


Supporting information
![]() | Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989015003837/xu5837sup1.cif |
![]() | Structure factor file (CIF format) https://doi.org/10.1107/S2056989015003837/xu5837Isup2.hkl |
![]() | Chemical Markup Language (CML) file https://doi.org/10.1107/S2056989015003837/xu5837Isup3.cml |
CCDC reference: 1051034
Key indicators
- Single-crystal X-ray study
- T = 250 K
- Mean
(C-C) = 0.002 Å
- Disorder in main residue
- R factor = 0.039
- wR factor = 0.116
- Data-to-parameter ratio = 16.2
checkCIF/PLATON results
No syntax errors found
Alert level C PLAT230_ALERT_2_C Hirshfeld Test Diff for S1 -- C10 .. 6.6 su PLAT234_ALERT_4_C Large Hirshfeld Difference C11 -- C12 .. 0.16 Ang. PLAT241_ALERT_2_C High Ueq as Compared to Neighbors for ..... C12 Check PLAT906_ALERT_3_C Large K value in the Analysis of Variance ...... 3.529 Check PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L= 0.600 8 Report PLAT913_ALERT_3_C Missing # of Very Strong Reflections in FCF .... 6 Note
Alert level G PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms .............. 2 Report PLAT154_ALERT_1_G The su's on the Cell Angles are Equal .......... 0.00500 Degree PLAT230_ALERT_2_G Hirshfeld Test Diff for C11' -- C12 .. 6.0 su PLAT300_ALERT_4_G Atom Site Occupancy of *C11 is Constrained at 0.500 Check PLAT300_ALERT_4_G Atom Site Occupancy of *C11' is Constrained at 0.500 Check PLAT301_ALERT_3_G Main Residue Disorder ............ Percentage = 6 Note PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels .......... 2 Note
0 ALERT level A = Most likely a serious problem - resolve or explain 0 ALERT level B = A potentially serious problem, consider carefully 6 ALERT level C = Check. Ensure it is not caused by an omission or oversight 7 ALERT level G = General information/check it is not something unexpected 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 3 ALERT type 2 Indicator that the structure model may be wrong or deficient 4 ALERT type 3 Indicator that the structure quality may be low 4 ALERT type 4 Improvement, methodology, query or suggestion 1 ALERT type 5 Informative message, check
Concerning our interest and on going research on thiosemicarbazone derivatives from natural products, we report herein the synthesis and crystal structure of 1-(2H-1,3-benzodioxol-5-yl)ethanone 4-ethylthiosemicarbazide. The carbonylated precursor is a secondary metabolite from Amazonian Magnoliid trees that belong to the Lauraceae family, the Aniba rosaeodora, (Mors et al., 1957).
The molecular structure of the title compound, which matches the asymmetric unit, is not planar [the mean deviation from planarity for non-H atoms, and excluding the disordered C11/C11' entity, amounts to 0.3794 (17) Å for C5]. The maximum deviation from the mean plane of the non-H atoms of the 1,3-benzodioxole fragment amounts to 0.0515 (14) Å for C7 and for the N1/N2/C10/S1/N3 fragment amounts 0.0480 (10) Å for N2, with the dihedral angle between the planes being 23.49 (10)°.
In the crystal, the molecules are connected by pairs of N2—H1N2···S1 intermolecular hydrogen bonds building dimers. The dimers are stacked along a-axis and although the neighbour columns have the same direction, the dimeric units show different orientations leading to a centrosymmetric structure (Figure 2 and Table 1).
Starting materials are commercially available and were used without further purification. The synthesis of the title compound was adapted from a previously procedure (Freund & Schander, 1902). In a hydrochloric acid catalized reaction, a mixture of 3',4'-(methylenedioxy)acetophenone (10 mmol) and 4-ethyl-3-thiosemicarbazide (10 mmol) in ethanol (80 mL) was refluxed for 4 h. After cooling and filtering, the title compound was obtained. Colourless crystal grown in DMSO by the slow evaporation of the solvent.
