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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 67| Part 7| July 2011| Pages o1743-o1744

(6aS,11aR,11cS)-8-Sulfanyl­idene-2,3,5,6,6a,7,11,11a,11b,11c-deca­hydro-3a,7a-di­aza-1H,4H-benzo[de]anthracen-3a-ium chloride hemihydrate

aSchool of Pharmacy, Yantai University, Yantai 264005, People's Republic of China, and bDepartment of Organic Chemistry, School of Pharmacy, Second Military Medical University, Shanghai 200433, People's Republic of China
*Correspondence e-mail: huhonggang_fox@msn.com

(Received 11 December 2010; accepted 15 March 2011; online 18 June 2011)

The title compound, C15H23N2S+·Cl·0.5H2O, was prepared from (6aS,11aR,11cS)-2,3,5,6,6a,7,11,11a,11b,11c-deca­hydro-3a,7a-diaza-1H,4H-benzo[de]anthracene-8-one (sophocarpine) and Lawesson's reagent. The thione-substituted ring is in an envelope conformation and the three other six-membered rings are in chair conformations. In the crystal, anions and cations are linked by N—H⋯Cl and weak C—H⋯Cl hydrogen bonds. One 0.5-occupancy solvent water mol­ecule lies on a twofold rotation axis and another 0.25-occupancy solvent water mol­ecule is in a general position. The H atoms of these water mol­ecules were not located or included in the refinement.

Related literature

For background to the medicinal uses of sophocarpine natural products, see: Gao et al. (2009[Gao, Y. L., Li, G. S., Li, C. M., Zhu, X. Y., Li, M., Fu, C. L. & Li, B. F. J. (2009). Ethnopharmacology, 125, 324-329.]); Jiang et al. (2007[Jiang, H., Hou, C., Zhang, S., Xie, H., Zhou, W., Jin, Q., Cheng, X., Qian, R. & Zhang, X. (2007). Eur. J. Pharmacol. 559, 98-108.]); Liu et al. (2007[Liu, J. Y., Hu, J. H., Zhu, Q. G., Li, F. Q., Wang, J. & Sun, H. J. (2007). Int. Immunopharmacol. 7, 816-823.]). For related structures, see: Ding et al. (2005[Ding, P. L., Liao, Z. X., Huang, H., Zhou, P. & Chen, D. F. (2005). Bioorg Med. Chem. Lett. pp. 1231-1235.]); Khan et al. (1992[Khan, M. A., Burrows, G. E. & Holt, E. M. (1992). Acta Cryst. C48, 2051-2053.]). For the synthesis, see: Kaleta et al. (2006[Kaleta, Z., Makowski, B. T., Soos, T. & Dembinski, R. (2006). Org. Lett. 8, 1625-1628.]).

[Scheme 1]

Experimental

Crystal data
  • C15H23N2S+·Cl·0.5H2O

  • Mr = 306.87

  • Tetragonal, P 41 21 2

  • a = 7.793 (5) Å

  • c = 52.59 (5) Å

  • V = 3194 (4) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.36 mm−1

  • T = 293 K

  • 0.25 × 0.20 × 0.18 mm

Data collection
  • Bruker SMART CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.915, Tmax = 0.937

  • 11100 measured reflections

  • 2816 independent reflections

  • 2489 reflections with I > 2σ(I)

  • Rint = 0.043

Refinement
  • R[F2 > 2σ(F2)] = 0.071

  • wR(F2) = 0.204

  • S = 1.23

  • 2816 reflections

  • 190 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.64 e Å−3

  • Δρmin = −0.25 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1023 Friedel pairs

  • Flack parameter: 0.1 (2)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯Cl1 1.10 (9) 2.01 (8) 3.019 (6) 151 (6)
C4—H4A⋯Cl1i 0.97 2.82 3.726 (7) 155
Symmetry code: (i) y, x, -z.

