organic compounds
(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
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 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); Jiang et al. (2007); Liu et al. (2007). For related structures, see: Ding et al. (2005); Khan et al. (1992). For the synthesis, see: Kaleta et al. (2006).
Experimental
Crystal data
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Data collection: SMART (Bruker, 1997); cell SAINT (Bruker, 1997); data reduction: SAINT; 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.
Supporting information
10.1107/S160053681100972X/lh5190sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S160053681100972X/lh5190Isup2.hkl
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.
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
although they are included in the formula.Data collection: SMART (Bruker, 1997); cell
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).Fig. 1. The molecular structure of the title compound with the atom-labeling scheme. Displacement ellipsoids are drawn at the 30% probability level. |
C15H23N2S+·Cl−·0.5H2O | Dx = 1.281 Mg m−3 |
Mr = 306.87 | Mo Kα radiation, λ = 0.71073 Å |
Tetragonal, P41212 | Cell parameters from 927 reflections |
Hall symbol: P 4abw 2nw | θ = 2.7–24.0° |
a = 7.793 (5) Å | µ = 0.36 mm−1 |
c = 52.59 (5) Å | T = 293 K |
V = 3194 (4) Å3 | Block, yellow |
Z = 8 | 0.25 × 0.20 × 0.18 mm |
F(000) = 1320 |
Bruker SMART CCD diffractometer | 2816 independent reflections |
Radiation source: fine-focus sealed tube | 2489 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.043 |
ϕ and ω scans | θmax = 25.0°, θmin = 2.6° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −9→7 |
Tmin = 0.915, Tmax = 0.937 | k = −7→9 |
11100 measured reflections | l = −54→62 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.071 | H 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 reflections | Δρmax = 0.64 e Å−3 |
190 parameters | Δρmin = −0.25 e Å−3 |
0 restraints | Absolute structure: Flack (1983), 1023 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.1 (2) |
C15H23N2S+·Cl−·0.5H2O | Z = 8 |
Mr = 306.87 | Mo Kα radiation |
Tetragonal, P41212 | µ = 0.36 mm−1 |
a = 7.793 (5) Å | T = 293 K |
c = 52.59 (5) Å | 0.25 × 0.20 × 0.18 mm |
V = 3194 (4) Å3 |
Bruker SMART CCD diffractometer | 2816 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 2489 reflections with I > 2σ(I) |
Tmin = 0.915, Tmax = 0.937 | Rint = 0.043 |
11100 measured reflections |
R[F2 > 2σ(F2)] = 0.071 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.204 | Δρmax = 0.64 e Å−3 |
S = 1.23 | Δρmin = −0.25 e Å−3 |
2816 reflections | Absolute structure: Flack (1983), 1023 Friedel pairs |
190 parameters | Absolute structure parameter: 0.1 (2) |
0 restraints |