The C—H H atoms were positioned with idealized geometry (methyl H atoms were allowed to rotate but not to tip) and refined isotropic with Uiso(H) = 1.2Ueq(C) (1.5 for methyl H atoms) using a riding model with C—H = 0.94 Å for aromatic, C—H = 0.98 Å for methylene and C—H = 0.97 Å for methyl H atoms. The N—H H atoms were located in a difference map and were refined isotropic with varying coordinates in the beginning. Finally, the N—H distances were set to ideal values of 0.87 Å and they were refined isotropic with Uiso(H) = 1.2Ueq(N) using a riding model. The methylene C atom C11 is disordered in two orientations and were refined using a split model with occupancy of 0.5:0.5.
Data collection: X-AREA (Stoe & Cie, 2008); cell refinement: X-AREA (Stoe & Cie, 2008); data reduction: X-RED32 (Stoe & Cie, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2013-2 (Sheldrick, 2015); molecular graphics: DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).
C12H15N3O2S | Z = 2 |
Mr = 265.33 | F(000) = 280 |
Triclinic, P1 | Dx = 1.371 Mg m−3 |
a = 5.7207 (3) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 10.6225 (6) Å | Cell parameters from 9389 reflections |
c = 10.8103 (6) Å | θ = 1.9–27.0° |
α = 83.908 (5)° | µ = 0.25 mm−1 |
β = 79.913 (5)° | T = 250 K |
γ = 87.029 (5)° | Parallelepiped, colourless |
V = 642.74 (6) Å3 | 0.15 × 0.15 × 0.10 mm |
Stoe IPDS-1 diffractometer | 2288 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube, Stoe IPDS-1 | Rint = 0.042 |
Graphite monochromator | θmax = 27.0°, θmin = 1.9° |
ϕ scans | h = −7→7 |
9389 measured reflections | k = −13→13 |
2811 independent reflections | l = −13→13 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.039 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.116 | H-atom parameters constrained |
S = 1.03 | w = 1/[σ2(Fo2) + (0.0649P)2 + 0.1118P] where P = (Fo2 + 2Fc2)/3 |
2811 reflections | (Δ/σ)max < 0.001 |
173 parameters | Δρmax = 0.28 e Å−3 |
0 restraints | Δρmin = −0.23 e Å−3 |
C12H15N3O2S | γ = 87.029 (5)° |
Mr = 265.33 | V = 642.74 (6) Å3 |
Triclinic, P1 | Z = 2 |
a = 5.7207 (3) Å | Mo Kα radiation |
b = 10.6225 (6) Å | µ = 0.25 mm−1 |
c = 10.8103 (6) Å | T = 250 K |
α = 83.908 (5)° | 0.15 × 0.15 × 0.10 mm |
β = 79.913 (5)° |
Stoe IPDS-1 diffractometer | 2288 reflections with I > 2σ(I) |
9389 measured reflections | Rint = 0.042 |
2811 independent reflections |
R[F2 > 2σ(F2)] = 0.039 | 0 restraints |
wR(F2) = 0.116 | H-atom parameters constrained |
S = 1.03 | Δρmax = 0.28 e Å−3 |
2811 reflections | Δρmin = −0.23 e Å−3 |
173 parameters |
