Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807036690/hk2302sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807036690/hk2302Isup2.hkl |
CCDC reference: 660180
Key indicators
- Single-crystal X-ray study
- T = 294 K
- Mean (C-C) = 0.003 Å
- R factor = 0.042
- wR factor = 0.121
- Data-to-parameter ratio = 15.2
checkCIF/PLATON results
No syntax errors found
Alert level C ABSTM02_ALERT_3_C The ratio of expected to reported Tmax/Tmin(RR') is < 0.90 Tmin and Tmax reported: 0.737 0.950 Tmin(prime) and Tmax expected: 0.945 0.955 RR(prime) = 0.784 Please check that your absorption correction is appropriate. PLAT061_ALERT_3_C Tmax/Tmin Range Test RR' too Large ............. 0.78 PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for C10 PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C9
Alert level G PLAT793_ALERT_1_G Check the Absolute Configuration of C8 = ... S
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 4 ALERT level C = Check and explain 1 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 2 ALERT type 2 Indicator that the structure model may be wrong or deficient 2 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
For general background, see: Langcake et al. (1983); Adams & Yang (1979); Nadler et al. (1988); Kamala & Rao (1989); Elbert et al. (2000). For bond-length data, see: Allen et al. (1987).
To a solution of NaSCN (0.49 g, 6 mmol) in anhydrous acetonitrile (10 ml) was added dropwise a solution of 2,2-dimethylcycloprpopanecarbonyl chloride (0.60 g, 4.5 mmol) in anhyrous acetonitrile (3 ml) at room temperature. The reaction mixture was kept at room temperature for half an hour and then at 333 K for 3 h. The solution was cooled, filtered and concentrated to about 4 ml. The residue was added dropwise to a solution of 2-aminopyridine (0.42 g, 4.5 mmol) in anhydrous acetonitrile (8 ml) at room temperature. The rection mixture refluxed for 5 h, and then was concentrated. The residue was separated by silica gel chromatography to afford the title compound, (I). Yellow single crystals were grown from a solution of AcOEt-cyclohexane (1:4).
H atoms were positioned geometrically with N—H = 0.86 Å (for NH), C—H = 0.93, 0.98, 0.97 and 0.96 Å for aromatic, methine, methylene and methyl H atoms, respectively, and constrained to ride on their parent atoms, with Uiso(H) = xUeq(C,N), where x = 1.5 for methyl H, and x = 1.2 for all other H atoms.
Cyclopropane derivatives have several biological activities. 2,2-Dichloro-3,3 -dimethylcyclopropanecarboxylic acid is an effective inducer against the rice blast fungus (Langcake et al., 1983). 1-Aminocyclopropane-1-carboxylic acid (ACC) is an intermediate in the biosynthesis of the ripening hormone ethylene (Adams & Yang, 1979), a component of bacterial phytotoxines, and azetidine-2 -carboxylic acid (Nadler et al., 1988). Thus, it is very important to synthesize other new compounds containing cyclopropane, and study their biological activities. Acyl thiourea derivatives have many biological activities, for example, they have been used as bactericides, fungicides and insecticides in many plants (Kamala & Rao, 1989). A pyridine ring is often used as an active component in pesticide discovery (Elbert et al., 2000). The title compound, (I), contains all these three active parts and may show some insecticidal activity. It was characterized by 1H NMR and elemental analysis, and we report herein its crystal structure.
In the molecule of the title compound, (I), (Fig. 1) the bond lengths and angles are within normal ranges (Allen et al., 1987). The intramolecular N—H···O hydrogen bond (Table 1) causes to the formation of a six-membered planar ring A (H2A/N2/C6/N3/C7/O1). Rings B (C8—C10) and C (N1/C1—C5) are, of course, planar and the dihedral angles between them are A/B = 79.14 (3)°, A/C = 14.60 (2)° and B/C = 83.45 (3)°.
In the crystal structure, intermolecular N—H····N hydrogen bonds (Table 1) link the molecules (Fig. 2). The intra- and intermolecular hydrogen bonds seem to be effective in the stabilization of the crystal structure.
For general background, see: Langcake et al. (1983); Adams & Yang (1979); Nadler et al. (1988); Kamala & Rao (1989); Elbert et al. (2000). For bond-length data, see: Allen et al. (1987).
Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 1997); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 1999); software used to prepare material for publication: SHELXTL.
C12H15N3OS | Dx = 1.236 Mg m−3 |
Mr = 249.33 | Melting point: 365 K |
Orthorhombic, Pbca | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ac 2ab | Cell parameters from 3793 reflections |
a = 13.785 (5) Å | θ = 2.2–23.3° |
b = 10.664 (4) Å | µ = 0.23 mm−1 |
c = 18.233 (6) Å | T = 294 K |
V = 2680.2 (16) Å3 | Block, colorless |
Z = 8 | 0.24 × 0.22 × 0.20 mm |
F(000) = 1056 |
Bruker SMART CCD area-detector diffractometer | 2371 independent reflections |
Radiation source: fine-focus sealed tube | 1825 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.024 |
φ and ω scans | θmax = 25.0°, θmin = 2.2° |
Absorption correction: multi-scan (SADABS; Bruker, 1997) | h = −16→15 |
Tmin = 0.737, Tmax = 0.950 | k = −12→10 |
13556 measured reflections | l = −21→21 |
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)] = 0.042 | H-atom parameters constrained |
wR(F2) = 0.121 | w = 1/[σ2(Fo2) + (0.0509P)2 + 1.1474P] where P = (Fo2 + 2Fc2)/3 |
S = 1.06 | (Δ/σ)max < 0.001 |
2371 reflections | Δρmax = 0.49 e Å−3 |
156 parameters | Δρmin = −0.50 e Å−3 |
0 restraints | Extinction correction: SHELXL97 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0045 (6) |
C12H15N3OS | V = 2680.2 (16) Å3 |
Mr = 249.33 | Z = 8 |
Orthorhombic, Pbca | Mo Kα radiation |
a = 13.785 (5) Å | µ = 0.23 mm−1 |
b = 10.664 (4) Å | T = 294 K |
c = 18.233 (6) Å | 0.24 × 0.22 × 0.20 mm |
Bruker SMART CCD area-detector diffractometer | 2371 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 1997) | 1825 reflections with I > 2σ(I) |
Tmin = 0.737, Tmax = 0.950 | Rint = 0.024 |
13556 measured reflections |
R[F2 > 2σ(F2)] = 0.042 | 0 restraints |
wR(F2) = 0.121 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.49 e Å−3 |
2371 reflections | Δρmin = −0.50 e Å−3 |
156 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 | ||
S1 | 0.20197 (6) | 0.31298 (7) | 0.39880 (4) | 0.0880 (3) | |
N1 | 0.06932 (13) | 0.68893 (15) | 0.47218 (10) | 0.0573 (5) | |
N2 | 0.17241 (13) | 0.52421 (15) | 0.47711 (9) | 0.0540 (4) | |
H2A | 0.1972 | 0.5695 | 0.5113 | 0.065* | |
N3 | 0.29367 (13) | 0.39256 (16) | 0.51506 (10) | 0.0562 (4) | |
H3A | 0.3287 | 0.3279 | 0.5056 | 0.067* | |
O1 | 0.28019 (13) | 0.55553 (14) | 0.59591 (9) | 0.0729 (5) | |
C1 | 0.03215 (16) | 0.5184 (2) | 0.39285 (12) | 0.0603 (6) | |
H1 | 0.0484 | 0.4401 | 0.3741 | 0.072* | |
C2 | −0.04982 (17) | 0.5802 (2) | 0.36940 (14) | 0.0669 (6) | |
H2 | −0.0898 | 0.5435 | 0.3343 | 0.080* | |
C3 | −0.07274 (17) | 0.6952 (2) | 0.39747 (13) | 0.0639 (6) | |
H3 | −0.1282 | 0.7378 | 0.3826 | 0.077* | |
