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Acta Crystallogr Sect E Struct Rep Online. 2009 May 1; 65(Pt 5): o1049.
Published online 2009 April 18. doi:  10.1107/S1600536809012550
PMCID: PMC2977731

1H-Pyrazolo[4,3-g]benzothia­zol-7-amine

Abstract

The mol­ecule of the title compound, C8H6N4S, is almost planar [maximum deviation from the mean plane = 0.020 (1) Å for the S atom]. In the crystal, a supra­molecular three-dimensional arrangement arises from N—H(...)N hydrogen bonds and weak aromatic stacking interactions along the a axis [centroid–centroid separation = 3.582 (2) Å].

Related literature

For background on DNA inter­calation agents, see: Cagnoli et al. (1968 [triangle]); Martínez & Chacón-García (2005 [triangle]); Chakrabarty et al. (2008 [triangle]). For further synthetic details, see: Salazar & Dorta (2004 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1049-scheme1.jpg

Experimental

Crystal data

  • C8H6N4S
  • M r = 190.23
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1049-efi1.jpg
  • a = 4.499 (2) Å
  • b = 14.979 (8) Å
  • c = 12.112 (7) Å
  • β = 92.442 (19)°
  • V = 815.6 (7) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.35 mm−1
  • T = 293 K
  • 0.50 × 0.48 × 0.28 mm

Data collection

  • Rigaku AFC7S Mercury diffractometer
  • Absorption correction: multi-scan (Jacobson, 1998 [triangle]) T min = 0.837, T max = 0.904
  • 8415 measured reflections
  • 1564 independent reflections
  • 1356 reflections with I > 2σ(I)
  • R int = 0.027

Refinement

  • R[F 2 > 2σ(F 2)] = 0.043
  • wR(F 2) = 0.117
  • S = 1.12
  • 1564 reflections
  • 118 parameters
  • H-atom parameters constrained
  • Δρmax = 0.21 e Å−3
  • Δρmin = −0.39 e Å−3

Data collection: CrystalClear (Rigaku, 2002 [triangle]); cell refinement: CrystalClear; data reduction: CrystalStructure (Rigaku/MSC, 2004 [triangle]); program(s) used to solve structure: SHELXTL-NT (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL-NT; molecular graphics: SHELXTL-NT and DIAMOND (Brandenburg, 1999 [triangle]); software used to prepare material for publication: SHELXTL-NT and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I. DOI: 10.1107/S1600536809012550/hb2931sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809012550/hb2931Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors thank DID Universidad Simón Bolívar for financial support (project: S1–IN–CB–001–08) and FONACIT–MCT Venezuela (project: LAB-199700821).

supplementary crystallographic information

Comment

Most of the significant advances against diseases have been made by designing and testing new structures, which are often heteroaromatic derivatives. Actually, the discovery of new compounds with antitumoral activity has become one of the most important goals in medicinal chemistry. One interesting group of potential chemotherapeutic agents includes molecules which interact with DNA like intercalator agents (Martínez & Chacón-García, 2005). Intercalation occurs when ligands of an appropriate size and chemical nature, fit themselves in between base pairs of DNA. Such ligands are mostly polycyclic, aromatic and planar. These kinds of agents are used in chemotherapeutic treatment to inhibit DNA replication in rapidly growing cancer cells. The title compound (I) is a polycyclic, aromatic and heterocyclic molecule and could be used to develop a new type of DNA intercalators agents (Chakrabarty et al. 2008).

The molecular structure is shown in figure 1, with its respective labels. The molecule adopts a conformation essenciality planar, with maximum deviation of the mean plane of 0.020 (1)Å for atom S1. The crystal structure of (I), consists of the self-assembly of the molecules through hydrogen bonding interactions of the kind N—H···N. The crystal packing (Fig. 2), consists of infinite chains in zigzag along the b axis generated by intermolecular interactions of hydrogen bond between the amino group and N atom of the imidazole ring [N1···N4 = 3.019 (3)Å]. These chains are connected through the interaction between the atoms N2 and N3 forming a two-dimensional wavy-like arrangement in the bc plane These layers are stacking through weak π–π interactions along the a axis (Cg3···Cg1, where Cg3 = C2/C3/C4/C5/C7/C8 and Cg1 = S1/C6/N3/C5/C7) together with an additional hydrogen bond lead to the formation of a three-dimensional hydrogen bonded network.

Experimental

To a solution of 6-aminoindazole (2.00 g, 15 mmol) and NH4SCN (2.29 g, 30 mmol) in acetic acid (25 ml) was added dropwise pentylpyridinium tribromide (5.86 g, 15 mmol) (Salazar & Dorta, 2004). The resulting solution was stirred for 3 h at room temperature and then, 3 h at 80°C. The reaction mixture was then poured into ice (50 g), the precipitate was filtered and discarded. The resulting solution was neutralized with K2CO3, and the formed precipitate was filtered, washed with AcOEt and dried; to give a yellow powder corresponding to the title compound. Yield: 1.80 g (63%). The melting point (uncorrected) was measured with a Fischer-Johns micro hot-stage apparatus: d 563 K.

