(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

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

doi:10.1107/S1600536810009165

organic compounds

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ISSN: 2056-9890

Volume 66| Part 4| April 2010| Page o853

doi:10.1107/S1600536810009165

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(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 and D. J. Watkin ^c

^aDepartment of Organic Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, England, ^bSummit PLC, 91 Milton Park, Abingdon, Oxon OX14 4RY, England, and ^cDepartment of Chemical Crystallography, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, England
^*Correspondence e-mail: sarah.jenkinson@chem.ox.ac.uk

(Received 24 February 2010; accepted 10 March 2010; online 17 March 2010)

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, P 2₁ 2₁ 2₁
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[F² > 2σ(F²)] = 0.042
wR(F²) = 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

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
Symmetry codes: (i) x+1, y, z; (ii) x, y-1, z; (iii) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ ; (iv) x, y+1, z; (v) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ .

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: 10.1107/S1600536810009165/lh5005sup1.cif

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

checkCIF report

Comment top

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.

Related literature top

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 top

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).

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 arbitary radius.
	Fig. 3. Packing diagram for the title compound projected along the a-axis. Hydrogen bonds are shown by dotted lines.
	Fig. 4. Packing diagram for the title compound projected along the b axis. Hydrogen bonds are shown by dotted lines.

(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 top

Crystal data top

C₁₂H₁₈N₂O₈	F(000) = 672
M_r = 318.28	D_x = 1.683 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 1646 reflections
a = 7.8711 (2) Å	θ = 5–27°
b = 8.1526 (2) Å	µ = 0.14 mm⁻¹
c = 19.5783 (5) Å	T = 150 K
V = 1256.34 (5) Å³	Plate, colourless
Z = 4	0.40 × 0.10 × 0.10 mm

Data collection top

Nonius KappaCCD area-detector diffractometer	1348 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.061
ω scans	θ_max = 27.5°, θ_min = 5.1°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −10→10
T_min = 0.85, T_max = 0.99	k = −10→10
12748 measured reflections	l = −25→25
1663 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)] = 0.042	H-atom parameters constrained
wR(F²) = 0.101	Method = Modified Sheldrick w = 1/[σ²(F²) + (0.06P)² + 0.76P], where P = [max(F_o²,0) + 2F_c²]/3
S = 0.93	(Δ/σ)_max = 0.000342
1662 reflections	Δρ_max = 0.35 e Å⁻³
199 parameters	Δρ_min = −0.43 e Å⁻³
0 restraints

Crystal data top

C₁₂H₁₈N₂O₈	V = 1256.34 (5) Å³
M_r = 318.28	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 7.8711 (2) Å	µ = 0.14 mm⁻¹
b = 8.1526 (2) Å	T = 150 K
c = 19.5783 (5) Å	0.40 × 0.10 × 0.10 mm

Data collection top

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

Refinement top

R[F² > 2σ(F²)] = 0.042	0 restraints
wR(F²) = 0.101	H-atom parameters constrained
S = 0.93	Δρ_max = 0.35 e Å⁻³
1662 reflections	Δρ_min = −0.43 e Å⁻³
199 parameters

