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Acta Crystallogr Sect E Struct Rep Online. 2009 March 1; 65(Pt 3): o474–o475.
Published online 2009 February 6. doi:  10.1107/S1600536809003766
PMCID: PMC2968537

3-Hydr­oxy-1,2,3,9-tetra­hydro­pyrrolo[2,1-b]quinazolin-4-ium chloride dihydrate: (+)-vasicinol hydro­chloride dihydrate from Peganum harmala L

Abstract

The title compound, C11H13N2O+·Cl·2H2O, the dihydrate of (+)-vasicinol hydro­chloride, is a pyrrolidinoquinazoline alkaloid. It was isolated from the ethyl acetate fraction of the leaves of Peganum harmala L. The pyrrolidine ring has an envelope conformation with the C atom at position 2 acting as the flap and the C atom at position 3, carrying the hydroxyl substituent, has an S configuration. The absolute configuration was determined as a result of the anomalous scattering of the Cl atom. In the crystal structure, mol­ecules stack along the a axis, connected to one another via inter­molecular O—H(...)Cl and N—H(...)Cl hydrogen bonds, forming approximately triangular-shaped R 2 1(7) rings, and O—H(...)Cl and O—H(...)O hydrogen bonds, forming penta­gonal-shaped R 5 4(10) rings. The overall effect is a ribbon-like arrangement running parallel to the a axis.

Related literature

For the isolation (+)-vasicinol and the crystal structure analysis of (+)-vasicinol hydro­bromide, see: Joshi et al. (1996 [triangle]). For general background on pyrrolidino-quinazoline alkaloids and their structures, see: Szulzewsky et al. (1976 [triangle]): Openshaw (1953 [triangle]); Bailey (1986 [triangle]); Rizk (1986 [triangle]); Tashkhodzhaev et al. (1995 [triangle]); Turgunov et al. (1995 [triangle]). For a study on the anti-Leishmaniasis activity of (+)-vasicinol hydro­chloride dihydrate, see: Misra et al. (2008 [triangle]). For further related literature on natural products, see: Hilal & Youngken (1983 [triangle]); Mirzakhmedov et al. (1975 [triangle]). For hydrogen-bond motifs, see: Bernstein et al. (1995 [triangle]). For puckering parameters, see: Cremer & Pople (1975 [triangle]).

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Object name is e-65-0o474-scheme1.jpg

Experimental

Crystal data

  • C11H13N2O+·Cl·2H2O
  • M r = 260.72
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-0o474-efi4.jpg
  • a = 7.0386 (6) Å
  • b = 9.5752 (10) Å
  • c = 18.4041 (18) Å
  • V = 1240.4 (2) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.31 mm−1
  • T = 173 (2) K
  • 0.42 × 0.19 × 0.11 mm

Data collection

  • Stoe IPDS diffractometer
  • Absorption correction: none
  • 8680 measured reflections
  • 2422 independent reflections
  • 1834 reflections with I > 2σ(I)
  • R int = 0.034

Refinement

  • R[F 2 > 2σ(F 2)] = 0.029
  • wR(F 2) = 0.061
  • S = 0.90
  • 2422 reflections
  • 216 parameters
  • 2 restraints
  • All H-atom parameters refined
  • Δρmax = 0.20 e Å−3
  • Δρmin = −0.14 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 984 Friedel pairs
  • Flack parameter: 0.004 (64)

Data collection: EXPOSE in IPDS-I (Stoe & Cie, 2000 [triangle]); cell refinement: CELL in IPDS-I; data reduction: INTEGRATE in IPDS-I; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]) and Mercury (Macrae et al., 2006 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809003766/lh2765sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809003766/lh2765Isup2.hkl

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

supplementary crystallographic information

Comment

Peganum harmala L is a member of the family Zygophyllaceae (Hilal and Youngken, 1983). This plant is commonly distributed in the Attock District, Islamabad, including the Margalla Hills. Several alkaloids have been isolated from the seeds and roots of this plant and have been identified as chemicals with a β-carboline structure, such as harmine, harmaline, harmalol, and harman (Bailey, 1986; Rizk, 1986), or with a quinazoline structure, such as vasicine and vasicinon (Openshaw, 1953; Bailey, 1986; Joshi et al., 1996). Here we report on the crystal structure of the title compound, the dihydrate of (+)Vasicinol hydrochloride. It is a pyrrolidino-quinazoline alkaloid and was isolated from the ethylacetate fraction of the leaves of Peganum harmala L, collected from the Margalla Hills, Islamabad.