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) | |
C1 | 0.7435 (3) | 0.18956 (14) | 0.16339 (15) | 0.0407 (3) | |
C2 | 0.8619 (3) | 0.24715 (14) | 0.24537 (15) | 0.0428 (3) | |
H2 | 0.8352 | 0.3334 | 0.2575 | 0.051* | |
C3 | 1.0167 (3) | 0.17309 (16) | 0.30646 (16) | 0.0457 (4) | |
C4 | 1.0618 (3) | 0.04644 (16) | 0.28893 (17) | 0.0516 (4) | |
C5 | 0.9543 (4) | −0.01187 (16) | 0.20857 (19) | 0.0581 (5) | |
H5 | 0.9863 | −0.0977 | 0.1962 | 0.070* | |
C6 | 0.7937 (3) | 0.06224 (16) | 0.14522 (17) | 0.0515 (4) | |
H6 | 0.7174 | 0.0250 | 0.0887 | 0.062* | |
O1 | 1.1441 (2) | 0.20752 (13) | 0.39317 (13) | 0.0621 (4) | |
C7 | 1.2882 (3) | 0.0980 (2) | 0.4229 (2) | 0.0615 (5) | |
H7A | 1.4562 | 0.1148 | 0.3917 | 0.074* | |
H7B | 1.2668 | 0.0771 | 0.5146 | 0.074* | |
O2 | 1.2191 (3) | −0.00457 (13) | 0.36476 (15) | 0.0698 (4) | |
C8 | 0.5558 (3) | 0.26302 (14) | 0.10543 (15) | 0.0407 (3) | |
C9 | 0.4637 (3) | 0.21798 (17) | −0.00254 (18) | 0.0541 (4) | |
H9A | 0.3116 | 0.1794 | 0.0280 | 0.081* | |
H9B | 0.5755 | 0.1560 | −0.0415 | 0.081* | |
H9C | 0.4440 | 0.2892 | −0.0643 | 0.081* | |
N1 | 0.4771 (2) | 0.36261 (12) | 0.15902 (13) | 0.0420 (3) | |
N2 | 0.2949 (2) | 0.43540 (12) | 0.11811 (13) | 0.0432 (3) | |
H1N2 | 0.2234 | 0.4229 | 0.0560 | 0.052* | |
C10 | 0.2019 (3) | 0.53176 (15) | 0.18658 (16) | 0.0461 (4) | |
S1 | −0.03625 (8) | 0.61725 (4) | 0.15015 (5) | 0.05451 (17) | |
N3 | 0.3122 (3) | 0.55269 (18) | 0.27906 (18) | 0.0732 (5) | |
H1N3 | 0.4362 | 0.5027 | 0.2843 | 0.088* | |
C11 | 0.2171 (16) | 0.6290 (8) | 0.3858 (8) | 0.071 (2) | 0.5 |
H11A | 0.1138 | 0.6987 | 0.3576 | 0.085* | 0.5 |
H11B | 0.1232 | 0.5758 | 0.4544 | 0.085* | 0.5 |
C11' | 0.2731 (18) | 0.6716 (7) | 0.3447 (8) | 0.0675 (19) | 0.5 |
H11C | 0.2989 | 0.7447 | 0.2812 | 0.081* | 0.5 |
H11D | 0.1073 | 0.6766 | 0.3872 | 0.081* | 0.5 |
C12 | 0.4155 (6) | 0.6790 (3) | 0.4304 (3) | 0.1149 (12) | |
H12A | 0.5616 | 0.6353 | 0.3959 | 0.172* | 0.5 |
H12B | 0.3914 | 0.6663 | 0.5219 | 0.172* | 0.5 |
H12C | 0.4259 | 0.7689 | 0.4032 | 0.172* | 0.5 |
H12D | 0.4978 | 0.5980 | 0.4444 | 0.172* | 0.5 |
H12E | 0.3205 | 0.7007 | 0.5092 | 0.172* | 0.5 |
H12F | 0.5307 | 0.7438 | 0.3993 | 0.172* | 0.5 |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0423 (7) | 0.0354 (7) | 0.0438 (8) | 0.0004 (6) | −0.0029 (6) | −0.0089 (6) |
C2 | 0.0447 (8) | 0.0345 (7) | 0.0491 (8) | −0.0006 (6) | −0.0058 (6) | −0.0077 (6) |
C3 | 0.0450 (8) | 0.0449 (8) | 0.0467 (8) | −0.0031 (6) | −0.0063 (6) | −0.0043 (6) |
C4 | 0.0492 (9) | 0.0433 (9) | 0.0588 (10) | 0.0060 (7) | −0.0064 (7) | 0.0028 (7) |
