supplementary materials


zl2432 scheme

Acta Cryst. (2012). E68, o94-o95    [ doi:10.1107/S1600536811052494 ]

2-(5-Fluoro-2,3-dioxoindolin-1-yl)ethyl 4-methylpiperazine-1-carbodithioate

Y. Wang, H.-H. Lin and S.-L. Cao

Abstract top

In the title compound, C16H18FN3O2S2, the methylpiperazine ring adopts a chair conformation, while the (2,3-dioxoindolin-1-yl)ethyl unit is linked to one of the N atoms of the piperazine ring via the carbodithioate group. In the crystal, each molecule is linked to its neighbors within the (\overline{1}03) plane through weak C-H(methylene)...O, C-H(aryl)...O and C-H(methylene)...S interactions. Perpendicular to this plane molecules are connected through intermolecular short N...[pi](pyrrole ring) contacts [N...C centroid = 3.232 (2) Å], another set of C-H(methylene)...O interactions and through short contacts between carbodithioate S atoms and the pyrrole rings [C...centroid = 3.695 (3), S...centroid = 3.403 (2) Å].

Comment top

Indoline-2,3-dione and its derivatives are well known for their broad spectrum biological and pharmacological properties including anticonvulsant (Bhattacharya & Chakrabarti, 1998), anti-inflammatory (Sridhar et al., 2001) and anxiogenic (Medvedev et al., 1996) activities. On the other hand, dithiocarbamates also exhibit a large range of biological activities such as fungicidal (Ozkirimli et al., 2005) and antitumor activities (Cao et al., 2005; Gaspari et al., 2006). In an attempt to obtain compounds that might also exhibit antitumor properties, but possibly with increased potency and selectivity, we designed and synthesized the title compoud (C16H18N3O2FS2), which consists of an indole core with a dithiocarbamate side chain (Scheme 1). In the present context, we report the crystal structure of the new compound.

In the crystalline structure of the title compound, the 1-methylpiperazine ring adopts a chair conformation, while the indoline-2,3-dione ethyl moiety is linked to one of the N atoms of the piperazine ring via the carbodithioate group, with the ethyl group in a trans-conformation (N1—C9—C10—S2 torsion angle of 175.74 (11)°, Fig. 1). This trans-conformation differentiates the title compound from the related compound 2-(2,3-dioxoindolin-1-yl)ethyl-4-(4-nitrophenyl)piperazine-1-carbodithioate reported by us recently (Wang et al., 2010), which was found to have a gauge-conformation with an N4(pyrrole)—C19—C20—S2 torsion angle of 66.16 (15)°. Through weak C13—H13B(methylene)···O2i, C—H(aryl)···O1ii and C12—H12B(methylene)···S2iii interactions each molecule is linked to its neighbors within the (-1 0 3) Miller plane (Table 1 and Fig. 2). Perpendicular to this plane molecules are connected through intermolecular short N···π (pyrrole ring) contacts, another set of C—H(methylene)···O interactions (Table 1) and through short contacts between carbodithioate sulfur atoms and the pyrrole rings (C11S1···Cg1iv, Table 2). A short contact is observed between the nitrogen atom N1 and the π-electron desnity of the pyrrole ring, with an N3···Cgv (Cg = C5-C6-C7-N1-C8, (v) = -x+1.5, y+0.5, -z+1.5) distance equal to 3.232 (2) Å, which is shorter than the van der Waals distance (3.40 Å) on the basis of Pauling's value for the half thickness of phenyl rings (1.85 Å) (Malone et al.,1997) and the van der Waals radius of N (1.55 Å) (Bondi, 1964). It is comparable to the N(pyrazinyl)···centroid(pyrazinyl) distance of 3.05 Å in {[Ni(L)(NO3)2]} (L = bis(2-pyraylmethyl)sulfide) reported by Black et al. (2007). Regarding the C11S1···π contact (Table 2), the CS bond is almost parallel to the pyrrole ring with a C11S1···Cg1(pyrrole) angle equal to 86.42 (2)°, a contact mode similar to that of the CO···π (pyridyl) contact in Cu(L)2(BF4)2 (L = 2,6-pyridinediylbis(3-pyridinyl)methanone) reported by Wan et al. (2008).