The molecular structure of the title compound is shown in Fig. 1. Dimensions are similar to those observed in other pyrrolidino-quinazoline alkaloids (Joshi et al., 1996; Tashkhodzhaev et al., 1995; Turgunov et al., 1995; Szulzewsky et al., 1976). The title compound crystallizes in the non-centrosymmetric orthorhombic space group P212121. The crystal structure of (+)-Vasicinol hydrobromide has been reported previously (Joshi et al., 1996), and crystallizes in the non-centrosymmetric monoclinic space group P21, with two independent molecules per asymmetric unit.

The pyrrolidine ring has an envelope conformation on atom C2; the puckering parameters (Cremer & Pople, 1975) are Q(2) = 0.243 (2) Å, and [var phi](2) = 253.8 (5)°. The carbon atom carrying the hydroxyl substituent, atom C3, has a S-configuration. The absolute configuration of the title compound was determined as a result of the anomalous scattering of the Cl-atom.

In the crystal the molecules stacks up the a axis and are connected to one another via a series of O—H···Cl, N—H···Cl hydrogen bonds, with approximately triangular-shaped R12(7) rings (Bernstein et al., 1995) and O—H···Cl and O—H···O hydrogen bonds, forming pentagonal-shaped R54(10) rings [see Fig. 2 and Table 1]. In this way a ribon-like arrangement is formed running parallel to the a axis. The same triangular arrangement, involving O—H···halide- and N—H···halide- hydrogen bonds, is also observed in the crystal packing of (+)-Vasicine hydrobromide (Fig. 3; Joshi et al., 1996).

Experimental

Peganum harmala L is a member of the family Zygophyllaceae (Hilal & Youngken, 1983). This plant is commonly distributed in the Attock District, Islamabad, including the Margalla Hills, Gilgit: Chilas, Yasin, Gupis, Phunder, Hunza, Skardu. The leaves of the plant were collected from the Margalla Hills, Islamabad and the sample was deposited in the herbarium of Quaid-i-Azam University (ISL) under the accession No. 123774 and 123775. The air dried leaves were powdered and extracted three times with methanol. The extracts were and concentrated to a semi-solid mass. Water was added to this semi-solid mass to form a paste. The extract was then fractioned using different solvents according to their increasing polarity. The title compound was isolated from the ethylacetate fraction of the leaves of Peganum harmala L as colourless rod-like crystals.

Refinement

The absolute configuration of the title compound was determined as a result of the anomalous scattering of the Cl-atom: Flack x parameter = -0.0044 with e.s.d. 0.0644; Hooft y Parameter Value = 0.0024 with e.s.d. 0.0478. The hydrogen atoms were located in difference Fourier maps. The C-bound H-atoms were freely refined: C—H = 0.92 (2) - 1.04 (2) Å. The O—H and N—H bond distances were restrained to 0.87 (2) and 0.82 (2) %A, respectively: O—H = 0.89 (2) Å and N—H = 0.821 (17) Å. The water H-atoms were refined with Uiso(H) = 1.5Ueq(O): O—H = 0.79 (4) - 0.89 (3) Å.

Figures

Fig. 1.
The molecular structure of the title compound, showing the atomic numbering scheme and displacement ellipsoids drawn at the 50% probability level.
Fig. 2.
View along the c direction of the crystal packing of the title compound, showing the formation of the triangular-shaped [R12(7)], and pentagonal-shaped [R54(10)] rings of hydrogen bonds (dashed blue lines; Cl- green ball; H-atoms not involved in hydrogen ...
Fig. 3.
View along the a axis of the crystal packing of (+)-Vasicinol hydrobromide (Joshi et al., 1996), showing the formation of the trianglular-shaped [R12(7)] rings of hydrogen bonds [Br- purple ball; H-atoms not involved in hydrogen bonding have been removed ...

