(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

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.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.007 Å
• H-atom completeness 96%
• Disorder in solvent or counterion
• R factor = 0.071
• wR factor = 0.204
• Data-to-parameter ratio = 14.8

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT353_ALERT_3_B Long    N-H Bond (0.87A)   N1     -   H1     ...       1.08 Ang.
PLAT430_ALERT_2_B Short Inter D...A Contact  O2     ..  O1      ..       2.54 Ang.
PLAT430_ALERT_2_B Short Inter D...A Contact  O2     ..  O1      ..       2.54 Ang.
PLAT431_ALERT_2_B Short Inter HL..A Contact  Cl1    ..  O1      ..       2.88 Ang.

Alert level C
CHEMW01_ALERT_1_C  The difference between the given and expected weight for
            compound is greater 1 mass unit. Check that all hydrogen
            atoms have been taken into account.
PLAT041_ALERT_1_C Calc. and Reported SumFormula    Strings  Differ          ?
PLAT042_ALERT_1_C Calc. and Reported MoietyFormula Strings  Differ          ?
PLAT045_ALERT_1_C Calculated and Reported Z Differ by ............       0.13 Ratio
PLAT068_ALERT_1_C Reported F000 Differs from Calcd (or Missing)...          ?
PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density ....       2.52
PLAT152_ALERT_1_C The Supplied and Calc. Volume s.u. Differ by ...        -33 Units
PLAT340_ALERT_3_C Low Bond Precision on  C-C Bonds (x 1000) Ang ..          7
PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) .....          1
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.595          3
PLAT918_ALERT_3_C Reflection(s) # with I(obs) much smaller I(calc)          1

Alert level G
FORMU01_ALERT_2_G  There is a discrepancy between the atom counts in the
            _chemical_formula_sum and the formula from the _atom_site* data.
            Atom count from _chemical_formula_sum:C15 H24 Cl1 N2 O0.5 S1
            Atom count from the _atom_site data:  C15 H23 Cl1 N2 O0.5 S1
CELLZ01_ALERT_1_G Difference between formula and atom_site contents detected.
CELLZ01_ALERT_1_G WARNING: H atoms missing from atom site list. Is this intentional?
           From the CIF: _cell_formula_units_Z    8
           From the CIF: _chemical_formula_sum  C15 H24 Cl N2 O0.5 S
           TEST: Compare cell contents of formula and atom_site data

           atom    Z*formula  cif sites diff
           C        120.00    120.00    0.00
           H        192.00    184.00    8.00
           Cl         8.00      8.00    0.00
           N         16.00     16.00    0.00
           O          4.00      4.00    0.00
           S          8.00      8.00    0.00
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           25.01
           From the CIF: _reflns_number_total               2816
           Count of symmetry unique reflns         1793
           Completeness (_total/calc)            157.06%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured      1023
           Fraction of Friedel pairs measured     0.571
           Are heavy atom types Z>Si present        yes
PLAT072_ALERT_2_G SHELXL First  Parameter in WGHT Unusually Large.       0.10
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported   _diffrn_ambient_temperature        293 K
PLAT302_ALERT_4_G Note: Anion/Solvent Disorder ...................         50 Perc.
PLAT791_ALERT_4_G Note: The Model has Chirality at N1     (Verify)          S
PLAT791_ALERT_4_G Note: The Model has Chirality at C5     (Verify)          R
PLAT791_ALERT_4_G Note: The Model has Chirality at C6     (Verify)          R
PLAT791_ALERT_4_G Note: The Model has Chirality at C13    (Verify)          S
PLAT791_ALERT_4_G Note: The Model has Chirality at C14    (Verify)          S
PLAT909_ALERT_3_G Percentage of Observed Data at Theta(Max) still          62 Perc.

   0 ALERT level A = Most likely a serious problem - resolve or explain
   4 ALERT level B = A potentially serious problem, consider carefully
  11 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  14 ALERT level G = General information/check it is not something unexpected

  10 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   6 ALERT type 2 Indicator that the structure model may be wrong or deficient
   6 ALERT type 3 Indicator that the structure quality may be low
   7 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

---

S1. Comment

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

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).

S2. Experimental

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.

S3. Refinement

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 U_iso(H) = 1.2U_eq(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

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

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

Crystal data

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) Å^3	Block, yellow
Z = 8	0.25 × 0.20 × 0.18 mm
F(000) = 1320

Data collection

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

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.071	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.204	w = 1/[σ^2(Fo^2) + (0.104P)^2 + 2.0841P] where P = (Fo^2 + 2Fc^2)/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)

Special details

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 (Ų)

	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)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

Geometric parameters (Å, º)

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—O1^i	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.

Hydrogen-bond geometry (Å, º)

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···Cl1^i	0.97	2.82	3.726 (7)	155

Symmetry code: (i) y, x, −z.