Data collection: SMART (Bruker, 1997[Bruker (1997). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 1997[Bruker (1997). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

Sophocarpine ((6aS,11aR,11cS)-2,3,5,6,6a,7,11,11a,11b,11c- decahydro-1H,4H -3a,7a-diaza-βenzo[de] anthracene-8-one) and its derivatives have been found to possess a variety of pharmacological effects (Jiang et al., 2007), including anti-inflammation (Liu et al., 2007) and immunity-regulation activity (Gao et al. 2009). As part of our ongoing investigation of sophocarpine and its derivatives, we report here the crystal structure of the title compound.

The molecular structure of the title compound is shown in Fig. 1. The bond lengths and angles are comparable to related structures (Khan et al., 1992; Ding et al., 2005). The C1/C2/C3/C4/C5/N2 ring is in an envelope conformation with C5 forming the flap. The three other six-membered rings A(N1/C6/C7/C8/C9/C14), B(N1/C10/C11/C12/C13/C14) and C(N2/C1/C2/C3/C4/C5) are in chair conformations. In the crystal, anions and cations are linked by N—H···Cl and weak C—H···Cl hydrogen bonds.

Related literature top

For background to the medicinal uses of sophocarpine natural products, see: Gao et al. (2009); Jiang et al. (2007); Liu et al. (2007). For related structures, see: Ding et al. (2005); Khan et al. (1992). For the synthetic procedure, see: Kaleta et al. (2006).

Experimental top

The synthetic procedure followed the methods of Kaleta et al. (2006). (6aS,11aR,11cS)-2,3,5,6,6a,7,11,11a,11b,11c-decahydro-1H, 4H-3a,7a-diaza-benzo[de] anthracene-8-one (0.01 mol) and Lawesson's reagent (0.04 mol) were mixed in toluene (100 ml) and stirred under reflux for 2 h. TLC showed that the reaction was completed. The mixture was concentrated and the residue was purified by a silica gel column. The products were stirred in dichloromethane and HCl was added. The resulting crystals were filtered and dried at room temperature. Single crystals suitable for X-ray measurements were obtained by recrystallization of a solution of the title compound in H2O at room temperature.

Refinement top

H atoms bonded to C atoms were fixed geometrically and allowed to ride on their attached atoms, with C—H distances in the range 0.93–0.98Å and with Uiso(H) = 1.2Ueq(C). The H atom bonded to N was refined independently with an isotropic displacement parameter. The H atoms of the partially occupied water molecules could not be located and are not included in the refinement although they are included in the formula.

