(2S,3R,4S,4aR)-2,3,4,7-Tetra­hydroxy-3,4,4a,5-tetra­hydro­[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one hemihydrate

Jucov, E.; Kornienko, A.; Masi, M.; Evidente, A.; Antipin, M.

doi:10.1107/S1600536812048763

Volume 69
Part 1
Pages o9-o10
January 2013

Received 12 November 2012
Accepted 27 November 2012
Online 5 December 2012

Key indicators
Single-crystal X-ray study
T = 100 K
Mean (C-C) = 0.003 Å
H completeness 99%
R = 0.047
wR = 0.122
Data-to-parameter ratio = 11.1
Details

(2S,3R,4S,4aR)-2,3,4,7-Tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one hemihydrate

Evgheni Jucov,^a ^* Alexander Kornienko,^b Marco Masi,^c Antonio Evidente ^c and Mikhail Antipin ^d

^aInstitute of Applied Physics of the Academy of Sciences of Moldova, 5 Academy Street, MD-2028, Chisinau, Republic of Moldova,^bDepartment of Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA,^cDipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, Napoli 80126, Italy, and ^dDepartment of Chemistry & Biology, New Mexico Highlands University, 803 University Avenue, Las Vegas, NM 87701, USA
Correspondence e-mail: evgheny.jukov@gmail.com

The title natural compound, isolated from Narcissus pseudonarcissus var. King Alfred crystallizes as a hemihydrate, C₁₄H₁₃NO₇·0.5H₂O, with four crystallographically independent dioxolophenanthridinone molecules and two crystallographically independent solvent water molecules in the asymmetric unit. All four crystallographically independent dioxolophenanthridinone molecules are geometrically very similar and differ only in the orientations of the three hydroxy groups at the terminal cyclohexene rings. The five-membered dioxolane ring has a planar conformation (the r.m.s. deviations are 0.010, 0.019, 0.025 and 0.004 Å, for the four crystallographically independent molecules), and the six-membered dihydropyridone and cyclohexene rings adopt sofa conformations in each molecule. The flattened structure of each dioxolophenanthridinone molecule is supported by a strong intramolecular O-HO hydrogen bond. The N atom has a slightly pyramidalized configuration. In the crystal, the dioxolophenanthridinone molecules form layers parallel to (101) with O-HO and N-HO hydrogen bonds linking the dioxolophenanthridinone molecules both within and between the layers and the water molecules, forming a three-dimensional framework. The absolute configurations of the chiral centers are 2S, 3R, 4S and 4aR.

Related literature

For general background to narciclasine, see: Ceriotti (1967a,b); Ceriotti et al. (1967); Kornienko & Evidente (2008). For the crystal structures of related compounds, see: Savona et al. (1970); Immirzi & Fuganti (1972); Bi et al. (1998); McNulty et al. (2011).

Experimental

Crystal data

C₁₄H₁₃NO₇·0.5H₂O
M_r = 316.26
Monoclinic, P 2₁
a = 10.90063 (8) Å
b = 20.37357 (17) Å
c = 11.88385 (9) Å
= 104.3549 (8)°
V = 2556.82 (4) Å³
Z = 8
Cu K radiation
= 1.16 mm^-1
T = 100 K
0.25 × 0.23 × 0.06 mm

Data collection

Agilent SuperNova (Dual, Cu at zero, Atlas CCD) diffractometer
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2012) T_min = 0.738, T_max = 1.000
57161 measured reflections
10051 independent reflections
9997 reflections with I > 2(I)
R_int = 0.028

Refinement

R[F² > 2(F²)] = 0.047
wR(F²) = 0.122
S = 1.05
10051 reflections
908 parameters
1 restraint
H atoms treated by a mixture of independent and constrained refinement
_max = 0.27 e Å^-3
_min = -0.21 e Å^-3
Absolute structure: Flack (1983), 4707 Friedel pairs
Flack parameter: 0.05 (8)

Table 1
Hydrogen-bond geometry (Å, °)

