organic compounds
1-Deoxy-1-fluoro-L-galactitol
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
The 6H13FO5 [6-deoxy-6-fluoro-D-galactitol or (2S,3R,4R,5S)-6-fluorohexane-1,2,3,4,5-pentaol]. The absolute stereochemistry was determined from the use of D-galactose as the starting material. In the crystal, the molecules are linked by O—H⋯O and O—H⋯F hydrogen bonds, forming a three-dimensional network with each molecule acting as a donor and acceptor for five hydrogen bonds.
unequivocally confirms the relative stereochemistry of the title compound, CRelated literature
For literature regarding fluorogalactitol and fluorogalactose, see: Kent & Wright (1972); Jenkinson et al. (2010).
Experimental
Crystal data
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Refinement
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Data collection: COLLECT (Nonius, 2001); cell 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.
Supporting information
https://doi.org/10.1107/S1600536810016624/lh5036sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810016624/lh5036Isup2.hkl
The title compound was recrystallised by vapour diffusion from a mixture of methanol and water: m.p. 445-447 K, [α]D25 +4.1 (c 1.06, H2O) {Lit. (Kent & Wright, 1972) m.p. 446-447 K, [α]D21 +4.2 (c 0.5, H2O)}.
In the absence of significant
Friedel pairs were merged and the was assigned from 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.
1-Deoxy-1-fluoro-L-galactitol [6-deoxy-6-fluoro-D-galactitol, (2S,3R,4R,5S)-6-fluorohexane-1,2,3,4,5-pentaol] 3 was prepared in 88% yield by reduction of 6-deoxy-6-fluoro-D-galactose 2, itself readily available from D-galactose (Jenkinson et al., 2010) with sodium borohydride in water (see fig. 1).
1-Deoxy-1-fluoro-L-galactitol 3 (Fig. 2) exists as an extensively hydrogen bonded lattice with each molecule acting as a donor and acceptor for 5 hydrogen bonds (Fig. 3 and Fig. 4). Only classical hydrogen bonding is considered.
For literature regarding fluorogalactitol and fluorogalactose, see: Kent & Wright (1972); Jenkinson et al. (2010).
Data collection: COLLECT (Nonius, 2001); cell
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).C6H13FO5 | F(000) = 196 |
Mr = 184.16 | Dx = 1.552 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2yb | Cell parameters from 828 reflections |
a = 4.7968 (3) Å | θ = 5–27° |
b = 8.5957 (5) Å | µ = 0.15 mm−1 |
c = 9.8194 (7) Å | T = 150 K |
β = 103.233 (3)° | Needle, colourless |
V = 394.12 (4) Å3 | 0.40 × 0.10 × 0.05 mm |
Z = 2 |
Area diffractometer | 788 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.039 |
ω scans | θmax = 27.5°, θmin = 5.2° |
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) | h = −6→6 |
Tmin = 0.88, Tmax = 0.99 | k = −10→11 |
3069 measured reflections | l = −12→12 |
947 independent reflections |
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)] = 0.040 | H-atom parameters constrained |
wR(F2) = 0.095 | Method = Modified Sheldrick w = 1/[σ2(F2) + ( 0.04P)2 + 0.16P], where P = [max(Fo2,0) + 2Fc2]/3 |
S = 0.99 | (Δ/σ)max = 0.000109 |
947 reflections | Δρmax = 0.35 e Å−3 |
109 parameters | Δρmin = −0.36 e Å−3 |
1 restraint |
C6H13FO5 | V = 394.12 (4) Å3 |
Mr = 184.16 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 4.7968 (3) Å | µ = 0.15 mm−1 |
b = 8.5957 (5) Å | T = 150 K |
c = 9.8194 (7) Å | 0.40 × 0.10 × 0.05 mm |