Computing details top

Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 1997); data reduction: SAINT (Bruker, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound with the atom-labeling scheme. Displacement ellipsoids are drawn at the 30% probability level.
(6aS,11aR,11cS)-8-Sulfanylidene- 2,3,5,6,6a,7,11,11a,11b,11c-decahydro- 3a,7a-diaza-1H,4H-benzo[de]anthracen-3a-ium chloride hemihydrate top
Crystal data top
C15H23N2S+·Cl·0.5H2ODx = 1.281 Mg m3
Mr = 306.87Mo Kα radiation, λ = 0.71073 Å
Tetragonal, P41212Cell parameters from 927 reflections
Hall symbol: P 4abw 2nwθ = 2.7–24.0°
a = 7.793 (5) ŵ = 0.36 mm1
c = 52.59 (5) ÅT = 293 K
V = 3194 (4) Å3Block, yellow
Z = 80.25 × 0.20 × 0.18 mm
F(000) = 1320
Data collection top
Bruker SMART CCD
diffractometer
2816 independent reflections
Radiation source: fine-focus sealed tube2489 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.043
ϕ and ω scansθmax = 25.0°, θmin = 2.6°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 97
Tmin = 0.915, Tmax = 0.937k = 79
11100 measured reflectionsl = 5462
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.071H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.204 w = 1/[σ2(Fo2) + (0.104P)2 + 2.0841P]
where P = (Fo2 + 2Fc2)/3
S = 1.23(Δ/σ)max = 0.002
2816 reflectionsΔρmax = 0.64 e Å3
190 parametersΔρmin = 0.25 e Å3
0 restraintsAbsolute structure: Flack (1983), 1023 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.1 (2)
Crystal data top
C15H23N2S+·Cl·0.5H2OZ = 8
Mr = 306.87Mo Kα radiation
Tetragonal, P41212µ = 0.36 mm1
a = 7.793 (5) ÅT = 293 K
c = 52.59 (5) Å0.25 × 0.20 × 0.18 mm
V = 3194 (4) Å3
Data collection top
Bruker SMART CCD
diffractometer
2816 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
2489 reflections with I > 2σ(I)
Tmin = 0.915, Tmax = 0.937Rint = 0.043
11100 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.071H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.204Δρmax = 0.64 e Å3
S = 1.23Δρmin = 0.25 e Å3
2816 reflectionsAbsolute structure: Flack (1983), 1023 Friedel pairs
190 parametersAbsolute structure parameter: 0.1 (2)
0 restraints
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
xyzUiso*/UeqOcc. (<1)
S10.6279 (2)0.2217 (2)0.11342 (2)0.0559 (4)
Cl10.2534 (2)0.6515 (3)0.01987 (3)0.0785 (6)
N10.4499 (5)0.8604 (6)0.05841 (7)0.0415 (9)
N20.6084 (5)0.4228 (5)0.07265 (6)0.0357 (9)
C10.7029 (6)0.3215 (6)0.08746 (8)0.0400 (11)
C20.8817 (7)0.2948 (7)0.08006 (9)0.0511 (12)
H2A0.95480.23860.09130.061*
C30.9422 (7)0.3467 (8)0.05836 (10)0.0543 (13)
H3A1.05660.32600.05440.065*
C40.8319 (7)0.4387 (7)0.03976 (9)0.0483 (13)
H4A0.78640.35700.02760.058*
H4B0.90110.52110.03050.058*
C50.6831 (6)0.5324 (6)0.05266 (7)0.0354 (10)
H5A0.59440.55400.03980.043*
C60.7298 (6)0.7046 (6)0.06520 (7)0.0352 (10)
H6A0.81280.67960.07870.042*
C70.8144 (7)0.8338 (7)0.04731 (10)0.0482 (12)
H7A0.85990.92850.05720.058*
H7B0.90960.77890.03870.058*
C80.6899 (7)0.9026 (7)0.02780 (10)0.0537 (13)
H8A0.64990.80970.01700.064*
H8B0.74720.98640.01710.064*
C90.5388 (7)0.9856 (7)0.04105 (10)0.0557 (14)
H9A0.57851.08320.05090.067*
H9B0.45801.02710.02840.067*
C100.2988 (7)0.9449 (8)0.07086 (11)0.0562 (15)
H10A0.33821.03900.08140.067*
H10B0.22360.99160.05790.067*
C110.2019 (7)0.8205 (8)0.08673 (10)0.0558 (14)
H11A0.15390.73190.07590.067*
H11B0.10760.87930.09500.067*
C120.3168 (7)0.7373 (8)0.10691 (10)0.0562 (14)
H12A0.35040.82330.11930.067*
H12B0.25230.64900.11570.067*
C130.4772 (6)0.6578 (7)0.09521 (8)0.0422 (11)
H13A0.55490.63090.10930.051*
C140.5717 (6)0.7830 (6)0.07802 (8)0.0382 (11)
H14A0.61220.87730.08880.046*
C150.4427 (6)0.4900 (7)0.08132 (8)0.0394 (11)
H15A0.38780.40860.09260.047*
H15B0.36760.50980.06690.047*
O10.2960 (17)0.2869 (17)0.0131 (3)0.049 (3)0.25
