1-De­oxy-1-fluoro-l-galactitol

Jenkinson, S.F.; Best, D.; Izumori, K.; Wilson, F.X.; Weymouth-Wilson, A.C.; Fleet, G.W.J.; Thompson, A.L.

doi:10.1107/S1600536810016624

organic compounds

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Volume 66| Part 6| June 2010| Page o1330

https://doi.org/10.1107/S1600536810016624

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1-Deoxy-1-fluoro-L-galactitol

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

^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, C₆H₁₃FO₅ [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.

Related literature

For literature regarding fluorogalactitol and fluorogalactose, see: Kent & Wright (1972 ); Jenkinson et al. (2010 ).

Experimental

Crystal data

C₆H₁₃FO₅
M_r = 184.16
Monoclinic, P 2₁
a = 4.7968 (3) Å
b = 8.5957 (5) Å
c = 9.8194 (7) Å
β = 103.233 (3)°
V = 394.12 (4) Å³
Z = 2
Mo Kα radiation
μ = 0.15 mm⁻¹
T = 150 K
0.40 × 0.10 × 0.05 mm

Data collection

Area diffractometer
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997 ) T_min = 0.88, T_max = 0.99
3069 measured reflections
947 independent reflections
788 reflections with I > 2σ(I)
R_int = 0.039

Refinement

R[F² > 2σ(F²)] = 0.040
wR(F²) = 0.095
S = 0.99
947 reflections
109 parameters
1 restraint
H-atom parameters constrained
Δρ_max = 0.35 e Å⁻³
Δρ_min = −0.36 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

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⋯O4^iv	0.82	1.89	2.703 (4)	170
O12—H121⋯F1^v	0.84	2.08	2.895 (3)	163
Symmetry codes: (i) $[-x+2, y-{\script{1\over 2}}, -z+1]$ ; (ii) $[-x+1, y+{\script{1\over 2}}, -z]$ ; (iii) x+1, y, z; (iv) x-1, y, z; (v) x-1, y, z-1.

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.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536810016624/lh5036sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810016624/lh5036Isup2.hkl

checkCIF report

Comment top

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.

Related literature top

For literature regarding fluorogalactitol and fluorogalactose, see: Kent & Wright (1972); Jenkinson et al. (2010).

Experimental top

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)}.

Structure description top

For literature regarding fluorogalactitol and fluorogalactose, see: Kent & Wright (1972); Jenkinson et al. (2010).

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

	Fig. 1. Synthetic Scheme.
	Fig. 2. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitrary radius.
	Fig. 3. Packing diagram for the title compound projected along the c-axis. Hydrogen bonds are indicated by dotted lines.
	Fig. 4. Packing diagram for the title compound projected along the b-axis. Hydrogen bonds are indicated by dotted lines.

1-Deoxy-1-fluoro-L-galactitol top

Crystal data top

C₆H₁₃FO₅	F(000) = 196
M_r = 184.16	D_x = 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

Data collection top

Area diffractometer	788 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.039
ω scans	θ_max = 27.5°, θ_min = 5.2°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −6→6
T_min = 0.88, T_max = 0.99	k = −10→11
3069 measured reflections	l = −12→12
947 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)] = 0.040	H-atom parameters constrained
wR(F²) = 0.095	Method = Modified Sheldrick w = 1/[σ²(F²) + ( 0.04P)² + 0.16P], where P = [max(F_o²,0) + 2F_c²]/3
S = 0.99	(Δ/σ)_max = 0.000109
947 reflections	Δρ_max = 0.35 e Å⁻³
109 parameters	Δρ_min = −0.36 e Å⁻³
1 restraint

Crystal data top

C₆H₁₃FO₅	V = 394.12 (4) Å³
M_r = 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)°

Data collection top

Area diffractometer	947 independent reflections
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	788 reflections with I > 2σ(I)
T_min = 0.88, T_max = 0.99	R_int = 0.039
3069 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.040	1 restraint
wR(F²) = 0.095	H-atom parameters constrained
S = 0.99	Δρ_max = 0.35 e Å⁻³
947 reflections	Δρ_min = −0.36 e Å⁻³
109 parameters

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

	x	y	z	U_iso*/U_eq
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*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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···O10^iv	0.82	1.87	2.691 (4)	172
O6—H61···O4^v	0.82	1.89	2.703 (4)	170
O12—H121···F1^vi	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
M_r	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)
T_min, T_max	0.88, 0.99
No. of measured, independent and observed [I > 2σ(I)] reflections	3069, 947, 788
R_int	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
Δρ_max, Δρ_min (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).

Hydrogen-bond geometry (Å, º) top

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···O4^iv	0.82	1.89	2.703 (4)	170
O12—H121···F1^v	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

Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435. CrossRef Web of Science IUCr Journals Google Scholar
Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487. Web of Science CrossRef IUCr Journals Google Scholar
Jenkinson, S. F., Best, D., Izumori, K., Wilson, F. X., Weymouth-Wilson, A. C., Fleet, G. W. J. & Thompson, A. L. (2010). Acta Cryst. E66, o1315. Web of Science CSD CrossRef IUCr Journals Google Scholar
Kent, P. W. & Wright, J. R. (1972). Carbohydr. Res. 22, 193–200. CrossRef CAS PubMed Web of Science Google Scholar
Nonius (2001). COLLECT. Nonius BV, Delft, The Netherlands. Google Scholar
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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CRYSTALLOGRAPHIC
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https://doi.org/10.1107/S1600536810016624

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