Related literature top

For background to indoline-2,3-dione and its derivatives, see: Bhattacharya & Chakrabarti (1998); Sridhar & Ramesh (2001); Medvedev et al. (1996) and to dithiocarbamates, see: Ozkirimli et al. (2005); Cao et al. (2005); Gaspari et al. (2006). For analogues of 5-fluoroindoline-2,3-dione, see: Wang et al. (2010). For N···π contacts, see: Black et al. (2007). For van der Waals radii, see Bondi (1964). For the thickness of phenyl rings, see: Malone et al. (1997). For CO···π (pyridyl) contacts, see: Wan et al. (2008)

Experimental top

A suspension of 1-methylpiperazine (2.4 mmol), carbon disulfide (0.72 mL, 12 mmol) and anhydrous potassium phosphate (0.51 g, 2.4 mmol) in N,N-dimethylformamide (15 mL) was stirred at room temperature for 30 minutes. Then, 1-(2-bromoethyl)-5-fluoroindoline-2,3-dione (2 mmol) was added and stirring was continued for 3.5 h. The reaction mixture was poured into water (100 mL) and the resulting precipitate was separated by filtration and further purified by column chromatography on silica gel with dichloromethane/methanol = 95:5 (v/v) as the eluent to give the title compound (Rf = 0.44, m.p. 472.2-473.2 K; yield 78%). After two weeks, the orange crystals of the title compound were deposited by slow evaporation from a solution of dichloromethane/N,N-dimethylformamide 1:1 (v/v) at room temperature.

Refinement top

All H atoms were discernible in the difference electron density maps. Nevertheless, the hydrogen atoms were placed into idealized positions and allowed to ride on their respective carrier atoms, with C—H = 0.93 and 0.97 Å for aryl and methylene hydrogens, respectively. Uiso(H) = 1.2Ueq(C)aryl/methylene.