D-HA	D-H	HA	DA	D-HA
O3-H3O4	0.96 (3)	1.57 (4)	2.4842 (19)	158 (3)
O5-H5O7Aⁱ	0.84 (4)	1.88 (4)	2.698 (2)	166 (4)
O6-H6O3Aⁱⁱ	0.85 (3)	1.98 (3)	2.745 (2)	150 (3)
O7-H7O7Cⁱⁱⁱ	0.89 (3)	1.89 (3)	2.768 (2)	170 (3)
N1-H1O4Bⁱ	0.91 (4)	2.25 (4)	3.105 (2)	157 (3)
O3A-H3AO4A	1.00 (4)	1.55 (4)	2.4656 (19)	151 (4)
O5A-H5AO7	0.87 (3)	2.23 (3)	3.050 (2)	157 (3)
O6A-H6AAO1ⁱⁱ	0.82 (4)	2.15 (4)	2.906 (2)	153 (3)
O7A-H7AO1A^iv	0.83 (4)	2.29 (4)	2.901 (2)	131 (3)
N1A-H1AAO4C	0.89 (3)	1.91 (3)	2.796 (2)	171 (3)
O3B-H3BO4B	1.01 (4)	1.57 (4)	2.537 (2)	159 (4)
O5B-H5BO2W^v	0.94 (4)	1.80 (4)	2.701 (2)	159 (4)
O6B-H6BO6^vi	0.89 (4)	2.03 (4)	2.8857 (19)	163 (3)
O7B-H7BO5^vii	0.86 (4)	1.86 (4)	2.714 (2)	175 (4)
N1B-H1BAO4^v	0.89 (4)	1.99 (4)	2.870 (2)	171 (3)
O3C-H3CO4C	0.95 (5)	1.59 (5)	2.4797 (18)	154 (5)
O5C-H5CO6B	0.82 (3)	2.01 (4)	2.829 (2)	175 (3)
O6C-H6CO6A^vi	0.88 (4)	1.93 (3)	2.7893 (19)	165 (3)
O7C-H7CO3C^vii	0.86 (4)	1.93 (4)	2.767 (2)	162 (3)
N1C-H1CO4A	0.91 (4)	2.03 (4)	2.911 (2)	164 (3)
O1W-H1WAO7Bⁱ	0.90 (4)	1.94 (4)	2.835 (2)	173 (4)
O1W-H1WBO5A^vii	0.89 (5)	2.22 (5)	3.036 (2)	153 (4)
O2W-H2WAO1W	0.90 (3)	1.94 (3)	2.833 (2)	167 (3)
O2W-H2WBO6C	0.87 (4)	2.00 (4)	2.869 (2)	172 (3)
Symmetry codes: (i) x, y, z-1; (ii) $[-x, y-{\script{1\over 2}}, -z+1]$ ; (iii) $[-x+1, y-{\script{1\over 2}}, -z+1]$ ; (iv) $[-x, y-{\script{1\over 2}}, -z+2]$ ; (v) x, y, z+1; (vi) $[-x, y+{\script{1\over 2}}, -z+1]$ ; (vii) $[-x+1, y+{\script{1\over 2}}, -z+1]$ .

Data collection: CrysAlis PRO (Agilent, 2012); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: RK2387 ).

Acknowledgements

The authors are grateful to Dr Sergey Lindeman for help with this work and to the NSF for support via DMR grant 0934212 (PREM) and CHE 0832622.

References

Agilent (2012). CrysAlis PRO. Agilent Technologies, Yarnton, England.
Bi, Y.-R., Yung, K.-H. & Wong, Y.-S. (1998). Plant. Sci. 135, 103-108.
Ceriotti, G. (1967a). Nature, 213, 595-596.
Ceriotti, G. (1967b). Tumori, 53, 437-445.
Ceriotti, G., Spandrio, L. & Gazzaniga, A. (1967). Tumori, 53, 359-371.
Flack, H. D. (1983). Acta Cryst. A39, 876-881.
Immirzi, A. & Fuganti, C. (1972). J. Chem. Soc. Chem. Commun. p. 240a.
Kornienko, A. & Evidente, A. (2008). Chem. Rev. 108, 1982-2014.
McNulty, J., Thorat, A., Vurgun, N., Nair, J. J., Makaji, E., Crankshaw, D. J., Holloway, A. C. & Pandey, S. (2011). J. Nat. Prod. 74, 106-108.
Savona, G., Piozzi, F., Marino, M. L., Knight, J. & Mays, M. J. (1970). J. Chem. Soc. Chem. Commun. p. 1006a.
Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.

organic compounds