C4 | −0.01104 (17) | 0.7452 (2) | 0.44817 (13) | 0.0637 (6) | |
H4 | −0.0260 | 0.8237 | 0.4672 | 0.076* | |
C5 | 0.08957 (14) | 0.57576 (17) | 0.44482 (11) | 0.0483 (5) | |
C6 | 0.22019 (15) | 0.41698 (19) | 0.46441 (11) | 0.0533 (5) | |
C7 | 0.31854 (17) | 0.45635 (19) | 0.57795 (13) | 0.0580 (5) | |
C8 | 0.39334 (18) | 0.3926 (2) | 0.62153 (13) | 0.0682 (6) | |
H8 | 0.4317 | 0.3302 | 0.5948 | 0.082* | |
C9 | 0.37782 (19) | 0.3640 (2) | 0.70296 (13) | 0.0662 (6) | |
C10 | 0.4473 (2) | 0.4617 (3) | 0.68099 (15) | 0.0853 (8) | |
H10A | 0.5158 | 0.4435 | 0.6869 | 0.102* | |
H10B | 0.4295 | 0.5483 | 0.6901 | 0.102* | |
C11 | 0.4160 (3) | 0.2389 (2) | 0.72840 (16) | 0.0987 (10) | |
H11A | 0.4792 | 0.2251 | 0.7080 | 0.148* | |
H11B | 0.3729 | 0.1736 | 0.7125 | 0.148* | |
H11C | 0.4200 | 0.2384 | 0.7810 | 0.148* | |
C12 | 0.2849 (2) | 0.4015 (3) | 0.73987 (16) | 0.0930 (9) | |
H12A | 0.2951 | 0.4065 | 0.7919 | 0.139* | |
H12B | 0.2358 | 0.3402 | 0.7296 | 0.139* | |
H12C | 0.2645 | 0.4818 | 0.7218 | 0.139* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.1028 (6) | 0.0876 (5) | 0.0736 (4) | 0.0359 (4) | −0.0289 (4) | −0.0302 (4) |
N1 | 0.0604 (11) | 0.0481 (10) | 0.0633 (11) | 0.0035 (8) | −0.0025 (9) | 0.0014 (8) |
N2 | 0.0589 (11) | 0.0453 (9) | 0.0578 (10) | 0.0006 (8) | −0.0089 (8) | −0.0005 (8) |
N3 | 0.0603 (11) | 0.0498 (9) | 0.0585 (10) | 0.0080 (8) | −0.0079 (8) | −0.0016 (8) |
O1 | 0.0922 (12) | 0.0477 (9) | 0.0788 (11) | 0.0052 (8) | −0.0285 (9) | −0.0096 (8) |
C1 | 0.0607 (13) | 0.0535 (12) | 0.0666 (14) | 0.0020 (10) | −0.0064 (11) | −0.0032 (10) |
C2 | 0.0616 (14) | 0.0668 (14) | 0.0723 (15) | 0.0002 (11) | −0.0125 (12) | 0.0005 (12) |
C3 | 0.0530 (13) | 0.0641 (14) | 0.0746 (15) | 0.0041 (10) | −0.0014 (11) | 0.0110 (12) |
C4 | 0.0662 (14) | 0.0500 (12) | 0.0750 (14) | 0.0073 (11) | 0.0027 (12) | 0.0020 (11) |
C5 | 0.0507 (11) | 0.0443 (10) | 0.0500 (11) | −0.0022 (9) | 0.0036 (9) | 0.0079 (9) |
C6 | 0.0575 (13) | 0.0521 (12) | 0.0503 (11) | 0.0018 (10) | −0.0005 (9) | 0.0045 (9) |
C7 | 0.0634 (13) | 0.0463 (12) | 0.0642 (13) | −0.0039 (10) | −0.0111 (10) | 0.0014 (10) |
C8 | 0.0709 (15) | 0.0659 (14) | 0.0680 (14) | 0.0114 (12) | −0.0183 (12) | −0.0063 (11) |
C9 | 0.0790 (17) | 0.0526 (12) | 0.0671 (14) | 0.0036 (11) | −0.0261 (12) | −0.0049 (11) |
C10 | 0.0817 (18) | 0.0794 (17) | 0.0947 (19) | −0.0100 (14) | −0.0385 (15) | 0.0026 (15) |
C11 | 0.140 (3) | 0.0620 (15) | 0.094 (2) | 0.0146 (17) | −0.0489 (19) | 0.0006 (14) |
C12 | 0.098 (2) | 0.108 (2) | 0.0722 (18) | 0.0091 (18) | −0.0160 (15) | 0.0025 (16) |
S1—C6 | 1.651 (2) | C4—H4 | 0.9300 |
N1—C4 | 1.334 (3) | C7—C8 | 1.469 (3) |
N1—C5 | 1.335 (2) | C8—C10 | 1.507 (3) |
N2—C6 | 1.340 (3) | C8—H8 | 0.9800 |
N2—C5 | 1.397 (3) | C9—C8 | 1.531 (3) |