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

	x	y	z	U_iso*/U_eq
O1	0.4593 (3)	0.7922 (2)	0.34949 (10)	0.0245
C2	0.5380 (4)	0.6635 (3)	0.34006 (13)	0.0181
N3	0.6870 (3)	0.6583 (3)	0.30476 (12)	0.0186
C4	0.8001 (3)	0.5165 (3)	0.30769 (13)	0.0178
C5	0.9227 (3)	0.5430 (3)	0.36900 (14)	0.0187
O6	1.0531 (3)	0.4227 (2)	0.36945 (10)	0.0233
C7	1.0081 (4)	0.7115 (3)	0.36672 (14)	0.0191
O8	1.0852 (2)	0.7438 (2)	0.43187 (9)	0.0238
C9	0.8851 (4)	0.8502 (3)	0.35308 (14)	0.0196
C10	0.7767 (4)	0.8115 (4)	0.29066 (15)	0.0202
O11	0.9812 (3)	0.9966 (2)	0.34507 (10)	0.0247
C12	0.7057 (4)	0.3552 (3)	0.31154 (14)	0.0192
O13	0.7761 (3)	0.2272 (2)	0.29231 (10)	0.0234
N14	0.5463 (3)	0.3566 (3)	0.33597 (12)	0.0186
C15	0.4689 (3)	0.5025 (3)	0.36625 (13)	0.0188
C16	0.4834 (3)	0.4874 (3)	0.44528 (13)	0.0187
O17	0.3887 (3)	0.6143 (2)	0.47677 (10)	0.0240
C18	0.4098 (4)	0.3245 (3)	0.46900 (13)	0.0203
O19	0.4442 (3)	0.3016 (3)	0.54059 (9)	0.0269
C20	0.4757 (4)	0.1754 (3)	0.43053 (13)	0.0201
C21	0.4581 (4)	0.2045 (3)	0.35390 (13)	0.0199
O22	0.3776 (3)	0.0390 (2)	0.45221 (10)	0.0310
H41	0.8655	0.5150	0.2656	0.0187*
H51	0.8535	0.5336	0.4109	0.0227*
H71	1.0974	0.7116	0.3316	0.0230*
H91	0.8058	0.8605	0.3927	0.0225*
H102	0.8459	0.7964	0.2509	0.0230*
H101	0.6975	0.8990	0.2835	0.0223*
H151	0.3443	0.5003	0.3557	0.0220*
H161	0.6054	0.4942	0.4588	0.0216*
H181	0.2825	0.3283	0.4634	0.0238*
H201	0.5996	0.1598	0.4417	0.0244*
H212	0.5077	0.1118	0.3286	0.0232*
H211	0.3349	0.2163	0.3433	0.0228*
H81	1.1809	0.7027	0.4365	0.0340*
H221	0.3488	−0.0299	0.4231	0.0459*
H191	0.4842	0.3832	0.5589	0.0407*
H111	0.9114	1.0645	0.3311	0.0377*
H171	0.4338	0.6804	0.5013	0.0351*
H61	1.0660	0.3593	0.4021	0.0354*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0253 (11)	0.0201 (10)	0.0280 (11)	0.0043 (9)	0.0024 (9)	−0.0012 (8)
C2	0.0189 (14)	0.0226 (14)	0.0128 (13)	0.0006 (13)	−0.0029 (11)	−0.0002 (10)
N3	0.0185 (12)	0.0171 (11)	0.0203 (13)	0.0000 (10)	0.0012 (10)	0.0030 (9)
C4	0.0153 (12)	0.0194 (13)	0.0186 (13)	0.0024 (12)	0.0012 (10)	0.0011 (11)
C5	0.0174 (13)	0.0198 (13)	0.0188 (13)	0.0017 (11)	0.0017 (11)	0.0014 (10)
O6	0.0206 (10)	0.0224 (10)	0.0270 (10)	0.0069 (9)	−0.0006 (9)	0.0050 (9)
C7	0.0193 (14)	0.0209 (13)	0.0170 (13)	0.0003 (11)	0.0006 (11)	−0.0014 (11)
O8	0.0191 (10)	0.0316 (11)	0.0208 (10)	0.0048 (9)	−0.0041 (8)	−0.0056 (8)
C9	0.0191 (14)	0.0192 (14)	0.0205 (14)	−0.0001 (12)	0.0020 (11)	−0.0008 (10)
C10	0.0200 (15)	0.0205 (13)	0.0203 (15)	0.0011 (12)	−0.0010 (11)	0.0004 (11)
O11	0.0265 (10)	0.0169 (10)	0.0307 (10)	0.0000 (10)	−0.0056 (8)	0.0012 (8)
C12	0.0212 (14)	0.0235 (15)	0.0129 (14)	0.0016 (12)	−0.0019 (11)	0.0007 (11)
O13	0.0274 (12)	0.0206 (10)	0.0223 (11)	0.0049 (9)	0.0016 (9)	−0.0027 (8)
N14	0.0182 (12)	0.0180 (12)	0.0197 (12)	−0.0009 (11)	0.0002 (10)	−0.0004 (9)
C15	0.0168 (12)	0.0208 (14)	0.0186 (12)	0.0026 (13)	0.0021 (10)	−0.0015 (12)
C16	0.0151 (12)	0.0214 (14)	0.0197 (12)	0.0014 (12)	0.0006 (10)	−0.0017 (11)
O17	0.0259 (11)	0.0240 (10)	0.0220 (10)	0.0037 (9)	0.0005 (9)	−0.0075 (8)
C18	0.0182 (14)	0.0270 (14)	0.0158 (14)	0.0028 (12)	−0.0007 (11)	0.0015 (11)
O19	0.0392 (12)	0.0261 (10)	0.0153 (9)	0.0003 (10)	−0.0045 (9)	0.0013 (8)
C20	0.0200 (13)	0.0183 (13)	0.0220 (14)	−0.0013 (12)	0.0010 (11)	0.0007 (11)
C21	0.0195 (14)	0.0200 (14)	0.0201 (14)	−0.0034 (12)	0.0015 (12)	−0.0005 (11)
O22	0.0468 (13)	0.0227 (11)	0.0235 (10)	−0.0087 (10)	0.0064 (10)	−0.0005 (8)