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: APEX2 and SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); 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) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The title molecule with the atomic numbering scheme. The displacement ellipsoids of the non-hydrogen atoms are shown at the 30% probability level.
[Figure 2] Fig. 2. The intermolecular C—H(aryl)···O, C—H(methylene)···S and C—H(methylene)···O interactions of the title compound within the (-1 0 3) Miller plane. View perpendicular to this plane.
[Figure 3] Fig. 3. View down the b direction of the stacking structure of the title compound. All weak non-covalent interactions are omitted for clarity.
2-(5-Fluoro-2,3-dioxoindolin-1-yl)ethyl 4-methylpiperazine-1-carbodithioate top
Crystal data top
C16H18FN3O2S2F(000) = 768
Mr = 367.45Dx = 1.444 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 222 reflections
a = 10.0258 (4) Åθ = 2.3–27.6°
b = 15.9925 (6) ŵ = 0.34 mm1
c = 11.0016 (5) ÅT = 296 K
β = 106.656 (3)°Block, colorless
V = 1689.96 (12) Å30.30 × 0.30 × 0.20 mm
Z = 4
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
3861 independent reflections
Radiation source: fine-focus sealed tube3058 reflections with I > 2σ(I)
graphiteRint = 0.031
CCD area detector scansθmax = 27.6°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Bruker 2007)
h = 1313
Tmin = 0.658, Tmax = 0.746k = 2020
18809 measured reflectionsl = 1114
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.100H-atom parameters constrained
S = 1.04 w = 1/[σ2(Fo2) + (0.0506P)2 + 0.3797P] P = (Fo2 + 2Fc2)/3
3861 reflections(Δ/σ)max = 0.001
217 parametersΔρmax = 0.22 e Å3
0 restraintsΔρmin = 0.20 e Å3
Crystal data top
C16H18FN3O2S2V = 1689.96 (12) Å3
Mr = 367.45Z = 4
Monoclinic, P21/nMo Kα radiation
a = 10.0258 (4) ŵ = 0.34 mm1
b = 15.9925 (6) ÅT = 296 K
c = 11.0016 (5) Å0.30 × 0.30 × 0.20 mm
β = 106.656 (3)°
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
3861 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker 2007)
3058 reflections with I > 2σ(I)
Tmin = 0.658, Tmax = 0.746Rint = 0.031
18809 measured reflectionsθmax = 27.6°
Refinement top
R[F2 > 2σ(F2)] = 0.035H-atom parameters constrained
wR(F2) = 0.100Δρmax = 0.22 e Å3
S = 1.04Δρmin = 0.20 e Å3
3861 reflectionsAbsolute structure: ?
217 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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*/Ueq
S10.91389 (4)0.66656 (2)0.57656 (4)0.04717 (13)
S20.69048 (4)0.53592 (2)0.54985 (5)0.04795 (14)
N11.04768 (13)0.40980 (8)0.72003 (13)0.0436 (3)
N20.64449 (12)0.69676 (7)0.54089 (14)0.0423 (3)
N30.42553 (14)0.81754 (8)0.50085 (14)0.0466 (3)
O11.22167 (14)0.21917 (7)0.75006 (15)0.0677 (4)
O20.93355 (12)0.28341 (8)0.68042 (13)0.0580 (3)
F11.60973 (12)0.46870 (8)0.86069 (15)0.0840 (4)
C11.24078 (19)0.51646 (9)0.77343 (17)0.0477 (4)
H1A1.18210.56260.76180.057*
C21.3845 (2)0.52580 (10)0.80939 (19)0.0554 (4)
H2A1.42330.57900.82240.066*
C31.46982 (18)0.45705 (11)0.82584 (19)0.0555 (5)
C41.41990 (17)0.37630 (10)0.80778 (18)0.0502 (4)
H4A1.47930.33050.81920.060*
C51.27711 (16)0.36716 (9)0.77186 (16)0.0419 (4)
C61.19005 (16)0.29208 (9)0.74546 (17)0.0465 (4)
C71.03847 (16)0.32457 (10)0.70982 (17)0.0449 (4)
C81.18809 (15)0.43610 (9)0.75556 (15)0.0397 (3)
C90.92604 (17)0.46265 (11)0.70586 (17)0.0488 (4)
H9A0.95530.51610.74650.059*
H9B0.86430.43650.74830.059*