β = 103.233 (3)° |
Area diffractometer | 947 independent reflections |
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) | 788 reflections with I > 2σ(I) |
Tmin = 0.88, Tmax = 0.99 | Rint = 0.039 |
3069 measured reflections |
R[F2 > 2σ(F2)] = 0.040 | 1 restraint |
wR(F2) = 0.095 | H-atom parameters constrained |
S = 0.99 | Δρmax = 0.35 e Å−3 |
947 reflections | Δρmin = −0.36 e Å−3 |
109 parameters |
x | y | z | Uiso*/Ueq | ||
F1 | 1.0608 (4) | 0.8416 (3) | 0.81046 (18) | 0.0300 | |
C2 | 0.8382 (7) | 0.7956 (4) | 0.6953 (3) | 0.0222 | |
C3 | 0.9617 (6) | 0.7729 (3) | 0.5690 (3) | 0.0165 | |
O4 | 1.1674 (4) | 0.6479 (3) | 0.5922 (2) | 0.0198 | |
C5 | 0.7225 (6) | 0.7433 (3) | 0.4383 (3) | 0.0161 | |
O6 | 0.5806 (5) | 0.6003 (2) | 0.4502 (2) | 0.0195 | |
C7 | 0.8349 (6) | 0.7338 (3) | 0.3047 (3) | 0.0157 | |
O8 | 0.9746 (4) | 0.8784 (3) | 0.2914 (2) | 0.0195 | |
C9 | 0.5959 (7) | 0.7026 (4) | 0.1752 (3) | 0.0192 | |
O10 | 0.3879 (4) | 0.8258 (3) | 0.1522 (2) | 0.0207 | |
C11 | 0.7088 (7) | 0.6776 (4) | 0.0451 (3) | 0.0215 | |
O12 | 0.4930 (5) | 0.6156 (3) | −0.0668 (2) | 0.0275 | |
H21 | 0.6950 | 0.8781 | 0.6774 | 0.0260* | |
H22 | 0.7491 | 0.6999 | 0.7173 | 0.0258* | |
H31 | 1.0631 | 0.8691 | 0.5540 | 0.0186* | |
H51 | 0.5826 | 0.8297 | 0.4297 | 0.0192* | |
H71 | 0.9744 | 0.6473 | 0.3126 | 0.0169* | |
H91 | 0.4965 | 0.6083 | 0.1918 | 0.0218* | |
H111 | 0.7818 | 0.7757 | 0.0180 | 0.0236* | |
H112 | 0.8650 | 0.6017 | 0.0659 | 0.0245* | |
H41 | 1.0976 | 0.5692 | 0.6169 | 0.0297* | |
H101 | 0.4579 | 0.9011 | 0.1221 | 0.0326* | |
H81 | 1.0943 | 0.8692 | 0.2436 | 0.0307* | |
H61 | 0.4434 | 0.6205 | 0.4847 | 0.0315* | |
H121 | 0.3696 | 0.6866 | −0.0851 | 0.0400* |
U11 | U22 | U33 | U12 | U13 | U23 | |
F1 | 0.0335 (11) | 0.0350 (11) | 0.0187 (9) | 0.0018 (10) | 0.0002 (8) | −0.0045 (8) |
C2 | 0.0217 (15) | 0.0270 (17) | 0.0166 (14) | 0.0023 (12) | 0.0019 (12) | −0.0039 (12) |
C3 | 0.0168 (14) | 0.0140 (13) | 0.0181 (13) | 0.0019 (11) | 0.0029 (11) | −0.0004 (11) |
O4 | 0.0176 (11) | 0.0202 (11) | 0.0222 (10) | 0.0029 (8) | 0.0054 (8) | 0.0048 (8) |
C5 | 0.0162 (14) | 0.0136 (14) | 0.0194 (14) | 0.0000 (11) | 0.0058 (11) | 0.0011 (11) |
O6 | 0.0229 (12) | 0.0169 (10) | 0.0215 (10) | −0.0052 (9) | 0.0109 (9) | −0.0024 (8) |
C7 | 0.0172 (14) | 0.0148 (15) | 0.0149 (13) | −0.0012 (12) | 0.0029 (11) | −0.0027 (11) |
O8 | 0.0208 (12) | 0.0165 (11) | 0.0233 (10) | −0.0033 (9) | 0.0094 (9) | −0.0024 (9) |
C9 | 0.0200 (14) | 0.0201 (15) | 0.0173 (14) | −0.0015 (12) | 0.0037 (12) | 0.0006 (12) |
O10 | 0.0190 (11) | 0.0217 (11) | 0.0223 (11) | 0.0015 (9) | 0.0064 (8) | 0.0042 (9) |
C11 | 0.0227 (16) | 0.0257 (17) | 0.0145 (14) | 0.0006 (13) | 0.0011 (12) | −0.0018 (13) |
O12 | 0.0312 (14) | 0.0274 (12) | 0.0201 (11) | 0.0025 (10) | −0.0017 (10) | −0.0078 (10) |
F1—C2 | 1.422 (3) | C7—O8 | 1.432 (4) |
C2—C3 | 1.504 (4) | C7—C9 | 1.528 (4) |
C2—H21 | 0.975 | C7—H71 | 0.992 |
C2—H22 | 0.974 | O8—H81 | 0.824 |
C3—O4 | 1.441 (4) | C9—O10 | 1.437 (4) |
C3—C5 | 1.534 (4) | C9—C11 | 1.513 (4) |
C3—H31 | 0.987 | C9—H91 | 0.973 |
O4—H41 | 0.816 | O10—H101 | 0.815 |
C5—O6 | 1.422 (4) | C11—O12 | 1.429 (3) |
C5—C7 | 1.530 (3) | C11—H111 | 0.973 |
C5—H51 | 0.992 | C11—H112 | 0.979 |
O6—H61 | 0.825 | O12—H121 | 0.840 |
F1—C2—C3 | 109.0 (3) | C5—C7—C9 | 112.2 (2) |
F1—C2—H21 | 108.1 | O8—C7—C9 | 110.7 (2) |
