(1R,2R,3S,5R,6R,7S,9aR,10aR)-4a,8a-Di­aza­per­hydro­anthracene-1,2,3,5,6,7-hexaol

Furneaux, R.H.; Gainsford, G.J.; Mason, J.M.; Tyler, P.C.

doi:10.1107/S1600536803018397

(1R,2R,3S,5R,6R,7S,9aR,10aR)-4a,8a-Diazaperhydroanthracene-1,2,3,5,6,7-hexaol

R. H. Furneaux, G. J. Gainsford, J. M. Mason and P. C. Tyler

The title compound, C₁₂H₂₂N₂O₆, is a linearly fused di(trihydroxypiperido)piperazine. The three six-membered rings adopt chair conformations with all the hydroxyl groups equatorial, and the ring fusion is the unusual trans-cisoid-cis.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536803018397/cv6223sup1.cif Contains datablocks global, II
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536803018397/cv6223IIsup2.hkl Contains datablock II

CCDC reference: 222899

checkCIF report

Key indicators

Single-crystal X-ray study
T = 173 K
Mean (C-C) = 0.005 Å
R factor = 0.046
wR factor = 0.094
Data-to-parameter ratio = 8.0

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT024_ALERT_4_C Merging of Friedel Data Preferred for Z<=Si ....          !
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          5

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           25.90
           From the CIF: _reflns_number_total               1504
           Count of symmetry unique reflns         1489
           Completeness (_total/calc)            101.01%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured        15
           Fraction of Friedel pairs measured     0.010
           Are heavy atom types Z>Si present           no

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion

Comment top

The title compound, (II), which is a condensation dimer of deoxynojirimycin, (I) (1-deoxy-D-glucopyranose having nitrogen in place of oxygen as the ring atom), was formed in low yield as a by-product on reaction of the latter compound with 2-bromobenzoylchloride in the presence of base. Presumably, the primary hydroxyl groups of the starting material were selectively esterified and the nitrogen nucleophiles of pairs of the product molecules then displaced the acyloxy groups to generate the central ring of the dimeric product.

The bond lengths and angles in (II) (Fig. 1) are normal (Table 1). The crystal lattice is bound tightly by five intermolecular O—H···O bonds and one O—H···N hydrogen bond, which involve all the hydroxyl H atoms [e.g. O3—H3O···O1(1 + x, y, z) with O···O = 2.782 (4) Å and O—H···O 162°; Spek, 1990].

There are no reported crystal structures of perhydrodiazaanthracene ring systems with ring fusion through the N atoms; the closest relatives are two sugar-derived fused-ring pyridopyrimidine compounds, with the former ring carrying three equatorial hydroxyl groups (Berges et al., 1999, and references therein). There are a few reported structures of piperazine compounds in which the N atoms are linked via aliphatic carbon chains [e.g. 1,7(1,4)-bis(2,5-diphenylpiperizina)dodecacyclophane; Fuji et al., 1996].

The six-membered rings of (II) adopt chair conformations and the ring fusion is unusual in being trans-cisoid-cis. This is also observed in a perhydroanthracene derivative with one N atom at a ring-junction position, a structure that occurs in the Veratrum alkaloids (Brambilla et al., 1982). The structures of perhydroanthracenes with the cis-cisoid-cis (van Koningsveld et al., 1984) and cis-transoid-cis (Hjortaas, 1967) configurations have also been reported.

Experimental top

A suspension of deoxynojirimycin (50 mg, 0.31 mmol), potassium carbonate (100 mg) and 2-bromobenzoyl chloride (200 µl) in water (1 ml) was sonicated for 15 min and then stirred at room temperature overnight. The solvent was removed under reduced pressure and the residue was chromatographed on a column of silica gel eluted with CH₂Cl₂/CH₃OH/NH₄OH (5:8:2) to give first deoxynojirimycin, (I), and then the title compound as an oil that gave suitable crystals on standing.

Computing details top

Data collection: SHELXTL (Siemens, 1983); cell refinement: SHELXTL; data reduction: SHELXTL; program(s) used to solve structure: SHELXS86 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: SHELXL97.

Figures top

Fig. 1. ORTEP-3 (Farrugia, 1997) view of (II), showing the atom-numbering scheme and displacement ellipsoids at the 50% probability level. H atoms are shown as circles of arbitrary radii.

