1756.]); Gullapalli et al. (2010[Gullapalli, P., Yoshihara, A., Morimoto, K., Rao, D., Akimitsu, K., Jenkinson, S. F., Fleet, G. W. J. & Izumori, K. (2010). Tetrahedron Lett. 51, 895-898.]). For literature relating to fluoro­sugars, see: Cobb et al. (2005[Cobb, S. L., Deng, H., Hamilton, J. T. G., McGlinchey, R. P., O'Hagan, D. & Schaffrath, C. (2005). Bioorg. Chem. 33, 393-401.]); Caravano et al. (2009[Caravano, A., Field, R. A., Percy, J. M., Rinaudo, G., Roig, R. & Singh, K. (2009). Org. Biomol. Chem. 7, 996-1008.]); Brackhagen et al. (2001[Brackhagen, M., Boye, H. & Vogel, C. (2001). J. Carbohydr. Chem. 20, 31-43.]); Taylor & Kent (1958[Taylor, N. F. & Kent, P. W. (1958). J. Chem. Soc. pp. 872-875.]).

[Scheme 1]

Experimental

Crystal data

  • C6H11FO5

  • Mr = 182.15

  • Orthorhombic, P 21 21 21

  • a = 6.7928 (3) Å

  • b = 7.5822 (3) Å

  • c = 14.1165 (6) Å

  • V = 727.06 (5) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.16 mm−1

  • T = 150 K

  • 0.25 × 0.15 × 0.15 mm
Data collection

  • Area diffractometer

  • Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]) Tmin = 0.88, Tmax = 0.98

  • 6912 measured reflections

  • 978 independent reflections

  • 855 reflections with I > 2σ(I)

  • Rint = 0.082
Refinement

  • R[F2 > 2σ(F2)] = 0.048

  • wR(F2) = 0.119

  • S = 1.00

  • 978 reflections

  • 109 parameters

  • H-atom parameters constrained

  • Δρmax = 0.39 e Å−3

  • Δρmin = −0.33 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O12—H121⋯O8i 0.82 1.95 2.769 (4) 177
O11—H111⋯O12ii 0.84 1.96 2.781 (4) 168
O6—H61⋯O4iii 0.84 1.91 2.747 (4) 174
O8—H81⋯O6i 0.82 1.93 2.739 (4) 169
Symmetry codes: (i) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]; (ii) [-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]; (iii) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1].

Data collection: COLLECT (Nonius, 2001[Nonius (2001). COLLECT. Nonius BV, Delft, The Netherlands.]); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994[Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.]); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003[Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487.]); molecular graphics: CAMERON (Watkin et al., 1996[Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, Oxford, England.]); software used to prepare material for publication: CRYSTALS.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536810016612/lh5035sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810016612/lh5035Isup2.hkl

checkCIF report


Comment top

Izumoring, a strategy for the biotechnological interconversion of aldoses, ketoses and alditols (Granström et al. 2004, Izumori 2006) allows convenient access to rare monosaccharides. Interconversions are achieved by regioselective microbial oxidation of alditols to give the corresponding ketoses, followed by enzymatic isomerisation to aldoses. Stereochemical diversity is introduced at C-2 in the keto-aldose isomerisation step and at C-3 by the epimerisation of ketoses, catalysed by D-tagatose-3-epimerase. In addition to the simple monosaccharides, this strategy is effective for the interconversion of deoxy (Gullapalli et al. 2010, Rao et al. 2009), methyl-branched (Jones et al. 2008) and azido (Jenkinson et al. 2009) sugars.

Fluorosugars have not been isolated from natural sources and consequently, in order to study metabolic processes, their passage along various biological pathways can be effectively tracked with the detection of fluorinated metabolites by 19F NMR (Cobb et al. 2005). The fluoro modification of sugars affects their hydrogen bonding capability and fluorosugars have been shown to resemble deoxy sugars such as fucose and rhamnose in terms of enzymatic recognition (Caravano et al. 2009). Application of the Izumoring strategy to fluorinated substrates would allow the bulk preparation of fluorosugars, an important and interesting class of carbohydrates.

6-Deoxy-6-fluoro-D-galactose was prepared from D-galactose diacetonide 1 (Fig. 1). Fluoride was introduced nucleophilically to give the protected fluorogalactose 2 in 68% yield as previously described for the enantiomer (Brackhagen et al. 2001). Dowex resin (H+) catalysed hydrolysis of the diacetonide gave the free 6-deoxy-6-fluoro-D-galactose 3 in 98% yield.