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. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
S1 | 0.6279 (2) | 0.2217 (2) | 0.11342 (2) | 0.0559 (4) | |
Cl1 | 0.2534 (2) | 0.6515 (3) | 0.01987 (3) | 0.0785 (6) | |
N1 | 0.4499 (5) | 0.8604 (6) | 0.05841 (7) | 0.0415 (9) | |
N2 | 0.6084 (5) | 0.4228 (5) | 0.07265 (6) | 0.0357 (9) | |
C1 | 0.7029 (6) | 0.3215 (6) | 0.08746 (8) | 0.0400 (11) | |
C2 | 0.8817 (7) | 0.2948 (7) | 0.08006 (9) | 0.0511 (12) | |
H2A | 0.9548 | 0.2386 | 0.0913 | 0.061* | |
C3 | 0.9422 (7) | 0.3467 (8) | 0.05836 (10) | 0.0543 (13) | |
H3A | 1.0566 | 0.3260 | 0.0544 | 0.065* | |
C4 | 0.8319 (7) | 0.4387 (7) | 0.03976 (9) | 0.0483 (13) | |
H4A | 0.7864 | 0.3570 | 0.0276 | 0.058* | |
H4B | 0.9011 | 0.5211 | 0.0305 | 0.058* | |
C5 | 0.6831 (6) | 0.5324 (6) | 0.05266 (7) | 0.0354 (10) | |
H5A | 0.5944 | 0.5540 | 0.0398 | 0.043* | |
C6 | 0.7298 (6) | 0.7046 (6) | 0.06520 (7) | 0.0352 (10) | |
H6A | 0.8128 | 0.6796 | 0.0787 | 0.042* | |
C7 | 0.8144 (7) | 0.8338 (7) | 0.04731 (10) | 0.0482 (12) | |
H7A | 0.8599 | 0.9285 | 0.0572 | 0.058* | |
H7B | 0.9096 | 0.7789 | 0.0387 | 0.058* | |
C8 | 0.6899 (7) | 0.9026 (7) | 0.02780 (10) | 0.0537 (13) | |
H8A | 0.6499 | 0.8097 | 0.0170 | 0.064* | |
H8B | 0.7472 | 0.9864 | 0.0171 | 0.064* | |
C9 | 0.5388 (7) | 0.9856 (7) | 0.04105 (10) | 0.0557 (14) | |
H9A | 0.5785 | 1.0832 | 0.0509 | 0.067* | |
H9B | 0.4580 | 1.0271 | 0.0284 | 0.067* | |
C10 | 0.2988 (7) | 0.9449 (8) | 0.07086 (11) | 0.0562 (15) | |
H10A | 0.3382 | 1.0390 | 0.0814 | 0.067* | |
H10B | 0.2236 | 0.9916 | 0.0579 | 0.067* | |
C11 | 0.2019 (7) | 0.8205 (8) | 0.08673 (10) | 0.0558 (14) | |
H11A | 0.1539 | 0.7319 | 0.0759 | 0.067* | |
H11B | 0.1076 | 0.8793 | 0.0950 | 0.067* | |
C12 | 0.3168 (7) | 0.7373 (8) | 0.10691 (10) | 0.0562 (14) | |
H12A | 0.3504 | 0.8233 | 0.1193 | 0.067* | |
H12B | 0.2523 | 0.6490 | 0.1157 | 0.067* | |
C13 | 0.4772 (6) | 0.6578 (7) | 0.09521 (8) | 0.0422 (11) | |
H13A | 0.5549 | 0.6309 | 0.1093 | 0.051* | |
C14 | 0.5717 (6) | 0.7830 (6) | 0.07802 (8) | 0.0382 (11) | |
H14A | 0.6122 | 0.8773 | 0.0888 | 0.046* | |
C15 | 0.4427 (6) | 0.4900 (7) | 0.08132 (8) | 0.0394 (11) | |
H15A | 0.3878 | 0.4086 | 0.0926 | 0.047* | |
H15B | 0.3676 | 0.5098 | 0.0669 | 0.047* | |
O1 | 0.2960 (17) | 0.2869 (17) | 0.0131 (3) | 0.049 (3) | 0.25 |
O2 | 0.0693 (14) | 0.0693 (14) | 0.0000 | 0.179 (12) | 0.50 |
H1 | 0.390 (8) | 0.755 (8) | 0.0486 (10) | 0.066 (17)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0630 (9) | 0.0610 (9) | 0.0436 (6) | 0.0009 (7) | −0.0016 (6) | 0.0180 (6) |
Cl1 | 0.0562 (9) | 0.1312 (17) | 0.0481 (7) | −0.0121 (10) | −0.0120 (7) | −0.0032 (8) |
N1 | 0.044 (2) | 0.041 (2) | 0.0398 (19) | 0.0012 (19) | −0.0050 (17) | 0.0082 (18) |