(II) top

Crystal data top

C₁₂H₂₂N₂O₆	F(000) = 624
M_r = 290.32	D_x = 1.475 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 24 reflections
a = 6.702 (2) Å	θ = 4.8–23.8°
b = 13.099 (5) Å	µ = 0.12 mm⁻¹
c = 14.893 (3) Å	T = 173 K
V = 1307.5 (7) Å³	Needle, colourless
Z = 4	0.42 × 0.30 × 0.15 mm

Data collection top

Siemens/Nicolet R3m 4-circle diffractometer	R_int = 0.039
Radiation source: fine-focus sealed tube	θ_max = 25.9°, θ_min = 2.1°
Graphite monochromator	h = 0→8
ω scan	k = 0→16
1608 measured reflections	l = 0→18
1504 independent reflections	3 standard reflections every 97 reflections
1146 reflections with I > 2σ(I)	intensity decay: 0.0%

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.046	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.094	H-atom parameters constrained
S = 0.98	w = 1/[σ²(F_o²) + (0.0441P)²] where P = (F_o² + 2F_c²)/3
1504 reflections	(Δ/σ)_max < 0.001
187 parameters	Δρ_max = 0.23 e Å⁻³
0 restraints	Δρ_min = −0.24 e Å⁻³

Crystal data top

C₁₂H₂₂N₂O₆	V = 1307.5 (7) Å³
M_r = 290.32	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 6.702 (2) Å	µ = 0.12 mm⁻¹
b = 13.099 (5) Å	T = 173 K
c = 14.893 (3) Å	0.42 × 0.30 × 0.15 mm

Data collection top

Siemens/Nicolet R3m 4-circle diffractometer	R_int = 0.039
1608 measured reflections	3 standard reflections every 97 reflections
1504 independent reflections	intensity decay: 0.0%
1146 reflections with I > 2σ(I)

Refinement top

R[F² > 2σ(F²)] = 0.046	0 restraints
wR(F²) = 0.094	H-atom parameters constrained
S = 0.98	Δρ_max = 0.23 e Å⁻³
1504 reflections	Δρ_min = −0.24 e Å⁻³
187 parameters

Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

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

	x	y	z	U_iso*/U_eq
O1	−0.2909 (4)	0.54689 (19)	0.40930 (17)	0.0200 (6)
H1O	−0.3155	0.5005	0.3720	0.024*
O2	0.0882 (4)	0.57543 (17)	0.32248 (15)	0.0171 (6)
H2O	0.1564	0.6215	0.2980	0.021*
O3	0.3816 (4)	0.67349 (18)	0.43697 (18)	0.0210 (6)
H3O	0.4911	0.6466	0.4232	0.025*
O5	0.2547 (4)	0.26556 (17)	0.72251 (17)	0.0172 (6)
H5O	0.3275	0.2139	0.7158	0.021*
O6	0.0154 (4)	0.08534 (18)	0.71468 (16)	0.0171 (6)
H6O	0.0145	0.0671	0.7687	0.021*
O7	−0.4163 (4)	0.13234 (17)	0.70110 (18)	0.0188 (6)
H7O	−0.3906	0.0696	0.7028	0.023*
N4A	0.0594 (4)	0.5401 (2)	0.6052 (2)	0.0136 (7)
N8A	−0.1842 (4)	0.3606 (2)	0.5991 (2)	0.0149 (7)
C1	−0.1007 (5)	0.5273 (3)	0.4517 (2)	0.0143 (8)
H1	−0.0582	0.4555	0.4394	0.017*
C2	0.0541 (5)	0.6012 (3)	0.4148 (2)	0.0134 (8)
H2	−0.0005	0.6721	0.4181	0.016*
C3	0.2473 (6)	0.5964 (3)	0.4683 (2)	0.0150 (8)
H3	0.3099	0.5278	0.4603	0.018*
C4	0.2039 (6)	0.6142 (2)	0.5678 (2)	0.0159 (8)
H4A	0.3303	0.6094	0.6020	0.019*
H4B	0.1506	0.6841	0.5758	0.019*
C5	0.0836 (5)	0.2572 (2)	0.6656 (2)	0.0129 (8)
H5	0.1248	0.2305	0.6055	0.016*
C6	−0.0675 (5)	0.1857 (2)	0.7072 (2)	0.0148 (8)
H6	−0.0980	0.2109	0.7691	0.018*
C7	−0.2591 (5)	0.1850 (3)	0.6542 (2)	0.0149 (8)
H7	−0.2360	0.1518	0.5946	0.018*
C8	−0.3350 (5)	0.2933 (3)	0.6401 (3)	0.0153 (8)
H8A	−0.4544	0.2913	0.6010	0.018*
H8B	−0.3757	0.3221	0.6988	0.018*
C9	0.1461 (5)	0.4365 (2)	0.6120 (2)	0.0145 (8)
H9A	0.2693	0.4389	0.6487	0.017*
H9B	0.1817	0.4114	0.5514	0.017*
C9A	−0.0033 (5)	0.3642 (3)	0.6551 (2)	0.0130 (8)
H9	−0.0396	0.3910	0.7158	0.016*
C10	−0.2718 (5)	0.4641 (3)	0.5941 (2)	0.0164 (8)
H10A	−0.3102	0.4862	0.6553	0.020*
H10B	−0.3946	0.4614	0.5572	0.020*
C10A	−0.1298 (5)	0.5425 (3)	0.5540 (2)	0.0137 (8)
H10	−0.1909	0.6114	0.5630	0.016*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0139 (14)	0.0215 (14)	0.0245 (15)	0.0016 (12)	−0.0068 (13)	−0.0025 (12)
O2	0.0211 (14)	0.0140 (11)	0.0163 (13)	−0.0033 (12)	0.0031 (13)	0.0039 (11)
O3	0.0162 (15)	0.0168 (12)	0.0302 (16)	−0.0035 (13)	0.0046 (14)	0.0023 (12)
O5	0.0114 (13)	0.0154 (13)	0.0249 (14)	0.0027 (12)	−0.0021 (13)	0.0017 (12)
O6	0.0198 (14)	0.0139 (12)	0.0177 (14)	0.0032 (12)	0.0043 (13)	0.0039 (11)
O7	0.0139 (14)	0.0115 (11)	0.0308 (15)	−0.0006 (12)	0.0041 (13)	0.0027 (12)
N4A	0.0107 (15)	0.0117 (14)	0.0184 (16)	−0.0019 (14)	0.0016 (14)	0.0004 (13)
N8A	0.0121 (15)	0.0135 (15)	0.0191 (15)	−0.0024 (14)	−0.0005 (14)	0.0026 (14)
C1	0.0094 (18)	0.0135 (17)	0.0199 (18)	−0.0002 (17)	−0.0018 (17)	0.0003 (15)
C2	0.015 (2)	0.0111 (17)	0.0141 (18)	−0.0007 (16)	−0.0002 (16)	0.0021 (15)
C3	0.0138 (19)	0.0105 (17)	0.0208 (19)	0.0002 (18)	−0.0004 (17)	0.0039 (16)
C4	0.017 (2)	0.0126 (17)	0.0180 (19)	−0.0034 (17)	−0.0022 (18)	0.0012 (15)
C5	0.0101 (17)	0.0167 (17)	0.0119 (17)	0.0023 (17)	−0.0033 (16)	−0.0002 (15)
C6	0.0179 (19)	0.0105 (16)	0.0161 (18)	0.0002 (17)	0.0007 (17)	−0.0001 (15)
C7	0.0147 (19)	0.0144 (17)	0.0158 (18)	−0.0017 (18)	0.0015 (16)	−0.0006 (15)
C8	0.0088 (18)	0.0172 (19)	0.0197 (19)	−0.0019 (16)	0.0008 (16)	−0.0001 (17)
C9	0.0127 (19)	0.0138 (18)	0.0170 (19)	−0.0010 (16)	0.0003 (16)	0.0006 (15)
C9A	0.0137 (18)	0.0128 (16)	0.0126 (17)	0.0008 (16)	−0.0021 (16)	−0.0001 (15)
C10	0.0140 (19)	0.0177 (19)	0.0175 (19)	0.0010 (18)	0.0027 (18)	0.0005 (17)
C10A	0.0107 (19)	0.0140 (18)	0.0164 (19)	0.0031 (16)	−0.0005 (16)	−0.0002 (15)