X-ray crystallography unequivocally confirmed the relative stereochemistry of the title compound. The absolute stereochemistry was determined by the use of D-galactose as the starting material. The compound exists as an extensively hydrogen-bonded lattice with each molecule acting as a donor and acceptor for 4 hydrogen bonds. Only classical hydrogen bonding is considered.

Related literature top

For literature relating to the biotechnological interconversion of carbohydrates (Izumoring) see: Granström et al. (2004); Izumori (2006); Jones et al. (2008); Rao et al. (2009); Jenkinson et al. (2009); Gullapalli et al. (2010). For literature relating to fluorosugars see: Cobb et al. (2005); Caravano et al. (2009); Brackhagen et al. (2001); Taylor & Kent (1958).

Experimental top

The title compound was recrystallised by vapour diffusion from a mixture of ethanol and water [m.p. 431-433 K;[α]D25 initial: +119.8, equilibrium: +69.4 (c 1.12, H2O) {Lit. (Taylor & Kent, 1958) m.p. 433 K; [α]D20 initial: +135, equilibrium: +76.5 (c 0.967, H2O)].

Refinement top

In the absence of significant anomalous scattering, Friedel pairs were merged and the absolute configuration was assigned from the use of D-galactose as the starting material.

The H atoms were all located in a difference map, but those attached to carbon 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 in the range 0.93–0.98, O—H = 0.82 Å) and Uiso(H) (in the range 1.2–1.5 times Ueq of the parent atom), after which the positions were refined with riding constraints.

Structure description top

Izumoring, a strategy for the biotechnological interconversion of aldoses, ketoses and alditols (Granström et al. 2004, Izumori 2006) allows convenient access to rare monosaccharides. Interconversions are achieved by regioselective microbial oxidation of alditols to give the corresponding ketoses, followed by enzymatic isomerisation to aldoses. Stereochemical diversity is introduced at C-2 in the keto-aldose isomerisation step and at C-3 by the epimerisation of ketoses, catalysed by D-tagatose-3-epimerase. In addition to the simple monosaccharides, this strategy is effective for the interconversion of deoxy (Gullapalli et al. 2010, Rao et al. 2009), methyl-branched (Jones et al. 2008) and azido (Jenkinson et al. 2009) sugars.

Fluorosugars have not been isolated from natural sources and consequently, in order to study metabolic processes, their passage along various biological pathways can be effectively tracked with the detection of fluorinated metabolites by 19F NMR (Cobb et al. 2005). The fluoro modification of sugars affects their hydrogen bonding capability and fluorosugars have been shown to resemble deoxy sugars such as fucose and rhamnose in terms of enzymatic recognition (Caravano et al. 2009). Application of the Izumoring strategy to fluorinated substrates would allow the bulk preparation of fluorosugars, an important and interesting class of carbohydrates.

6-Deoxy-6-fluoro-D-galactose was prepared from D-galactose diacetonide 1 (Fig. 1). Fluoride was introduced nucleophilically to give the protected fluorogalactose 2 in 68% yield as previously described for the enantiomer (Brackhagen et al. 2001). Dowex resin (H+) catalysed hydrolysis of the diacetonide gave the free 6-deoxy-6-fluoro-D-galactose 3 in 98% yield.

X-ray crystallography unequivocally confirmed the relative stereochemistry of the title compound. The absolute stereochemistry was determined by the use of D-galactose as the starting material. The compound exists as an extensively hydrogen-bonded lattice with each molecule acting as a donor and acceptor for 4 hydrogen bonds. Only classical hydrogen bonding is considered.

For literature relating to the biotechnological interconversion of carbohydrates (Izumoring) see: Granström et al. (2004); Izumori (2006); Jones et al. (2008); Rao et al. (2009); Jenkinson et al. (2009); Gullapalli et al. (2010). For literature relating to fluorosugars see: Cobb et al. (2005); Caravano et al. (2009); Brackhagen et al. (2001); Taylor & Kent (1958).

Computing details top

Data collection: COLLECT (Nonius, 2001); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); 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 (Betteridge et al., 2003).