Crystal data

C11H13N2O+·Cl·2H2OF(000) = 552
Mr = 260.72Dx = 1.396 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 6244 reflections
a = 7.0386 (6) Åθ = 2.2–25.9°
b = 9.5752 (10) ŵ = 0.31 mm1
c = 18.4041 (18) ÅT = 173 K
V = 1240.4 (2) Å3Rod, colourless
Z = 40.42 × 0.19 × 0.11 mm

Data collection

Stoe IPDS diffractometer1834 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.034
graphiteθmax = 26.1°, θmin = 2.2°
phi rotation scansh = −8→8
8680 measured reflectionsk = −11→11
2422 independent reflectionsl = −22→22

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.029All H-atom parameters refined
wR(F2) = 0.061w = 1/[σ2(Fo2) + (0.033P)2] where P = (Fo2 + 2Fc2)/3
S = 0.90(Δ/σ)max < 0.001
2422 reflectionsΔρmax = 0.20 e Å3
216 parametersΔρmin = −0.14 e Å3
2 restraintsAbsolute structure: Flack (1983), 984 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.004 (64)

Special details

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles
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)

xyzUiso*/Ueq
O10.3510 (2)0.15059 (15)0.24928 (8)0.0409 (5)
N90.2235 (3)0.16767 (15)0.09484 (8)0.0249 (5)
N100.2348 (2)0.40126 (14)0.12323 (8)0.0246 (5)
C10.2373 (4)0.4955 (2)0.18629 (12)0.0348 (8)
C20.2861 (4)0.3982 (2)0.24882 (11)0.0348 (7)
C30.2264 (4)0.2536 (2)0.22362 (10)0.0280 (7)
C40.2242 (3)0.0847 (2)−0.02920 (11)0.0310 (7)
C50.2242 (3)0.1121 (3)−0.10295 (10)0.0373 (7)
C60.2232 (4)0.2484 (3)−0.12768 (11)0.0398 (8)
C70.2228 (3)0.3570 (2)−0.07828 (10)0.0339 (7)
C80.2231 (4)0.45209 (19)0.04834 (10)0.0287 (7)
C110.2303 (3)0.27062 (18)0.14208 (9)0.0223 (6)
C120.2237 (3)0.33226 (19)−0.00429 (9)0.0253 (6)
C130.2242 (3)0.19435 (18)0.01937 (9)0.0227 (6)
O1W0.4964 (3)0.7633 (3)0.06429 (11)0.0639 (8)
O2W0.1191 (3)0.2477 (2)0.42346 (11)0.0598 (8)
Cl10.80565 (8)0.38150 (5)0.32092 (3)0.0358 (2)
H1A0.329 (3)0.563 (2)0.1789 (12)0.033 (6)*
H1B0.113 (4)0.540 (2)0.1877 (14)0.049 (7)*