N2 | 0.037 (2) | 0.040 (2) | 0.0303 (17) | −0.0046 (17) | −0.0017 (15) | 0.0024 (15) |
C1 | 0.046 (3) | 0.037 (3) | 0.037 (2) | 0.001 (2) | −0.006 (2) | −0.0013 (19) |
C2 | 0.047 (3) | 0.057 (3) | 0.049 (3) | 0.005 (3) | −0.007 (2) | 0.007 (2) |
C3 | 0.046 (3) | 0.062 (4) | 0.055 (3) | 0.014 (3) | 0.010 (2) | −0.001 (3) |
C4 | 0.054 (3) | 0.055 (3) | 0.036 (2) | −0.002 (3) | 0.008 (2) | −0.002 (2) |
C5 | 0.034 (2) | 0.046 (3) | 0.0256 (19) | 0.000 (2) | −0.0053 (17) | 0.0039 (18) |
C6 | 0.028 (2) | 0.045 (3) | 0.033 (2) | 0.001 (2) | −0.0038 (17) | −0.0006 (19) |
C7 | 0.041 (3) | 0.048 (3) | 0.056 (3) | −0.004 (2) | 0.003 (2) | 0.007 (2) |
C8 | 0.056 (3) | 0.052 (3) | 0.052 (3) | −0.006 (3) | 0.006 (2) | 0.018 (2) |
C9 | 0.056 (4) | 0.048 (3) | 0.064 (3) | 0.002 (3) | 0.000 (3) | 0.021 (3) |
C10 | 0.047 (3) | 0.059 (3) | 0.062 (3) | 0.020 (3) | 0.002 (3) | 0.001 (3) |
C11 | 0.044 (3) | 0.074 (4) | 0.049 (3) | 0.013 (3) | 0.011 (2) | 0.008 (3) |
C12 | 0.049 (3) | 0.072 (4) | 0.047 (3) | 0.011 (3) | 0.009 (2) | 0.008 (3) |
C13 | 0.038 (3) | 0.056 (3) | 0.032 (2) | 0.003 (2) | −0.0029 (18) | 0.007 (2) |
C14 | 0.042 (3) | 0.045 (3) | 0.0281 (19) | 0.000 (2) | −0.0086 (18) | −0.0039 (19) |
C15 | 0.029 (2) | 0.049 (3) | 0.040 (2) | −0.001 (2) | −0.0022 (19) | 0.012 (2) |
O1 | 0.033 (7) | 0.026 (7) | 0.089 (9) | −0.006 (6) | 0.007 (7) | 0.002 (6) |
O2 | 0.074 (7) | 0.074 (7) | 0.39 (3) | −0.027 (9) | 0.080 (13) | −0.080 (13) |
S1—C1 | 1.676 (5) | C7—H7B | 0.9700 |
N1—C10 | 1.499 (7) | C8—C9 | 1.513 (8) |
N1—C9 | 1.505 (6) | C8—H8A | 0.9700 |
N1—C14 | 1.526 (6) | C8—H8B | 0.9700 |
N1—H1 | 1.07 (6) | C9—H9A | 0.9700 |
N2—C1 | 1.331 (6) | C9—H9B | 0.9700 |
N2—C15 | 1.466 (6) | C10—C11 | 1.485 (8) |
N2—C5 | 1.474 (5) | C10—H10A | 0.9700 |
C1—C2 | 1.462 (8) | C10—H10B | 0.9700 |
C2—C3 | 1.299 (7) | C11—C12 | 1.532 (7) |
C2—H2A | 0.9300 | C11—H11A | 0.9700 |
C3—C4 | 1.486 (8) | C11—H11B | 0.9700 |
C3—H3A | 0.9300 | C12—C13 | 1.525 (7) |
C4—C5 | 1.529 (7) | C12—H12A | 0.9700 |
C4—H4A | 0.9700 | C12—H12B | 0.9700 |
C4—H4B | 0.9700 | C13—C14 | 1.520 (6) |
C5—C6 | 1.539 (6) | C13—C15 | 1.522 (7) |
C5—H5A | 0.9800 | C13—H13A | 0.9800 |
C6—C7 | 1.527 (6) | C14—H14A | 0.9800 |
C6—C14 | 1.531 (6) | C15—H15A | 0.9700 |
C6—H6A | 0.9800 | C15—H15B | 0.9700 |
C7—C8 | 1.511 (7) | O1—O1i | 1.38 (3) |
C7—H7A | 0.9700 | ||
C10—N1—C9 | 110.0 (4) | C7—C8—H8B | 109.7 |
C10—N1—C14 | 111.5 (4) | C9—C8—H8B | 109.7 |
C9—N1—C14 | 112.3 (4) | H8A—C8—H8B | 108.2 |
C10—N1—H1 | 102 (3) | N1—C9—C8 | 111.1 (4) |
C9—N1—H1 | 114 (3) | N1—C9—H9A | 109.4 |
C14—N1—H1 | 107 (3) | C8—C9—H9A | 109.4 |
C1—N2—C15 | 121.2 (4) | N1—C9—H9B | 109.4 |
C1—N2—C5 | 122.8 (4) | C8—C9—H9B | 109.4 |
C15—N2—C5 | 111.2 (4) | H9A—C9—H9B | 108.0 |
N2—C1—C2 | 117.2 (4) | C11—C10—N1 | 111.0 (4) |
N2—C1—S1 | 123.9 (4) | C11—C10—H10A | 109.4 |