Figures top
[Figure 1] Fig. 1. Synthetic Scheme.
[Figure 2] Fig. 2. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitrary radius.
[Figure 3] Fig. 3. Packing diagram of the title compound projected along the b-axis. Hydrogen bonds are shown by dotted lines.
[Figure 4] Fig. 4. Packing diagram of the title compound projected along the a-axis. Hydrogen bonds are shown by dotted lines.
6-Deoxy-6-fluoro-D-galactose top
Crystal data top
C6H11FO5F(000) = 384
Mr = 182.15Dx = 1.664 Mg m−3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 976 reflections
a = 6.7928 (3) Åθ = 5–27°
b = 7.5822 (3) ŵ = 0.16 mm−1
c = 14.1165 (6) ÅT = 150 K
V = 727.06 (5) Å3Plate, colourless
Z = 40.25 × 0.15 × 0.15 mm
Data collection top
Area
diffractometer		855 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.082
ω scansθmax = 27.4°, θmin = 5.1°
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)		h = −8→8
Tmin = 0.88, Tmax = 0.98k = −9→9
6912 measured reflectionsl = −18→18
978 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.048H-atom parameters constrained
wR(F2) = 0.119 Method = Modified Sheldrick w = 1/[σ2(F2) + ( 0.06P)2 + 0.71P],
where P = [max(Fo2,0) + 2Fc2]/3
S = 1.00(Δ/σ)max = 0.000180
978 reflectionsΔρmax = 0.39 e Å−3
109 parametersΔρmin = −0.33 e Å−3
0 restraints
Crystal data top
C6H11FO5V = 727.06 (5) Å3
Mr = 182.15Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 6.7928 (3) ŵ = 0.16 mm−1
b = 7.5822 (3) ÅT = 150 K
c = 14.1165 (6) Å0.25 × 0.15 × 0.15 mm
Data collection top
Area
diffractometer		978 independent reflections
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)		855 reflections with I > 2σ(I)
Tmin = 0.88, Tmax = 0.98Rint = 0.082
6912 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0480 restraints
wR(F2) = 0.119H-atom parameters constrained
S = 1.00Δρmax = 0.39 e Å−3
978 reflectionsΔρmin = −0.33 e Å−3
109 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
F10.9642 (3)0.0074 (3)0.67642 (15)0.0322
C20.8064 (5)0.1203 (4)0.7000 (2)0.0241
C30.8368 (5)0.2957 (4)0.6533 (2)0.0197
O40.8221 (3)0.2665 (3)0.55221 (14)0.0197
C50.8651 (5)0.4205 (4)0.4981 (2)0.0199
O61.0586 (3)0.4776 (3)0.51563 (17)0.0249
C70.7217 (5)0.5681 (4)0.5230 (2)0.0193
O80.7765 (3)0.7197 (3)0.46922 (16)0.0253
C90.7242 (5)0.6033 (4)0.6292 (2)0.0196
C100.6857 (5)0.4332 (4)0.6843 (2)0.0207
O110.4899 (3)0.3738 (3)0.66532 (15)0.0234
O120.5874 (3)0.7379 (3)0.65554 (15)0.0225
H210.68890.06620.67380.0302*
H220.79790.13190.77010.0295*
H310.97230.33770.66700.0229*
H510.84630.39020.42780.0240*
H710.58580.53330.50640.0246*
H910.85390.64540.64600.0234*
H1010.70440.45570.75410.0250*
H1210.49800.74880.61700.0346*
H1110.44890.33610.71750.0347*
H611.13200.39830.49310.0374*
H810.71700.81190.48110.0389*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
F10.0339 (11)0.0274 (10)0.0352 (11)0.0100 (9)0.0011 (9)0.0051 (9)
C20.0227 (16)0.0222 (15)0.0273 (15)0.0057 (15)0.0012 (14)0.0016 (13)
C30.0187 (14)0.0211 (14)0.0193 (14)0.0019 (13)0.0003 (12)0.0014 (12)
O40.0221 (11)0.0165 (10)0.0205 (10)−0.0024 (9)0.0011 (9)0.0005 (9)
C50.0189 (15)0.0168 (14)0.0241 (14)−0.0029 (12)0.0029 (12)0.0020 (12)
O60.0193 (12)0.0195 (10)0.0359 (12)0.0006 (9)0.0060 (10)−0.0002 (9)
C70.0205 (16)0.0171 (14)0.0204 (14)0.0006 (12)0.0028 (12)0.0018 (12)
O80.0307 (12)0.0176 (10)0.0277 (11)0.0021 (10)0.0077 (10)0.0035 (9)
C90.0172 (15)0.0171 (14)0.0246 (15)0.0033 (13)0.0001 (12)−0.0020 (12)
C100.0192 (16)0.0228 (15)0.0203 (14)0.0005 (13)−0.0016 (12)0.0012 (12)
O110.0185 (11)0.0281 (12)0.0236 (11)−0.0034 (10)0.0013 (9)0.0023 (10)
O120.0220 (11)0.0230 (11)0.0226 (10)0.0054 (10)−0.0005 (9)−0.0038 (10)
Geometric parameters (Å, º) top
F1—C21.412 (4)C7—O81.428 (4)
C2—C31.499 (4)C7—C91.522 (4)
C2—H210.971C7—H710.988
C2—H220.995O8—H810.824
C3—O41.448 (3)C9—C101.528 (4)
C3—C101.527 (4)C9—O121.430 (4)
C3—H310.992C9—H910.967
O4—C51.426 (4)C10—O111.430 (4)
C5—O61.406 (4)C10—H1011.008
C5—C71.524 (4)O11—H1110.838
C5—H511.027O12—H1210.820
O6—H610.843
F1—C2—C3109.2 (3)C5—C7—C9110.4 (2)
F1—C2—H21106.2O8—C7—C9112.3 (2)
C3—C2—H21108.7C5—C7—H71110.3
F1—C2—H22109.4O8—C7—H71109.4
C3—C2—H22111.5C9—C7—H71106.9
H21—C2—H22111.7C7—O8—H81116.5
C2—C3—O4106.8 (2)C7—C9—C10110.5 (3)
C2—C3—C10112.8 (3)C7—C9—O12112.0 (2)
O4—C3—C10109.9 (2)C10—C9—O12111.0 (2)
C2—C3—H31109.1C7—C9—H91108.1
O4—C3—H31107.8C10—C9—H91108.0
C10—C3—H31110.3O12—C9—H91107.0
C3—O4—C5112.9 (2)C9—C10—C3108.4 (3)
O4—C5—O6110.4 (3)C9—C10—O11109.2 (3)
O4—C5—C7110.3 (2)C3—C10—O11110.9 (3)
O6—C5—C7109.3 (2)C9—C10—H101109.5
O4—C5—H51108.0C3—C10—H101108.1
O6—C5—H51110.8O11—C10—H101110.7
C7—C5—H51107.9C10—O11—H111104.6
C5—O6—H61105.5C9—O12—H121112.3
C5—C7—O8107.6 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H21···O12i0.972.603.318 (4)131
C5—H51···O11ii1.032.593.320 (4)128
O12—H121···O8iii0.821.952.769 (4)177
O11—H111···O12iv0.841.962.781 (4)168
O6—H61···O4ii0.841.912.747 (4)174
O8—H81···O6iii0.821.932.739 (4)169
Symmetry codes: (i) x, y−1, z; (ii) x+1/2, −y+1/2, −z+1; (iii) x−1/2, −y+3/2, −z+1; (iv) −x+1, y−1/2, −z+3/2.