Geometric parameters (Å, º) top

O1—C2	1.232 (3)	O11—H111	0.826
C2—N3	1.362 (4)	C12—O13	1.240 (3)
C2—C15	1.510 (4)	C12—N14	1.343 (4)
N3—C4	1.461 (3)	N14—C15	1.462 (3)
N3—C10	1.461 (4)	N14—C21	1.464 (3)
C4—C5	1.555 (4)	C15—C16	1.556 (3)
C4—C12	1.513 (4)	C15—H151	1.002
C4—H41	0.972	C16—O17	1.416 (3)
C5—O6	1.420 (3)	C16—C18	1.521 (4)
C5—C7	1.530 (4)	C16—H161	0.998
C5—H51	0.988	O17—H171	0.804
O6—H61	0.829	C18—O19	1.440 (3)
C7—O8	1.437 (3)	C18—C20	1.521 (4)
C7—C9	1.513 (4)	C18—H181	1.008
C7—H71	0.983	O19—H191	0.819
O8—H81	0.830	C20—C21	1.525 (4)
C9—C10	1.523 (4)	C20—O22	1.419 (3)
C9—O11	1.422 (3)	C20—H201	1.008
C9—H91	1.000	C21—H212	0.984
C10—H102	0.958	C21—H211	0.996
C10—H101	0.957	O22—H221	0.832