C100.84770 (16)0.47709 (10)0.56780 (17)0.0446 (4)
H10A0.82470.42350.52570.054*
H10B0.90730.50690.52690.054*
C110.74743 (15)0.64129 (9)0.55535 (15)0.0368 (3)
C120.50387 (16)0.67350 (10)0.5460 (2)0.0531 (5)
H12A0.50050.67630.63310.064*
H12B0.48420.61640.51680.064*
C130.39430 (17)0.73083 (11)0.4648 (2)0.0545 (4)
H13A0.39030.72350.37630.065*
H13B0.30400.71630.47450.065*
C140.55667 (18)0.83880 (10)0.47625 (18)0.0507 (4)
H14A0.57650.89760.49460.061*
H14B0.54820.82970.38720.061*
C150.67565 (16)0.78703 (9)0.55582 (18)0.0470 (4)
H15A0.75900.79890.53090.056*
H15B0.69350.80240.64430.056*
C160.3137 (2)0.87270 (12)0.4299 (2)0.0615 (5)
H16A0.22760.85630.44490.092*
H16B0.30510.86860.34100.092*
H16C0.33500.92940.45750.092*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.03141 (19)0.0426 (2)0.0657 (3)0.00238 (15)0.01100 (18)0.00061 (18)
S20.03104 (19)0.03047 (19)0.0770 (3)0.00221 (13)0.00697 (18)0.00188 (17)
N10.0375 (6)0.0350 (6)0.0536 (9)0.0071 (5)0.0055 (6)0.0042 (6)
N20.0310 (6)0.0303 (6)0.0618 (9)0.0001 (5)0.0072 (6)0.0043 (6)
N30.0431 (7)0.0370 (7)0.0530 (9)0.0105 (5)0.0030 (6)0.0005 (6)
O10.0549 (7)0.0274 (6)0.1107 (12)0.0032 (5)0.0075 (7)0.0003 (6)
O20.0407 (6)0.0551 (7)0.0713 (9)0.0104 (5)0.0047 (6)0.0008 (6)
F10.0452 (6)0.0693 (8)0.1238 (12)0.0187 (5)0.0025 (7)0.0018 (7)
C10.0571 (9)0.0290 (7)0.0549 (10)0.0053 (7)0.0127 (8)0.0033 (7)
C20.0618 (11)0.0337 (8)0.0655 (12)0.0110 (7)0.0102 (9)0.0015 (7)
C30.0416 (9)0.0483 (9)0.0680 (12)0.0110 (7)0.0019 (8)0.0006 (8)
C40.0386 (8)0.0371 (8)0.0670 (12)0.0029 (6)0.0026 (8)0.0035 (7)
C50.0388 (8)0.0278 (7)0.0531 (10)0.0014 (6)0.0039 (7)0.0020 (6)
C60.0402 (8)0.0306 (7)0.0621 (11)0.0000 (6)0.0041 (7)0.0013 (7)
C70.0378 (8)0.0399 (8)0.0516 (10)0.0002 (6)0.0042 (7)0.0028 (7)
C80.0403 (7)0.0315 (7)0.0434 (9)0.0046 (6)0.0058 (7)0.0038 (6)
C90.0428 (8)0.0481 (9)0.0556 (11)0.0139 (7)0.0144 (8)0.0060 (7)
C100.0357 (7)0.0366 (7)0.0582 (10)0.0080 (6)0.0083 (7)0.0004 (7)
C110.0326 (7)0.0332 (7)0.0411 (8)0.0000 (5)0.0047 (6)0.0016 (6)
C120.0321 (7)0.0320 (7)0.0921 (14)0.0004 (6)0.0130 (8)0.0041 (8)
C130.0341 (8)0.0466 (9)0.0742 (12)0.0037 (7)0.0014 (8)0.0134 (8)
C140.0519 (9)0.0373 (8)0.0588 (11)0.0038 (7)0.0092 (8)0.0006 (7)
C150.0410 (8)0.0300 (7)0.0660 (11)0.0022 (6)0.0090 (8)0.0053 (7)
C160.0582 (11)0.0553 (11)0.0632 (12)0.0224 (9)0.0050 (9)0.0085 (9)
Geometric parameters (Å, °) top
S1—C111.6673 (15)C4—H4A0.9300
S2—C111.7747 (15)C5—C81.397 (2)
S2—C101.7973 (15)C5—C61.464 (2)
N1—C71.369 (2)C6—C71.547 (2)
N1—C81.413 (2)C9—C101.514 (2)
N1—C91.4550 (19)C9—H9A0.9700
N2—C111.3353 (19)C9—H9B0.9700
N2—C121.4746 (19)C10—H10A0.9700
N2—C151.4763 (19)C10—H10B0.9700
N3—C131.452 (2)C12—C131.511 (2)
N3—C141.457 (2)C12—H12A0.9700
N3—C161.464 (2)C12—H12B0.9700
O1—C61.2056 (18)C13—H13A0.9700
O2—C71.2039 (19)C13—H13B0.9700
F1—C31.357 (2)C14—C151.509 (2)
C1—C81.382 (2)C14—H14A0.9700
C1—C21.389 (3)C14—H14B0.9700
C1—H1A0.9300C15—H15A0.9700
C2—C31.373 (3)C15—H15B0.9700
C2—H2A0.9300C16—H16A0.9600
C3—C41.379 (2)C16—H16B0.9600
C4—C51.379 (2)C16—H16C0.9600
C11—S2—C10103.29 (7)C9—C10—S2112.11 (11)
C7—N1—C8110.95 (12)C9—C10—H10A109.2
C7—N1—C9122.35 (14)S2—C10—H10A109.2
C8—N1—C9126.50 (13)C9—C10—H10B109.2
C11—N2—C12122.86 (13)S2—C10—H10B109.2
C11—N2—C15120.31 (13)H10A—C10—H10B107.9
C12—N2—C15114.61 (12)N2—C11—S1124.34 (11)
C13—N3—C14107.92 (13)N2—C11—S2113.37 (11)
C13—N3—C16110.97 (14)S1—C11—S2122.29 (8)
C14—N3—C16110.77 (14)N2—C12—C13111.44 (14)