O20.0693 (14)0.0693 (14)0.00000.179 (12)0.50
H10.390 (8)0.755 (8)0.0486 (10)0.066 (17)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0630 (9)0.0610 (9)0.0436 (6)0.0009 (7)0.0016 (6)0.0180 (6)
Cl10.0562 (9)0.1312 (17)0.0481 (7)0.0121 (10)0.0120 (7)0.0032 (8)
N10.044 (2)0.041 (2)0.0398 (19)0.0012 (19)0.0050 (17)0.0082 (18)
N20.037 (2)0.040 (2)0.0303 (17)0.0046 (17)0.0017 (15)0.0024 (15)
C10.046 (3)0.037 (3)0.037 (2)0.001 (2)0.006 (2)0.0013 (19)
C20.047 (3)0.057 (3)0.049 (3)0.005 (3)0.007 (2)0.007 (2)
C30.046 (3)0.062 (4)0.055 (3)0.014 (3)0.010 (2)0.001 (3)
C40.054 (3)0.055 (3)0.036 (2)0.002 (3)0.008 (2)0.002 (2)
C50.034 (2)0.046 (3)0.0256 (19)0.000 (2)0.0053 (17)0.0039 (18)
C60.028 (2)0.045 (3)0.033 (2)0.001 (2)0.0038 (17)0.0006 (19)
C70.041 (3)0.048 (3)0.056 (3)0.004 (2)0.003 (2)0.007 (2)
C80.056 (3)0.052 (3)0.052 (3)0.006 (3)0.006 (2)0.018 (2)
C90.056 (4)0.048 (3)0.064 (3)0.002 (3)0.000 (3)0.021 (3)
C100.047 (3)0.059 (3)0.062 (3)0.020 (3)0.002 (3)0.001 (3)
C110.044 (3)0.074 (4)0.049 (3)0.013 (3)0.011 (2)0.008 (3)
C120.049 (3)0.072 (4)0.047 (3)0.011 (3)0.009 (2)0.008 (3)
C130.038 (3)0.056 (3)0.032 (2)0.003 (2)0.0029 (18)0.007 (2)
C140.042 (3)0.045 (3)0.0281 (19)0.000 (2)0.0086 (18)0.0039 (19)
C150.029 (2)0.049 (3)0.040 (2)0.001 (2)0.0022 (19)0.012 (2)
O10.033 (7)0.026 (7)0.089 (9)0.006 (6)0.007 (7)0.002 (6)
O20.074 (7)0.074 (7)0.39 (3)0.027 (9)0.080 (13)0.080 (13)
Geometric parameters (Å, º) top
S1—C11.676 (5)C7—H7B0.9700
N1—C101.499 (7)C8—C91.513 (8)
N1—C91.505 (6)C8—H8A0.9700
N1—C141.526 (6)C8—H8B0.9700
N1—H11.07 (6)C9—H9A0.9700
N2—C11.331 (6)C9—H9B0.9700
N2—C151.466 (6)C10—C111.485 (8)
N2—C51.474 (5)C10—H10A0.9700
C1—C21.462 (8)C10—H10B0.9700
C2—C31.299 (7)C11—C121.532 (7)
C2—H2A0.9300C11—H11A0.9700
C3—C41.486 (8)C11—H11B0.9700
C3—H3A0.9300C12—C131.525 (7)
C4—C51.529 (7)C12—H12A0.9700
C4—H4A0.9700C12—H12B0.9700
C4—H4B0.9700C13—C141.520 (6)
C5—C61.539 (6)C13—C151.522 (7)
C5—H5A0.9800C13—H13A0.9800
C6—C71.527 (6)C14—H14A0.9800
C6—C141.531 (6)C15—H15A0.9700
C6—H6A0.9800C15—H15B0.9700
C7—C81.511 (7)O1—O1i1.38 (3)
C7—H7A0.9700
C10—N1—C9110.0 (4)C7—C8—H8B109.7
C10—N1—C14111.5 (4)C9—C8—H8B109.7
C9—N1—C14112.3 (4)H8A—C8—H8B108.2
C10—N1—H1102 (3)N1—C9—C8111.1 (4)
C9—N1—H1114 (3)N1—C9—H9A109.4
C14—N1—H1107 (3)C8—C9—H9A109.4
C1—N2—C15121.2 (4)N1—C9—H9B109.4
C1—N2—C5122.8 (4)C8—C9—H9B109.4
C15—N2—C5111.2 (4)H9A—C9—H9B108.0
N2—C1—C2117.2 (4)C11—C10—N1111.0 (4)
N2—C1—S1123.9 (4)C11—C10—H10A109.4
C2—C1—S1118.9 (4)N1—C10—H10A109.4
C3—C2—C1122.3 (5)C11—C10—H10B109.4
C3—C2—H2A118.8N1—C10—H10B109.4
C1—C2—H2A118.8H10A—C10—H10B108.0
C2—C3—C4121.2 (5)C10—C11—C12111.6 (5)
C2—C3—H3A119.4C10—C11—H11A109.3
C4—C3—H3A119.4C12—C11—H11A109.3
C3—C4—C5112.1 (4)C10—C11—H11B109.3
C3—C4—H4A109.2C12—C11—H11B109.3
C5—C4—H4A109.2H11A—C11—H11B108.0
C3—C4—H4B109.2C13—C12—C11111.8 (4)
C5—C4—H4B109.2C13—C12—H12A109.3
H4A—C4—H4B107.9C11—C12—H12A109.3
N2—C5—C4109.8 (4)C13—C12—H12B109.3
N2—C5—C6107.0 (3)C11—C12—H12B109.3
C4—C5—C6115.3 (4)H12A—C12—H12B107.9
N2—C5—H5A108.2C14—C13—C15110.6 (3)
C4—C5—H5A108.2C14—C13—C12112.1 (4)
C6—C5—H5A108.2C15—C13—C12113.5 (4)
C7—C6—C14110.8 (4)C14—C13—H13A106.7
C7—C6—C5114.4 (4)C15—C13—H13A106.7
C14—C6—C5110.3 (4)C12—C13—H13A106.7
C7—C6—H6A107.0C13—C14—N1110.7 (4)
C14—C6—H6A107.0C13—C14—C6113.3 (4)
C5—C6—H6A107.0N1—C14—C6111.1 (3)
C8—C7—C6112.0 (4)C13—C14—H14A107.1
C8—C7—H7A109.2N1—C14—H14A107.1
C6—C7—H7A109.2C6—C14—H14A107.1
C8—C7—H7B109.2N2—C15—C13107.5 (4)
C6—C7—H7B109.2N2—C15—H15A110.2
H7A—C7—H7B107.9C13—C15—H15A110.2
C7—C8—C9109.8 (4)N2—C15—H15B110.2
C7—C8—H8A109.7C13—C15—H15B110.2
C9—C8—H8A109.7H15A—C15—H15B108.5
Symmetry code: (i) y, x, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···Cl11.10 (9)2.01 (8)3.019 (6)151 (6)
C4—H4A···Cl1i0.972.823.726 (7)155
Symmetry code: (i) y, x, z.