Geometric parameters (Å, º) top

O1—C1	1.446 (4)	C2—H2	1.0000
O1—H1O	0.8400	C3—C4	1.528 (5)
O2—C2	1.434 (4)	C3—H3	1.0000
O2—H2O	0.8400	C4—H4A	0.9900
O3—C3	1.431 (4)	C4—H4B	0.9900
O3—H3O	0.8400	C5—C6	1.512 (5)
O5—C5	1.431 (4)	C5—C9A	1.526 (4)
O5—H5O	0.8400	C5—H5	1.0000
O6—C6	1.432 (4)	C6—C7	1.508 (5)
O6—H6O	0.8400	C6—H6	1.0000
O7—C7	1.440 (4)	C7—C8	1.521 (5)
O7—H7O	0.8400	C7—H7	1.0000
N4A—C4	1.480 (4)	C8—H8A	0.9900
N4A—C9	1.480 (4)	C8—H8B	0.9900
N4A—C10A	1.480 (4)	C9—C9A	1.520 (5)
N8A—C9A	1.472 (4)	C9—H9A	0.9900
N8A—C8	1.473 (4)	C9—H9B	0.9900
N8A—C10	1.479 (4)	C9A—H9	1.0000
C1—C2	1.522 (5)	C10—C10A	1.523 (5)
C1—C10A	1.548 (5)	C10—H10A	0.9900
C1—H1	1.0000	C10—H10B	0.9900
C2—C3	1.522 (5)	C10A—H10	1.0000

C1—O1—H1O	109.5	O6—C6—C7	111.4 (3)
C2—O2—H2O	109.5	O6—C6—C5	109.9 (3)
C3—O3—H3O	109.5	C7—C6—C5	111.1 (3)
C5—O5—H5O	109.5	O6—C6—H6	108.1
C6—O6—H6O	109.5	C7—C6—H6	108.1
C7—O7—H7O	109.5	C5—C6—H6	108.1
C4—N4A—C9	111.7 (3)	O7—C7—C6	111.8 (3)
C4—N4A—C10A	110.7 (3)	O7—C7—C8	105.6 (3)
C9—N4A—C10A	113.0 (3)	C6—C7—C8	110.5 (3)
C9A—N8A—C8	110.5 (3)	O7—C7—H7	109.6
C9A—N8A—C10	109.0 (3)	C6—C7—H7	109.6
C8—N8A—C10	107.3 (3)	C8—C7—H7	109.6
O1—C1—C2	109.3 (3)	N8A—C8—C7	112.7 (3)
O1—C1—C10A	107.2 (3)	N8A—C8—H8A	109.1
C2—C1—C10A	111.1 (3)	C7—C8—H8A	109.1
O1—C1—H1	109.7	N8A—C8—H8B	109.1
C2—C1—H1	109.7	C7—C8—H8B	109.1
C10A—C1—H1	109.7	H8A—C8—H8B	107.8
O2—C2—C1	107.8 (3)	N4A—C9—C9A	110.0 (3)
O2—C2—C3	110.9 (3)	N4A—C9—H9A	109.7
C1—C2—C3	111.4 (3)	C9A—C9—H9A	109.7
O2—C2—H2	108.9	N4A—C9—H9B	109.7
C1—C2—H2	108.9	C9A—C9—H9B	109.7
C3—C2—H2	108.9	H9A—C9—H9B	108.2
O3—C3—C2	109.6 (3)	N8A—C9A—C9	108.9 (3)
O3—C3—C4	109.2 (3)	N8A—C9A—C5	110.1 (3)
C2—C3—C4	109.9 (3)	C9—C9A—C5	111.3 (3)
O3—C3—H3	109.4	N8A—C9A—H9	108.8
C2—C3—H3	109.4	C9—C9A—H9	108.8
C4—C3—H3	109.4	C5—C9A—H9	108.8
N4A—C4—C3	112.9 (3)	N8A—C10—C10A	113.0 (3)
N4A—C4—H4A	109.0	N8A—C10—H10A	109.0
C3—C4—H4A	109.0	C10A—C10—H10A	109.0
N4A—C4—H4B	109.0	N8A—C10—H10B	109.0
C3—C4—H4B	109.0	C10A—C10—H10B	109.0
H4A—C4—H4B	107.8	H10A—C10—H10B	107.8
O5—C5—C6	110.0 (3)	N4A—C10A—C10	108.6 (3)
O5—C5—C9A	107.3 (3)	N4A—C10A—C1	113.3 (3)
C6—C5—C9A	110.8 (3)	C10—C10A—C1	112.2 (3)
O5—C5—H5	109.6	N4A—C10A—H10	107.5
C6—C5—H5	109.6	C10—C10A—H10	107.5
C9A—C5—H5	109.6	C1—C10A—H10	107.5