H1O0.298 (4)0.071 (2)0.2333 (13)0.0610*
H2A0.225 (4)0.422 (2)0.2921 (12)0.038 (6)*
H2B0.431 (3)0.395 (2)0.2595 (11)0.040 (6)*
H30.095 (3)0.231 (2)0.2387 (11)0.036 (6)*
H40.233 (3)−0.012 (2)−0.0084 (10)0.034 (6)*
H50.222 (4)0.034 (2)−0.1392 (12)0.053 (7)*
H60.224 (3)0.266 (2)−0.1810 (13)0.047 (6)*
H70.217 (4)0.454 (2)−0.0961 (12)0.051 (7)*
H8A0.108 (3)0.502 (2)0.0441 (11)0.029 (6)*
H8B0.331 (3)0.517 (2)0.0407 (11)0.033 (6)*
H9N0.211 (4)0.0872 (17)0.1102 (11)0.0370*
H1WA0.432 (5)0.792 (4)0.099 (2)0.0960*
H1WB0.603 (5)0.764 (4)0.077 (2)0.0960*
H2WA0.033 (5)0.282 (4)0.3988 (19)0.0900*
H2WB0.081 (5)0.245 (4)0.4695 (18)0.0900*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0538 (11)0.0371 (9)0.0319 (8)0.0022 (7)−0.0108 (7)0.0022 (7)
N90.0323 (11)0.0191 (7)0.0233 (8)−0.0015 (8)−0.0018 (8)0.0007 (7)
N100.0296 (11)0.0206 (8)0.0235 (7)0.0004 (8)−0.0027 (7)0.0010 (6)
C10.0445 (17)0.0241 (10)0.0357 (11)−0.0014 (10)0.0015 (12)−0.0078 (9)
C20.0439 (15)0.0338 (10)0.0268 (10)−0.0057 (12)0.0001 (11)−0.0084 (9)
C30.0337 (16)0.0272 (10)0.0230 (10)−0.0018 (10)0.0003 (9)0.0000 (8)
C40.0307 (14)0.0319 (11)0.0305 (10)0.0038 (9)−0.0018 (10)−0.0054 (8)
C50.0312 (14)0.0536 (12)0.0272 (10)0.0024 (13)−0.0031 (9)−0.0119 (11)
C60.0360 (15)0.0600 (14)0.0234 (10)0.0003 (13)−0.0011 (11)0.0050 (10)
C70.0318 (13)0.0429 (13)0.0270 (10)0.0017 (11)−0.0002 (9)0.0090 (9)
C80.0317 (14)0.0253 (10)0.0292 (11)−0.0001 (11)−0.0030 (10)0.0075 (8)
C110.0194 (13)0.0225 (9)0.0249 (9)0.0014 (8)0.0003 (8)−0.0017 (8)
C120.0182 (12)0.0323 (9)0.0253 (9)0.0002 (9)−0.0014 (9)0.0027 (8)
C130.0199 (12)0.0281 (9)0.0200 (9)−0.0006 (8)−0.0001 (8)0.0004 (7)
O1W0.0428 (12)0.1035 (16)0.0453 (11)0.0043 (12)0.0030 (9)−0.0184 (11)
O2W0.0432 (13)0.0885 (15)0.0477 (11)0.0093 (11)0.0014 (9)0.0226 (11)
Cl10.0414 (3)0.0279 (2)0.0380 (3)0.0034 (2)0.0001 (3)−0.0046 (2)

Geometric parameters (Å, °)