C8—C1—C2117.62 (14)N2—C12—H12A109.3
C8—C1—H1A121.2C13—C12—H12A109.3
C2—C1—H1A121.2N2—C12—H12B109.3
C3—C2—C1120.51 (15)C13—C12—H12B109.3
C3—C2—H2A119.7H12A—C12—H12B108.0
C1—C2—H2A119.7N3—C13—C12110.78 (14)
F1—C3—C2118.80 (16)N3—C13—H13A109.5
F1—C3—C4118.20 (16)C12—C13—H13A109.5
C2—C3—C4123.00 (16)N3—C13—H13B109.5
C3—C4—C5116.40 (15)C12—C13—H13B109.5
C3—C4—H4A121.8H13A—C13—H13B108.1
C5—C4—H4A121.8N3—C14—C15111.70 (14)
C4—C5—C8121.70 (14)N3—C14—H14A109.3
C4—C5—C6130.89 (14)C15—C14—H14A109.3
C8—C5—C6107.41 (13)N3—C14—H14B109.3
O1—C6—C5130.57 (15)C15—C14—H14B109.3
O1—C6—C7124.27 (15)H14A—C14—H14B107.9
C5—C6—C7105.15 (12)N2—C15—C14111.42 (13)
O2—C7—N1126.86 (15)N2—C15—H15A109.3
O2—C7—C6127.14 (15)C14—C15—H15A109.3
N1—C7—C6106.00 (13)N2—C15—H15B109.3
C1—C8—C5120.76 (14)C14—C15—H15B109.3
C1—C8—N1128.76 (14)H15A—C15—H15B108.0
C5—C8—N1110.48 (13)N3—C16—H16A109.5
N1—C9—C10111.95 (14)N3—C16—H16B109.5
N1—C9—H9A109.2H16A—C16—H16B109.5
C10—C9—H9A109.2N3—C16—H16C109.5
N1—C9—H9B109.2H16A—C16—H16C109.5
C10—C9—H9B109.2H16B—C16—H16C109.5
H9A—C9—H9B107.9
C8—C1—C2—C30.2 (3)C7—N1—C8—C1178.77 (17)
C1—C2—C3—F1179.83 (18)C9—N1—C8—C16.3 (3)
C1—C2—C3—C40.3 (3)C7—N1—C8—C50.9 (2)
F1—C3—C4—C5179.72 (18)C9—N1—C8—C5174.01 (15)
C2—C3—C4—C50.1 (3)C7—N1—C9—C1080.2 (2)
C3—C4—C5—C80.4 (3)C8—N1—C9—C10105.47 (19)
C3—C4—C5—C6179.75 (19)N1—C9—C10—S2175.74 (11)
C4—C5—C6—O11.0 (4)C11—S2—C10—C987.13 (13)
C8—C5—C6—O1178.4 (2)C12—N2—C11—S1168.35 (14)
C4—C5—C6—C7179.90 (19)C15—N2—C11—S16.2 (2)
C8—C5—C6—C70.70 (19)C12—N2—C11—S211.7 (2)
C8—N1—C7—O2179.46 (18)C15—N2—C11—S2173.86 (12)
C9—N1—C7—O25.4 (3)C10—S2—C11—N2178.69 (12)
C8—N1—C7—C61.28 (18)C10—S2—C11—S11.28 (13)
C9—N1—C7—C6173.87 (15)C11—N2—C12—C13150.62 (16)
O1—C6—C7—O21.3 (3)C15—N2—C12—C1346.3 (2)
C5—C6—C7—O2179.54 (18)C14—N3—C13—C1263.3 (2)
O1—C6—C7—N1177.94 (19)C16—N3—C13—C12175.16 (16)
C5—C6—C7—N11.21 (18)N2—C12—C13—N355.4 (2)
C2—C1—C8—C50.7 (3)C13—N3—C14—C1562.61 (18)
C2—C1—C8—N1179.63 (17)C16—N3—C14—C15175.73 (14)
C4—C5—C8—C10.9 (3)C11—N2—C15—C14151.30 (15)
C6—C5—C8—C1179.65 (16)C12—N2—C15—C1445.1 (2)
C4—C5—C8—N1179.43 (16)N3—C14—C15—N253.36 (19)
C6—C5—C8—N10.04 (19)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
C13—H13B···O2i0.972.503.225 (2)131
C12—H12A···O2ii0.972.613.385 (2)137
C15—H15B···O2ii0.972.623.383 (2)136
C1—H1A···O1iii0.932.703.282 (3)121
C2—H2A···O1iii0.932.673.275 (2)124
C12—H12B···S2i0.972.973.866 (3)155
C11—S1···Cg1iv1.6673 (15)3.403 (2)3.695 (3)86.43 (6)
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+3/2, y+1/2, −z+3/2; (iii) −x+5/2, y+1/2, −z+3/2; (iv) −x+5/2, y+3/2, −z+3/2.
Table 1
Hydrogen-bond geometry (Å, °)
top
D—H···AD—HH···AD···AD—H···A
C13—H13B···O2i0.972.503.225 (2)131
C12—H12A···O2ii0.972.613.385 (2)137
C15—H15B···O2ii0.972.623.383 (2)136
C1—H1A···O1iii0.932.703.282 (3)121
C2—H2A···O1iii0.932.673.275 (2)124
C12—H12B···S2i0.972.973.866 (3)155
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+3/2, y+1/2, −z+3/2; (iii) −x+5/2, y+1/2, −z+3/2.
Table 2
CS···π-electron ring interactions (Å)
top
CS···CgC···CgS···Cg
C11S1···Cg1i3.695 (3)3.403 (2)
Symmetry code: (i) -x+2,-y+1,-z+1. Cg1 is the centroid of N1-C8-C5-C6-C7 (pyrrole).
Acknowledgements top

The authors are grateful to the National Natural Science Foundation of China (project No. 20972099) and the Beijing Municipal Commission of Education for financial support.

references
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