O1—C1—C2—O2	−67.9 (4)	C4—N4A—C9—C9A	177.1 (3)
C10A—C1—C2—O2	174.0 (3)	C10A—N4A—C9—C9A	−57.3 (4)
O1—C1—C2—C3	170.2 (3)	C8—N8A—C9A—C9	−178.4 (3)
C10A—C1—C2—C3	52.1 (4)	C10—N8A—C9A—C9	−60.8 (3)
O2—C2—C3—O3	65.4 (4)	C8—N8A—C9A—C5	59.2 (4)
C1—C2—C3—O3	−174.6 (3)	C10—N8A—C9A—C5	176.9 (3)
O2—C2—C3—C4	−174.6 (3)	N4A—C9—C9A—N8A	60.1 (4)
C1—C2—C3—C4	−54.6 (4)	N4A—C9—C9A—C5	−178.4 (3)
C9—N4A—C4—C3	70.0 (4)	O5—C5—C9A—N8A	−178.4 (3)
C10A—N4A—C4—C3	−56.8 (4)	C6—C5—C9A—N8A	−58.3 (4)
O3—C3—C4—N4A	177.7 (3)	O5—C5—C9A—C9	60.8 (4)
C2—C3—C4—N4A	57.5 (4)	C6—C5—C9A—C9	−179.2 (3)
O5—C5—C6—O6	−62.9 (4)	C9A—N8A—C10—C10A	59.5 (4)
C9A—C5—C6—O6	178.7 (3)	C8—N8A—C10—C10A	179.2 (3)
O5—C5—C6—C7	173.4 (3)	C4—N4A—C10A—C10	179.2 (3)
C9A—C5—C6—C7	55.0 (4)	C9—N4A—C10A—C10	53.0 (4)
O6—C6—C7—O7	67.6 (4)	C4—N4A—C10A—C1	53.7 (4)
C5—C6—C7—O7	−169.5 (3)	C9—N4A—C10A—C1	−72.4 (4)
O6—C6—C7—C8	−175.1 (3)	N8A—C10—C10A—N4A	−54.2 (4)
C5—C6—C7—C8	−52.2 (4)	N8A—C10—C10A—C1	71.8 (4)
C9A—N8A—C8—C7	−58.0 (4)	O1—C1—C10A—N4A	−171.4 (3)
C10—N8A—C8—C7	−176.7 (3)	C2—C1—C10A—N4A	−52.1 (4)
O7—C7—C8—N8A	175.3 (3)	O1—C1—C10A—C10	65.1 (4)
C6—C7—C8—N8A	54.1 (4)

Experimental details

Crystal data
Chemical formula	C₁₂H₂₂N₂O₆
M_r	290.32
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	173
a, b, c (Å)	6.702 (2), 13.099 (5), 14.893 (3)
V (Å³)	1307.5 (7)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.12
Crystal size (mm)	0.42 × 0.30 × 0.15

Data collection
Diffractometer	Siemens/Nicolet R3m 4-circle diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	1608, 1504, 1146
R_int	0.039
(sin θ/λ)_max (Å⁻¹)	0.615

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.046, 0.094, 0.98
No. of reflections	1504
No. of parameters	187
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.23, −0.24

Computer programs: SHELXTL (Siemens, 1983), SHELXTL, SHELXS86 (Sheldrick, 1990), SHELXL97 (Sheldrick, 1997), ORTEP-3 for Windows (Farrugia, 1997), SHELXL97.

Selected geometric parameters (Å, º) top

N4A—C4	1.480 (4)	N4A—C10A	1.480 (4)
N4A—C9	1.480 (4)	N8A—C9A	1.472 (4)

C9—N4A—C10A	113.0 (3)	C8—N8A—C10	107.3 (3)

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Format		BIBTeX
		EndNote
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		Refer
		Medline
		CIF
		SGML
		Text
		Plain Text

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(1R,2R,3S,5R,6R,7S,9aR,10aR)-4a,8a-Di­aza­per­hydro­anthracene-1,2,3,5,6,7-hexaol

Supporting information

Key indicators

checkCIF/PLATON results

(1R,2R,3S,5R,6R,7S,9aR,10aR)-4a,8a-Diazaperhydroanthracene-1,2,3,5,6,7-hexaol