C3—C2—H21 | 109.9 | C5—C7—H71 | 109.7 |
F1—C2—H22 | 110.2 | O8—C7—H71 | 109.6 |
C3—C2—H22 | 110.4 | C9—C7—H71 | 107.3 |
H21—C2—H22 | 109.1 | C7—O8—H81 | 111.8 |
C2—C3—O4 | 110.5 (2) | C7—C9—O10 | 111.3 (2) |
C2—C3—C5 | 110.6 (2) | C7—C9—C11 | 112.5 (2) |
O4—C3—C5 | 111.3 (2) | O10—C9—C11 | 110.0 (2) |
C2—C3—H31 | 108.3 | C7—C9—H91 | 108.0 |
O4—C3—H31 | 107.7 | O10—C9—H91 | 107.0 |
C5—C3—H31 | 108.3 | C11—C9—H91 | 107.8 |
C3—O4—H41 | 110.6 | C9—O10—H101 | 108.3 |
C3—C5—O6 | 110.8 (2) | C9—C11—O12 | 111.5 (3) |
C3—C5—C7 | 112.5 (2) | C9—C11—H111 | 109.2 |
O6—C5—C7 | 107.1 (2) | O12—C11—H111 | 110.9 |
C3—C5—H51 | 108.0 | C9—C11—H112 | 108.9 |
O6—C5—H51 | 109.1 | O12—C11—H112 | 107.3 |
C7—C5—H51 | 109.3 | H111—C11—H112 | 109.2 |
C5—O6—H61 | 107.1 | C11—O12—H121 | 104.2 |
C5—C7—O8 | 107.3 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H21···O6i | 0.97 | 2.49 | 3.409 (4) | 157 |
O4—H41···O8ii | 0.82 | 1.94 | 2.738 (4) | 165 |
O10—H101···O12iii | 0.82 | 1.95 | 2.730 (4) | 160 |
O8—H81···O10iv | 0.82 | 1.87 | 2.691 (4) | 172 |
O6—H61···O4v | 0.82 | 1.89 | 2.703 (4) | 170 |
O12—H121···F1vi | 0.84 | 2.08 | 2.895 (3) | 163 |
Symmetry codes: (i) −x+1, y+1/2, −z+1; (ii) −x+2, y−1/2, −z+1; (iii) −x+1, y+1/2, −z; (iv) x+1, y, z; (v) x−1, y, z; (vi) x−1, y, z−1. |
Experimental details
Crystal data | |
Chemical formula | C6H13FO5 |
Mr | 184.16 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 150 |
a, b, c (Å) | 4.7968 (3), 8.5957 (5), 9.8194 (7) |
β (°) | 103.233 (3) |
V (Å3) | 394.12 (4) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.15 |
Crystal size (mm) | 0.40 × 0.10 × 0.05 |
Data collection | |
Diffractometer | Area |
Absorption correction | Multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) |
Tmin, Tmax | 0.88, 0.99 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3069, 947, 788 |
Rint | 0.039 |
(sin θ/λ)max (Å−1) | 0.650 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.040, 0.095, 0.99 |
No. of reflections | 947 |
No. of parameters | 109 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.35, −0.36 |
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).
D—H···A | D—H | H···A | D···A | D—H···A |
O4—H41···O8i | 0.82 | 1.94 | 2.738 (4) | 165 |
O10—H101···O12ii | 0.82 | 1.95 | 2.730 (4) | 160 |
O8—H81···O10iii | 0.82 | 1.87 | 2.691 (4) | 172 |
O6—H61···O4iv | 0.82 | 1.89 | 2.703 (4) | 170 |
O12—H121···F1v | 0.84 | 2.08 | 2.895 (3) | 163 |
Symmetry codes: (i) −x+2, y−1/2, −z+1; (ii) −x+1, y+1/2, −z; (iii) x+1, y, z; (iv) x−1, y, z; (v) x−1, y, z−1. |
References
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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. Google Scholar
Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, Oxford, England. Google Scholar
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1-Deoxy-1-fluoro-L-galactitol [6-deoxy-6-fluoro-D-galactitol, (2S,3R,4R,5S)-6-fluorohexane-1,2,3,4,5-pentaol] 3 was prepared in 88% yield by reduction of 6-deoxy-6-fluoro-D-galactose 2, itself readily available from D-galactose (Jenkinson et al., 2010) with sodium borohydride in water (see fig. 1).
1-Deoxy-1-fluoro-L-galactitol 3 (Fig. 2) exists as an extensively hydrogen bonded lattice with each molecule acting as a donor and acceptor for 5 hydrogen bonds (Fig. 3 and Fig. 4). Only classical hydrogen bonding is considered.