C5 | 0.0666 (11) | 0.0355 (8) | 0.0716 (12) | 0.0095 (7) | −0.0103 (9) | −0.0106 (8) |
C6 | 0.0577 (10) | 0.0395 (8) | 0.0594 (10) | 0.0034 (7) | −0.0105 (8) | −0.0161 (7) |
O1 | 0.0644 (8) | 0.0599 (8) | 0.0684 (8) | 0.0018 (6) | −0.0293 (7) | −0.0074 (6) |
C7 | 0.0524 (10) | 0.0694 (12) | 0.0607 (11) | 0.0010 (9) | −0.0142 (8) | 0.0083 (9) |
O2 | 0.0699 (9) | 0.0565 (8) | 0.0853 (10) | 0.0114 (6) | −0.0292 (7) | 0.0024 (7) |
C8 | 0.0417 (7) | 0.0357 (7) | 0.0449 (8) | −0.0012 (6) | −0.0050 (6) | −0.0095 (6) |
C9 | 0.0538 (9) | 0.0522 (10) | 0.0617 (10) | 0.0070 (7) | −0.0156 (8) | −0.0245 (8) |
N1 | 0.0417 (6) | 0.0370 (6) | 0.0485 (7) | 0.0033 (5) | −0.0086 (5) | −0.0108 (5) |
N2 | 0.0430 (7) | 0.0398 (7) | 0.0501 (7) | 0.0048 (5) | −0.0128 (5) | −0.0150 (5) |
C10 | 0.0464 (8) | 0.0403 (8) | 0.0539 (9) | 0.0033 (6) | −0.0106 (7) | −0.0150 (7) |
S1 | 0.0481 (2) | 0.0521 (3) | 0.0700 (3) | 0.01332 (18) | −0.02210 (19) | −0.0241 (2) |
N3 | 0.0788 (11) | 0.0749 (11) | 0.0815 (11) | 0.0404 (9) | −0.0444 (9) | −0.0480 (9) |
C11 | 0.070 (4) | 0.073 (5) | 0.081 (6) | 0.027 (4) | −0.029 (4) | −0.046 (4) |
C11' | 0.087 (5) | 0.057 (4) | 0.068 (5) | 0.027 (3) | −0.032 (4) | −0.033 (3) |
C12 | 0.109 (2) | 0.133 (3) | 0.122 (2) | 0.029 (2) | −0.0365 (19) | −0.089 (2) |
C1—C6 | 1.395 (2) | N1—N2 | 1.3730 (18) |
C1—C2 | 1.410 (2) | N2—C10 | 1.358 (2) |
C1—C8 | 1.483 (2) | N2—H1N2 | 0.8699 |
C2—C3 | 1.364 (2) | C10—N3 | 1.315 (2) |
C2—H2 | 0.9400 | C10—S1 | 1.6792 (17) |
C3—O1 | 1.372 (2) | N3—C11 | 1.489 (9) |
C3—C4 | 1.383 (2) | N3—C11' | 1.501 (9) |
C4—C5 | 1.363 (3) | N3—H1N3 | 0.8700 |
C4—O2 | 1.375 (2) | C11—C12 | 1.453 (10) |
C5—C6 | 1.401 (3) | C11—H11A | 0.9800 |
C5—H5 | 0.9400 | C11—H11B | 0.9800 |
C6—H6 | 0.9400 | C11'—C12 | 1.347 (10) |
O1—C7 | 1.432 (2) | C11'—H11C | 0.9800 |
C7—O2 | 1.420 (3) | C11'—H11D | 0.9800 |
C7—H7A | 0.9800 | C12—H12A | 0.9700 |
C7—H7B | 0.9800 | C12—H12B | 0.9700 |
C8—N1 | 1.2832 (19) | C12—H12C | 0.9700 |
C8—C9 | 1.493 (2) | C12—H12D | 0.9700 |
C9—H9A | 0.9700 | C12—H12E | 0.9700 |
C9—H9B | 0.9700 | C12—H12F | 0.9700 |
C9—H9C | 0.9700 | ||
C6—C1—C2 | 119.34 (15) | C10—N2—N1 | 117.50 (13) |
C6—C1—C8 | 121.30 (15) | C10—N2—H1N2 | 115.4 |
C2—C1—C8 | 119.22 (13) | N1—N2—H1N2 | 126.9 |
C3—C2—C1 | 117.54 (14) | N3—C10—N2 | 115.66 (15) |
C3—C2—H2 | 121.2 | N3—C10—S1 | 123.92 (12) |
C1—C2—H2 | 121.2 | N2—C10—S1 | 120.41 (13) |
C2—C3—O1 | 127.54 (15) | C10—N3—C11 | 126.2 (4) |
C2—C3—C4 | 122.40 (16) | C10—N3—C11' | 123.1 (4) |
O1—C3—C4 | 110.05 (15) | C10—N3—H1N3 | 113.3 |
