(1R,2R,3S,6aS,7R,8R,9S,12aS)-1,2,3,7,8,9-Hexahydroxy­perhydro­dipyrido[1,2-a:1′,2′-d]pyrazine-6,12-dione

S F Jenkinson; D Best; F X Wilson; G W J Fleet; D J Watkin

doi:10.1107/S1600536810009165

. 2010 Mar 17;66(Pt 4):o853. doi: 10.1107/S1600536810009165

(1R,2R,3S,6aS,7R,8R,9S,12aS)-1,2,3,7,8,9-Hexahydroxyperhydrodipyrido[1,2-a:1′,2′-d]pyrazine-6,12-dione

S F Jenkinson ^a,^*, D Best ^a, F X Wilson ^b, G W J Fleet ^a, D J Watkin ^c

PMCID: PMC2983886 PMID: 21580677

Abstract

The crystal structure of the title compound, C₁₂H₁₈N₂O₈, exists as O—H⋯O hydrogen-bonded layers of molecules running parallel to the ab plane. Each molecule is a donor and acceptor for six hydrogen bonds. The absolute stereochemistry was determined by the use of d-glucuronolactone as the starting material.

Related literature

For the isolation and biological activity of pipecolic acids, see: Manning et al. (1985 ▶); di Bello et al. (1984 ▶). For the synthesis of pipecolic acids, see: Bashyal et al. (1986 ▶); Bashyal, Chow & Fleet (1987 ▶); Bashyal, Chow, Fellows & Fleet (1987 ▶).

Experimental

Crystal data

C₁₂H₁₈N₂O₈
M _r = 318.28
Orthorhombic,
a = 7.8711 (2) Å
b = 8.1526 (2) Å
c = 19.5783 (5) Å
V = 1256.34 (5) Å³
Z = 4
Mo Kα radiation
μ = 0.14 mm⁻¹
T = 150 K
0.40 × 0.10 × 0.10 mm

Data collection

Nonius KappaCCD area-detector diffractometer
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997 ▶) T _min = 0.85, T _max = 0.99
12748 measured reflections
1663 independent reflections
1348 reflections with I > 2σ(I)
R _int = 0.061

Refinement

R[F ² > 2σ(F ²)] = 0.042
wR(F ²) = 0.101
S = 0.93
1662 reflections
199 parameters
H-atom parameters constrained
Δρ_max = 0.35 e Å⁻³
Δρ_min = −0.43 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.

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810009165/lh5005sup1.cif

e-66-0o853-sup1.cif^{(17.1KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810009165/lh5005Isup2.hkl

e-66-0o853-Isup2.hkl^{(83.5KB, hkl)}

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O8—H81⋯O17ⁱ	0.83	1.95	2.756 (4)	162
O22—H221⋯O1ⁱⁱ	0.83	2.22	2.917 (4)	141
O19—H191⋯O11ⁱⁱⁱ	0.82	2.12	2.793 (4)	139
O11—H111⋯O13^iv	0.83	1.86	2.685 (4)	173
O17—H171⋯O8ⁱⁱⁱ	0.80	1.87	2.633 (4)	157
O6—H61⋯O19^v	0.83	1.97	2.680 (4)	143

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) ; (v) .

Acknowledgments

We would like to thank the Chemical Crystallography department and ALT at the University of Oxford for use of the diffractometers.

supplementary crystallographic information

Comment

2S,3R,4R,5S-Trihydroxypipecolicacid (BR1) 2 (Fig.1), a sugar mimic of glucuronic acid, has been isolated from the seeds of Baphia racemosa (Manning et al., 1985) and shown to inhibit both glucuronidase and iduronidase activity (di Bello et al., 1984). In a modification of the original synthesis of BR1 from D-glucuronolactone (Bashyal et al., 1986, Bashyal, Chow & Fleet, 1987, Bashyal, Chow, Fellows & Fleet, 1987), reduction of the azide 1 afforded a low yield of 2 together with by-products. One of the components of the mixture was crystallized; the structure of this material was determined unequivocally by X-ray crystallographic analysis and shown to be the diketopiperazine 3 (Fig. 2). The absolute stereochemistry was determined by the use of D-glucuronolactone as the starting material. The structure consists of layers of hydrogen bonded molecules running parallel to the ab plane (Fig. 3, Fig. 4). Each molecule is a donor and acceptor for 6 hydrogen bonds. Only classical hydrogen bonding was considered.

Experimental

The title compound was recrystallised by diffusion from a mixture of water and acetonitrile: m.p. 511 K decomposed; [α]_D²⁰ + 29.7 (c, 0.35 in H₂O).