Experimental details

Crystal data
Chemical formulaC6H11FO5
Mr182.15
Crystal system, space groupOrthorhombic, P212121
Temperature (K)150
a, b, c (Å)6.7928 (3), 7.5822 (3), 14.1165 (6)
V (Å3)727.06 (5)
Z4
Radiation typeMo Kα
µ (mm−1)0.16
Crystal size (mm)0.25 × 0.15 × 0.15
Data collection
DiffractometerArea
Absorption correctionMulti-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
Tmin, Tmax0.88, 0.98
No. of measured, independent and
observed [I > 2σ(I)] reflections		6912, 978, 855
Rint0.082
(sin θ/λ)max (Å−1)0.648
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.048, 0.119, 1.00
No. of reflections978
No. of parameters109
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.39, −0.33

Computer programs: COLLECT (Nonius, 2001), DENZO/SCALEPACK (Otwinowski & Minor, 1997), SIR92 (Altomare et al., 1994), CRYSTALS (Betteridge et al., 2003), CAMERON (Watkin et al., 1996).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O12—H121···O8i0.821.952.769 (4)177
O11—H111···O12ii0.841.962.781 (4)168
O6—H61···O4iii0.841.912.747 (4)174
O8—H81···O6i0.821.932.739 (4)169
Symmetry codes: (i) x−1/2, −y+3/2, −z+1; (ii) −x+1, y−1/2, −z+3/2; (iii) x+1/2, −y+1/2, −z+1.
 

References

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ISSN: 2056-9890
Volume 66| Part 6| June 2010| Page o1315
https://doi.org/10.1107/S1600536810016612
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