C5—C4—O2 | 128.69 (16) | C11—N3—H1N3 | 119.0 |
C5—C4—C3 | 121.73 (16) | C11'—N3—H1N3 | 121.5 |
O2—C4—C3 | 109.57 (17) | C12—C11—N3 | 108.7 (6) |
C4—C5—C6 | 116.86 (15) | C12—C11—H11A | 110.0 |
C4—C5—H5 | 121.6 | N3—C11—H11A | 110.0 |
C6—C5—H5 | 121.6 | C12—C11—H11B | 110.0 |
C1—C6—C5 | 122.10 (17) | N3—C11—H11B | 110.0 |
C1—C6—H6 | 118.9 | H11A—C11—H11B | 108.3 |
C5—C6—H6 | 118.9 | C12—C11'—N3 | 114.0 (6) |
C3—O1—C7 | 105.38 (14) | C12—C11'—H11C | 108.7 |
O2—C7—O1 | 108.49 (15) | N3—C11'—H11C | 108.7 |
O2—C7—H7A | 110.0 | C12—C11'—H11D | 108.7 |
O1—C7—H7A | 110.0 | N3—C11'—H11D | 108.7 |
O2—C7—H7B | 110.0 | H11C—C11'—H11D | 107.6 |
O1—C7—H7B | 110.0 | C11—C12—H12A | 109.5 |
H7A—C7—H7B | 108.4 | C11—C12—H12B | 109.5 |
C4—O2—C7 | 105.90 (14) | H12A—C12—H12B | 109.5 |
N1—C8—C1 | 114.42 (14) | C11—C12—H12C | 109.5 |
N1—C8—C9 | 124.48 (15) | H12A—C12—H12C | 109.5 |
C1—C8—C9 | 121.04 (13) | H12B—C12—H12C | 109.5 |
C8—C9—H9A | 109.5 | C11'—C12—H12D | 109.5 |
C8—C9—H9B | 109.5 | C11'—C12—H12E | 109.5 |
H9A—C9—H9B | 109.5 | H12D—C12—H12E | 109.5 |
C8—C9—H9C | 109.5 | C11'—C12—H12F | 109.5 |
H9A—C9—H9C | 109.5 | H12D—C12—H12F | 109.5 |
H9B—C9—H9C | 109.5 | H12E—C12—H12F | 109.5 |
C8—N1—N2 | 120.07 (14) | ||
C6—C1—C2—C3 | −1.9 (2) | C6—C1—C8—N1 | 159.25 (15) |
C8—C1—C2—C3 | 173.75 (14) | C2—C1—C8—N1 | −16.3 (2) |
C1—C2—C3—O1 | −177.54 (15) | C6—C1—C8—C9 | −18.1 (2) |
C1—C2—C3—C4 | 1.0 (2) | C2—C1—C8—C9 | 166.30 (15) |
C2—C3—C4—C5 | 0.3 (3) | C1—C8—N1—N2 | −176.84 (12) |
O1—C3—C4—C5 | 179.06 (16) | C9—C8—N1—N2 | 0.4 (2) |
C2—C3—C4—O2 | −178.38 (15) | C8—N1—N2—C10 | 173.15 (14) |
O1—C3—C4—O2 | 0.34 (19) | N1—N2—C10—N3 | 6.2 (2) |
O2—C4—C5—C6 | 177.85 (17) | N1—N2—C10—S1 | −174.75 (11) |
C3—C4—C5—C6 | −0.6 (3) | N2—C10—N3—C11 | −164.2 (4) |
C2—C1—C6—C5 | 1.7 (3) | S1—C10—N3—C11 | 16.8 (5) |
C8—C1—C6—C5 | −173.86 (16) | N2—C10—N3—C11' | 165.3 (4) |
C4—C5—C6—C1 | −0.4 (3) | S1—C10—N3—C11' | −13.8 (5) |
C2—C3—O1—C7 | −176.90 (16) | C10—N3—C11—C12 | −153.3 (4) |
C4—C3—O1—C7 | 4.46 (18) | C11'—N3—C11—C12 | −61.3 (15) |
C3—O1—C7—O2 | −7.55 (19) | C10—N3—C11'—C12 | −175.3 (4) |
C5—C4—O2—C7 | 176.35 (19) | C11—N3—C11'—C12 | 79.0 (15) |
C3—C4—O2—C7 | −5.04 (19) | N3—C11'—C12—C11 | −73.0 (13) |
O1—C7—O2—C4 | 7.8 (2) | N3—C11—C12—C11' | 68.3 (14) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H1N2···S1i | 0.87 | 2.72 | 3.5842 (14) | 175 |
Symmetry code: (i) −x, −y+1, −z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H1N2···S1i | 0.87 | 2.72 | 3.5842 (14) | 175.2 |
Symmetry code: (i) −x, −y+1, −z. |