N2—H2A | 0.8600 | C9—C10 | 1.471 (4) |
N3—C7 | 1.377 (3) | C9—C11 | 1.507 (3) |
N3—C6 | 1.395 (3) | C9—C12 | 1.501 (4) |
N3—H3A | 0.8600 | C10—H10A | 0.9700 |
O1—C7 | 1.227 (3) | C10—H10B | 0.9700 |
C1—C2 | 1.376 (3) | C11—H11A | 0.9600 |
C1—C5 | 1.378 (3) | C11—H11B | 0.9600 |
C1—H1 | 0.9300 | C11—H11C | 0.9600 |
C2—H2 | 0.9300 | C12—H12A | 0.9600 |
C3—C4 | 1.365 (3) | C12—H12B | 0.9600 |
C3—C2 | 1.366 (3) | C12—H12C | 0.9600 |
C3—H3 | 0.9300 | ||
C4—N1—C5 | 117.24 (19) | C7—C8—C9 | 121.3 (2) |
C6—N2—C5 | 131.66 (18) | C10—C8—C9 | 57.90 (16) |
C6—N2—H2A | 114.2 | C7—C8—H8 | 115.1 |
C5—N2—H2A | 114.2 | C10—C8—H8 | 115.1 |
C7—N3—C6 | 129.78 (18) | C9—C8—H8 | 115.1 |
C7—N3—H3A | 115.1 | C10—C9—C12 | 119.3 (2) |
C6—N3—H3A | 115.1 | C10—C9—C11 | 118.9 (2) |
C2—C1—C5 | 118.2 (2) | C12—C9—C11 | 113.3 (3) |
C2—C1—H1 | 120.9 | C10—C9—C8 | 60.25 (17) |
C5—C1—H1 | 120.9 | C12—C9—C8 | 120.1 (2) |
C3—C2—C1 | 120.2 (2) | C11—C9—C8 | 115.2 (2) |
C3—C2—H2 | 119.9 | C9—C10—C8 | 61.85 (17) |
C1—C2—H2 | 119.9 | C9—C10—H10A | 117.6 |
C4—C3—C2 | 117.4 (2) | C8—C10—H10A | 117.6 |
C4—C3—H3 | 121.3 | C9—C10—H10B | 117.6 |
C2—C3—H3 | 121.3 | C8—C10—H10B | 117.6 |
N1—C4—C3 | 124.4 (2) | H10A—C10—H10B | 114.7 |
N1—C4—H4 | 117.8 | C9—C11—H11A | 109.5 |
C3—C4—H4 | 117.8 | C9—C11—H11B | 109.5 |
N1—C5—C1 | 122.53 (19) | H11A—C11—H11B | 109.5 |
N1—C5—N2 | 111.65 (18) | C9—C11—H11C | 109.5 |
C1—C5—N2 | 125.78 (19) | H11A—C11—H11C | 109.5 |
N2—C6—N3 | 113.69 (17) | H11B—C11—H11C | 109.5 |
N2—C6—S1 | 128.60 (16) | C9—C12—H12A | 109.5 |
N3—C6—S1 | 117.70 (15) | C9—C12—H12B | 109.5 |
O1—C7—N3 | 122.8 (2) | H12A—C12—H12B | 109.5 |
O1—C7—C8 | 123.8 (2) | C9—C12—H12C | 109.5 |
N3—C7—C8 | 113.38 (19) | H12A—C12—H12C | 109.5 |
C7—C8—C10 | 120.7 (2) | H12B—C12—H12C | 109.5 |
C5—N1—C4—C3 | −0.6 (3) | C4—C3—C2—C1 | 0.7 (4) |
C4—N1—C5—C1 | 1.3 (3) | C2—C3—C4—N1 | −0.4 (4) |
C4—N1—C5—N2 | −176.82 (18) | O1—C7—C8—C10 | −16.7 (4) |
C6—N2—C5—N1 | −176.9 (2) | N3—C7—C8—C10 | 164.6 (2) |
C6—N2—C5—C1 | 5.1 (3) | O1—C7—C8—C9 | 52.1 (3) |
C5—N2—C6—N3 | −172.60 (19) | N3—C7—C8—C9 | −126.7 (2) |
C5—N2—C6—S1 | 6.5 (3) | C7—C8—C10—C9 | 109.9 (3) |
C7—N3—C6—N2 | 5.6 (3) | C10—C9—C8—C7 | −108.9 (3) |
C7—N3—C6—S1 | −173.64 (18) | C12—C9—C8—C7 | −0.2 (3) |
C6—N3—C7—O1 | −5.6 (4) | C11—C9—C8—C7 | 140.9 (2) |
C6—N3—C7—C8 | 173.2 (2) | C12—C9—C8—C10 | 108.7 (3) |
C5—C1—C2—C3 | 0.0 (3) | C11—C9—C8—C10 | −110.3 (3) |
C2—C1—C5—N1 | −1.0 (3) | C12—C9—C10—C8 | −109.9 (2) |
C2—C1—C5—N2 | 176.8 (2) | C11—C9—C10—C8 | 104.2 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···O1 | 0.86 | 1.93 | 2.648 (2) | 141 |
N3—H3A···N1i | 0.86 | 2.13 | 2.982 (3) | 170 |
Symmetry code: (i) −x+1/2, y−1/2, z. |
Experimental details
Crystal data | |