O1—C31.402 (3)C5—C61.382 (4)
O1—H1O0.90 (2)C6—C71.381 (3)
O1W—H1WB0.79 (4)C7—C121.382 (2)
O1W—H1WA0.83 (4)C8—C121.502 (3)
O2W—H2WA0.83 (4)C12—C131.391 (2)
O2W—H2WB0.89 (3)C1—H1B0.97 (3)
N9—C131.412 (2)C1—H1A0.92 (2)
N9—C111.315 (2)C2—H2A0.93 (2)
N10—C111.299 (2)C2—H2B1.04 (2)
N10—C81.464 (2)C3—H30.99 (2)
N10—C11.470 (3)C4—H41.004 (19)
N9—H9N0.825 (17)C5—H51.00 (2)
C1—C21.520 (3)C6—H61.00 (2)
C2—C31.519 (3)C7—H70.99 (2)
C3—C111.510 (2)C8—H8A0.94 (2)
C4—C51.382 (3)C8—H8B0.99 (2)
C4—C131.379 (3)
C3—O1—H1O103.1 (16)C4—C13—C12121.34 (16)
H1WA—O1W—H1WB107 (4)N10—C1—H1A108.8 (14)
H2WA—O2W—H2WB108 (3)C2—C1—H1B116.8 (15)
C11—N9—C13120.96 (15)N10—C1—H1B106.2 (14)
C1—N10—C11112.38 (15)C2—C1—H1A112.5 (13)
C1—N10—C8122.67 (14)H1A—C1—H1B109.0 (18)
C8—N10—C11124.78 (15)C1—C2—H2B112.5 (11)
C13—N9—H9N120.4 (14)C3—C2—H2A110.8 (13)
C11—N9—H9N118.5 (14)H2A—C2—H2B107 (2)
N10—C1—C2102.95 (15)C3—C2—H2B107.6 (11)
C1—C2—C3105.36 (17)C1—C2—H2A113.1 (13)
O1—C3—C2111.4 (2)O1—C3—H3109.7 (12)
O1—C3—C11113.54 (17)C11—C3—H3108.6 (12)
C2—C3—C11101.54 (15)C2—C3—H3111.9 (11)
C5—C4—C13119.47 (19)C13—C4—H4117.1 (11)
C4—C5—C6120.2 (2)C5—C4—H4123.3 (11)
C5—C6—C7119.61 (19)C4—C5—H5120.8 (12)
C6—C7—C12121.29 (19)C6—C5—H5119.0 (12)
N10—C8—C12110.68 (14)C7—C6—H6121.4 (11)
N9—C11—C3125.13 (16)C5—C6—H6119.0 (11)
N10—C11—C3111.72 (15)C12—C7—H7119.3 (13)
N9—C11—N10123.11 (16)C6—C7—H7119.4 (13)
C8—C12—C13121.58 (15)N10—C8—H8B107.4 (12)
C7—C12—C8120.30 (16)N10—C8—H8A107.1 (12)
C7—C12—C13118.12 (16)H8A—C8—H8B109.2 (17)
N9—C13—C4119.99 (16)C12—C8—H8A109.6 (12)
N9—C13—C12118.67 (15)C12—C8—H8B112.7 (12)
C13—N9—C11—N101.2 (3)O1—C3—C11—N10−135.24 (18)
C13—N9—C11—C3178.7 (2)C2—C3—C11—N9166.7 (2)
C11—N9—C13—C4177.6 (2)C2—C3—C11—N10−15.5 (3)
C11—N9—C13—C12−2.8 (3)C13—C4—C5—C6−0.3 (3)
C8—N10—C1—C2−170.1 (2)C5—C4—C13—N9179.8 (2)
C11—N10—C1—C214.5 (3)C5—C4—C13—C120.2 (3)
C1—N10—C8—C12179.9 (2)C4—C5—C6—C70.2 (4)
C11—N10—C8—C12−5.3 (3)C5—C6—C7—C120.1 (4)
C1—N10—C11—N9178.6 (2)C6—C7—C12—C8−180.0 (2)
C1—N10—C11—C30.7 (3)C6—C7—C12—C13−0.3 (3)
C8—N10—C11—N93.3 (3)N10—C8—C12—C7−176.89 (19)
C8—N10—C11—C3−174.5 (2)N10—C8—C12—C133.4 (3)
N10—C1—C2—C3−23.3 (3)C7—C12—C13—N9−179.5 (2)
C1—C2—C3—O1144.52 (19)C7—C12—C13—C40.1 (3)
C1—C2—C3—C1123.3 (3)C8—C12—C13—N90.2 (3)
O1—C3—C11—N947.0 (3)C8—C12—C13—C4179.8 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1—H1O···Cl1i0.90 (2)2.20 (2)3.086 (2)171 (2)
N9—H9N···Cl1i0.83 (2)2.35 (2)3.155 (2)167 (2)
O1W—H1WA···Cl1ii0.83 (4)2.39 (4)3.204 (2)167 (3)
O1W—H1WB···O2Wii0.79 (4)1.96 (4)2.720 (3)162 (4)
O2W—H2WA···Cl1iii0.83 (4)2.35 (4)3.173 (2)175 (3)
O2W—H2WB···O1Wiv0.89 (3)1.83 (3)2.718 (3)179 (5)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH2765).

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