C2—C1—S1 | 118.9 (4) | N1—C10—H10A | 109.4 |
C3—C2—C1 | 122.3 (5) | C11—C10—H10B | 109.4 |
C3—C2—H2A | 118.8 | N1—C10—H10B | 109.4 |
C1—C2—H2A | 118.8 | H10A—C10—H10B | 108.0 |
C2—C3—C4 | 121.2 (5) | C10—C11—C12 | 111.6 (5) |
C2—C3—H3A | 119.4 | C10—C11—H11A | 109.3 |
C4—C3—H3A | 119.4 | C12—C11—H11A | 109.3 |
C3—C4—C5 | 112.1 (4) | C10—C11—H11B | 109.3 |
C3—C4—H4A | 109.2 | C12—C11—H11B | 109.3 |
C5—C4—H4A | 109.2 | H11A—C11—H11B | 108.0 |
C3—C4—H4B | 109.2 | C13—C12—C11 | 111.8 (4) |
C5—C4—H4B | 109.2 | C13—C12—H12A | 109.3 |
H4A—C4—H4B | 107.9 | C11—C12—H12A | 109.3 |
N2—C5—C4 | 109.8 (4) | C13—C12—H12B | 109.3 |
N2—C5—C6 | 107.0 (3) | C11—C12—H12B | 109.3 |
C4—C5—C6 | 115.3 (4) | H12A—C12—H12B | 107.9 |
N2—C5—H5A | 108.2 | C14—C13—C15 | 110.6 (3) |
C4—C5—H5A | 108.2 | C14—C13—C12 | 112.1 (4) |
C6—C5—H5A | 108.2 | C15—C13—C12 | 113.5 (4) |
C7—C6—C14 | 110.8 (4) | C14—C13—H13A | 106.7 |
C7—C6—C5 | 114.4 (4) | C15—C13—H13A | 106.7 |
C14—C6—C5 | 110.3 (4) | C12—C13—H13A | 106.7 |
C7—C6—H6A | 107.0 | C13—C14—N1 | 110.7 (4) |
C14—C6—H6A | 107.0 | C13—C14—C6 | 113.3 (4) |
C5—C6—H6A | 107.0 | N1—C14—C6 | 111.1 (3) |
C8—C7—C6 | 112.0 (4) | C13—C14—H14A | 107.1 |
C8—C7—H7A | 109.2 | N1—C14—H14A | 107.1 |
C6—C7—H7A | 109.2 | C6—C14—H14A | 107.1 |
C8—C7—H7B | 109.2 | N2—C15—C13 | 107.5 (4) |
C6—C7—H7B | 109.2 | N2—C15—H15A | 110.2 |
H7A—C7—H7B | 107.9 | C13—C15—H15A | 110.2 |
C7—C8—C9 | 109.8 (4) | N2—C15—H15B | 110.2 |
C7—C8—H8A | 109.7 | C13—C15—H15B | 110.2 |
C9—C8—H8A | 109.7 | H15A—C15—H15B | 108.5 |
Symmetry code: (i) y, x, −z. |
D—H···A | D—H | H···A | D···A | 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. |
Experimental details
Crystal data | |
Chemical formula | C15H23N2S+·Cl−·0.5H2O |
Mr | 306.87 |
Crystal system, space group | Tetragonal, P41212 |
Temperature (K) | 293 |
a, c (Å) | 7.793 (5), 52.59 (5) |
V (Å3) | 3194 (4) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.36 |
Crystal size (mm) | 0.25 × 0.20 × 0.18 |
Data collection | |
Diffractometer | Bruker SMART CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1996) |
Tmin, Tmax | 0.915, 0.937 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 11100, 2816, 2489 |
Rint | 0.043 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.071, 0.204, 1.23 |
No. of reflections | 2816 |
No. of parameters | 190 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.64, −0.25 |
Absolute structure | Flack (1983), 1023 Friedel pairs |
Absolute structure parameter | 0.1 (2) |
Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | 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. |
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)
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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.