Chemical formula | C12H15N3OS |
Mr | 249.33 |
Crystal system, space group | Orthorhombic, Pbca |
Temperature (K) | 294 |
a, b, c (Å) | 13.785 (5), 10.664 (4), 18.233 (6) |
V (Å3) | 2680.2 (16) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.23 |
Crystal size (mm) | 0.24 × 0.22 × 0.20 |
Data collection | |
Diffractometer | Bruker SMART CCD area-detector |
Absorption correction | Multi-scan (SADABS; Bruker, 1997) |
Tmin, Tmax | 0.737, 0.950 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 13556, 2371, 1825 |
Rint | 0.024 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.042, 0.121, 1.06 |
No. of reflections | 2371 |
No. of parameters | 156 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.49, −0.50 |
Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 1997), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Bruker, 1999), SHELXTL.
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···O1 | 0.86 | 1.93 | 2.648 (2) | 141 |
N3—H3A···N1i | 0.86 | 2.13 | 2.982 (3) | 170 |
Symmetry code: (i) −x+1/2, y−1/2, z. |
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Cyclopropane derivatives have several biological activities. 2,2-Dichloro-3,3 -dimethylcyclopropanecarboxylic acid is an effective inducer against the rice blast fungus (Langcake et al., 1983). 1-Aminocyclopropane-1-carboxylic acid (ACC) is an intermediate in the biosynthesis of the ripening hormone ethylene (Adams & Yang, 1979), a component of bacterial phytotoxines, and azetidine-2 -carboxylic acid (Nadler et al., 1988). Thus, it is very important to synthesize other new compounds containing cyclopropane, and study their biological activities. Acyl thiourea derivatives have many biological activities, for example, they have been used as bactericides, fungicides and insecticides in many plants (Kamala & Rao, 1989). A pyridine ring is often used as an active component in pesticide discovery (Elbert et al., 2000). The title compound, (I), contains all these three active parts and may show some insecticidal activity. It was characterized by 1H NMR and elemental analysis, and we report herein its crystal structure.
In the molecule of the title compound, (I), (Fig. 1) the bond lengths and angles are within normal ranges (Allen et al., 1987). The intramolecular N—H···O hydrogen bond (Table 1) causes to the formation of a six-membered planar ring A (H2A/N2/C6/N3/C7/O1). Rings B (C8—C10) and C (N1/C1—C5) are, of course, planar and the dihedral angles between them are A/B = 79.14 (3)°, A/C = 14.60 (2)° and B/C = 83.45 (3)°.
In the crystal structure, intermolecular N—H····N hydrogen bonds (Table 1) link the molecules (Fig. 2). The intra- and intermolecular hydrogen bonds seem to be effective in the stabilization of the crystal structure.