Literature DB >> 21579420

1-De-oxy-1-fluoro-l-galactitol.

Sarah F Jenkinson, Daniel Best, Ken Izumori, Francis X Wilson, Alexander C Weymouth-Wilson, George W J Fleet, Amber L Thompson.

Abstract

The crystal structure unequivocally confirms the relative stereochemistry of the title compound, C(6)H(13)FO(5) [6-de-oxy-6-fluoro-d-galactitol or (2S,3R,4R,5S)-6-fluoro-hexane-1,2,3,4,5-penta-ol]. 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 mol-ecule acting as a donor and acceptor for five hydrogen bonds.

Entities: Chemical Disease Gene Species

Year: 2010 PMID： 21579420 PMCID： PMC2979521 DOI： 10.1107/S1600536810016624

Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN： 1600-5368

Related literature

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

Experimental

Crystal data

C6H13FO5 M = 184.16 Monoclinic, 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[F 2 > 2σ(F 2)] = 0.040 wR(F 2) = 0.095 S = 0.99 947 reflections 109 parameters 1 restraint H-atom parameters constrained Δρmax = 0.35 e Å−3 Δρmin = −0.36 e Å−3 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. Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810016624/lh5036sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536810016624/lh5036Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report

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

Area diffractometer	788 reflections with I > 2σ(I)
graphite	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 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 = 0.0001
947 reflections	Δρ_max = 0.35 e Å⁻³
109 parameters	Δρ_min = −0.36 e Å⁻³
1 restraint

	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*

	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···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

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) ; (ii) ; (iii) ; (iv) ; (v) .

2 in total

1. Fluorocarbohydrates. XXIV. Chemical and enzymic reduction and phosphorylation of 6-deoxy-6-fluoro- -D-galactose.

Authors: P W Kent; J R Wright
Journal: Carbohydr Res Date: 1972-04 Impact factor: 2.104

2. 6-De-oxy-6-fluoro-d-galactose.

Authors: Sarah F Jenkinson; Daniel Best; Ken Izumori; Francis X Wilson; Alexander C Weymouth-Wilson; George W J Fleet; Amber L Thompson
Journal: Acta Crystallogr Sect E Struct Rep Online Date: 2010-05-12

2 in total