Experimental details

Crystal data
Chemical formulaC15H23N2S+·Cl·0.5H2O
Mr306.87
Crystal system, space groupTetragonal, P41212
Temperature (K)293
a, c (Å)7.793 (5), 52.59 (5)
V3)3194 (4)
Z8
Radiation typeMo Kα
µ (mm1)0.36
Crystal size (mm)0.25 × 0.20 × 0.18
Data collection
DiffractometerBruker SMART CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.915, 0.937
No. of measured, independent and
observed [I > 2σ(I)] reflections
11100, 2816, 2489
Rint0.043
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.071, 0.204, 1.23
No. of reflections2816
No. of parameters190
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.64, 0.25
Absolute structureFlack (1983), 1023 Friedel pairs
Absolute structure parameter0.1 (2)

Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···Cl11.10 (9)2.01 (8)3.019 (6)151 (6)
C4—H4A···Cl1i0.972.823.726 (7)155
Symmetry code: (i) y, x, z.
 

Acknowledgements

The authors are grateful to Weng Linhong and Dr Cheng of the Department of Chemistry of Fudan University for the data acquisition and inter­pretation. This work was supported by grants from the National Natural Science Foundation (No. 20902109) and the Science & Technology Commission of Shanghai Municipality (No. 08JC1405500)

References

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Volume 67| Part 7| July 2011| Pages o1743-o1744
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