O1—C2—N3	122.3 (3)	C4—C12—O13	119.8 (3)
O1—C2—C15	120.5 (2)	C4—C12—N14	118.0 (2)
N3—C2—C15	117.1 (2)	O13—C12—N14	122.2 (3)
C2—N3—C4	122.0 (2)	C12—N14—C15	122.7 (2)
C2—N3—C10	119.1 (2)	C12—N14—C21	121.4 (2)
C4—N3—C10	112.9 (2)	C15—N14—C21	113.2 (2)
N3—C4—C5	107.4 (2)	C2—C15—N14	114.8 (2)
N3—C4—C12	113.0 (2)	C2—C15—C16	112.3 (2)
C5—C4—C12	112.8 (2)	N14—C15—C16	108.0 (2)
N3—C4—H41	107.4	C2—C15—H151	107.3
C5—C4—H41	109.1	N14—C15—H151	108.0
C12—C4—H41	106.9	C16—C15—H151	105.9
C4—C5—O6	110.9 (2)	C15—C16—O17	109.7 (2)
C4—C5—C7	112.0 (2)	C15—C16—C18	110.2 (2)
O6—C5—C7	107.6 (2)	O17—C16—C18	107.7 (2)
C4—C5—H51	106.8	C15—C16—H161	109.3
O6—C5—H51	109.8	O17—C16—H161	110.5
C7—C5—H51	109.7	C18—C16—H161	109.5
C5—O6—H61	121.6	C16—O17—H171	121.1
C5—C7—O8	108.9 (2)	C16—C18—O19	109.8 (2)
C5—C7—C9	113.3 (2)	C16—C18—C20	114.6 (2)
O8—C7—C9	106.9 (2)	O19—C18—C20	108.3 (2)
C5—C7—H71	109.6	C16—C18—H181	108.6
O8—C7—H71	108.6	O19—C18—H181	107.2
C9—C7—H71	109.5	C20—C18—H181	108.0
C7—O8—H81	114.0	C18—O19—H191	113.2
C7—C9—C10	110.2 (2)	C18—C20—C21	109.4 (2)
C7—C9—O11	107.8 (2)	C18—C20—O22	107.0 (2)
C10—C9—O11	112.5 (2)	C21—C20—O22	111.5 (2)
C7—C9—H91	109.0	C18—C20—H201	108.8
C10—C9—H91	106.9	C21—C20—H201	108.8
O11—C9—H91	110.3	O22—C20—H201	111.2
C9—C10—N3	107.2 (2)	C20—C21—N14	108.9 (2)
C9—C10—H102	111.1	C20—C21—H212	109.8
N3—C10—H102	108.5	N14—C21—H212	110.0
C9—C10—H101	109.1	C20—C21—H211	107.9
N3—C10—H101	110.5	N14—C21—H211	109.3
H102—C10—H101	110.3	H212—C21—H211	110.9
C9—O11—H111	104.2	C20—O22—H221	118.2

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C4—H41···O11ⁱ	0.97	2.48	3.455 (4)	176
C15—H151···O6ⁱⁱ	1.00	2.39	3.337 (4)	157
O8—H81···O17ⁱⁱⁱ	0.83	1.95	2.756 (4)	162
O22—H221···O1^iv	0.83	2.22	2.917 (4)	141
O19—H191···O11^v	0.82	2.12	2.793 (4)	139
O11—H111···O13^vi	0.83	1.86	2.685 (4)	173
O17—H171···O8^v	0.80	1.87	2.633 (4)	157
O6—H61···O19^vii	0.83	1.97	2.680 (4)	143

Symmetry codes: (i) −x+2, y−1/2, −z+1/2; (ii) x−1, y, z; (iii) x+1, y, z; (iv) x, y−1, z; (v) x−1/2, −y+3/2, −z+1; (vi) x, y+1, z; (vii) x+1/2, −y+1/2, −z+1.

Experimental details

Crystal data
Chemical formula	C₁₂H₁₈N₂O₈
M_r	318.28
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	150
a, b, c (Å)	7.8711 (2), 8.1526 (2), 19.5783 (5)
V (Å³)	1256.34 (5)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.14
Crystal size (mm)	0.40 × 0.10 × 0.10

Data collection
Diffractometer	Nonius KappaCCD area-detector diffractometer
Absorption correction	Multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)
T_min, T_max	0.85, 0.99
No. of measured, independent and observed [I > 2σ(I)] reflections	12748, 1663, 1348
R_int	0.061
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.042, 0.101, 0.93
No. of reflections	1662
No. of parameters	199
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.35, −0.43

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
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

Symmetry codes: (i) x+1, y, z; (ii) x, y−1, z; (iii) x−1/2, −y+3/2, −z+1; (iv) x, y+1, z; (v) x+1/2, −y+1/2, −z+1.

Acknowledgements

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

References

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

(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

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Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

(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