The yellow powder was dissolved in a minimum amount of 1,4-dioxane and the solution was left for several days at room temperature, during which the solution gradually reduced its volume to give light brown blocks of (I).

IR data [KBr pellets, (cm-1)]: 3367, 3314, 3181, 1629. 1H NMR [500 MHz, DMSO-d6, d (p.p.m.)]: 13.04 (brs, 1H, NH), 8.05 (s, 1H,), 7.57 (d, 1H, J = 6.84 Hz), 7.45 (brs, 2H, NH2), 7.21 (d, 1H, J = 6.88 Hz).13 C NMR [126 MHz, DMSO-d6, d (p.p.m.)]: 166.97 (C6), 152.21 (C5), 135.41 (C1), 134.99 (C2), 119.13 (C8), 118.01 (C3), 113.95 (C4), 109.39 (C7).

Refinement

The N-bound H atoms were located in difference maps and refined as riding in their as found relative positions with Uiso(H) = 1.2Ueq(N). The C-bound H atoms were placed in idealized positions (C—H = 0.93–0.98 Å) and refined as riding with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The molecular structure of (I), showing displacement elipsoids drawn at the 35% probability level and H atoms shown as spheres of arbitrary radius.
Fig. 2.
View of the hydrogen bonded layer in the bc plane in (I). The H atoms have been omitted for clarity and dashed lines indicate the donor···acceptor interactions for hydrogen bonds.

Crystal data

C8H6N4SF(000) = 392
Mr = 190.23Dx = 1.549 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71070 Å
Hall symbol: -P 2ybcCell parameters from 5546 reflections
a = 4.499 (2) Åθ = 1.4–27.8°
b = 14.979 (8) ŵ = 0.35 mm1
c = 12.112 (7) ÅT = 293 K
β = 92.442 (19)°Block, light brown
V = 815.6 (7) Å30.50 × 0.48 × 0.28 mm
Z = 4

Data collection

Rigaku AFC7S Mercury diffractometer1564 independent reflections
Radiation source: Normal-focus sealed tube1356 reflections with I > 2σ(I)
graphiteRint = 0.027
ω scansθmax = 27.8°, θmin = 2.2°
Absorption correction: multi-scan (Jacobson, 1998)h = −5→5
Tmin = 0.837, Tmax = 0.904k = −17→17
8415 measured reflectionsl = −10→13

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.043Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.117H-atom parameters constrained
S = 1.12w = 1/[σ2(Fo2) + (0.0537P)2 + 0.4259P] where P = (Fo2 + 2Fc2)/3
1564 reflections(Δ/σ)max = 0.001
118 parametersΔρmax = 0.21 e Å3
0 restraintsΔρmin = −0.38 e Å3

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 (Å2)

xyzUiso*/Ueq
S11.01959 (12)0.29819 (4)0.80928 (4)0.0375 (2)
N10.4558 (5)0.03847 (13)0.69844 (15)0.0469 (5)
N20.6362 (4)0.11194 (12)0.70868 (14)0.0399 (5)
H20.72750.13050.64320.048*
N30.8801 (4)0.31237 (12)1.01512 (15)0.0374 (4)
N41.2153 (5)0.42105 (13)0.95801 (16)0.0467 (5)
H61.32020.44790.89990.056*
H51.24080.44241.03450.056*
C10.3414 (6)0.02732 (16)0.79596 (19)0.0447 (6)
H10.2103−0.01830.81250.054*
C20.4424 (5)0.09335 (14)0.87253 (17)0.0364 (5)
C30.3893 (5)0.11384 (15)0.98363 (18)0.0425 (5)
H30.26000.07901.02330.051*
C40.5305 (5)0.18567 (15)1.03243 (18)0.0408 (5)
H40.49760.19961.10570.049*
C50.7267 (5)0.23892 (14)0.97160 (16)0.0352 (5)
C61.0420 (5)0.34903 (14)0.94037 (17)0.0354 (5)
C70.7767 (5)0.22046 (13)0.86132 (16)0.0319 (5)
C80.6336 (5)0.14676 (14)0.81177 (16)0.0333 (5)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0429 (4)0.0374 (4)0.0325 (4)−0.0007 (2)0.0051 (2)0.00195 (19)
N10.0621 (14)0.0372 (11)0.0414 (11)−0.0055 (9)0.0022 (9)−0.0022 (8)
N20.0526 (12)0.0365 (10)0.0308 (10)−0.0003 (9)0.0058 (8)−0.0021 (7)
N30.0424 (11)0.0372 (10)0.0326 (10)0.0027 (8)0.0028 (8)−0.0032 (7)
N40.0574 (13)0.0421 (11)0.0405 (11)−0.0088 (9)0.0014 (9)0.0000 (8)
C10.0550 (15)0.0365 (12)0.0426 (13)−0.0047 (10)0.0028 (10)0.0023 (9)
C20.0414 (13)0.0312 (11)0.0367 (11)0.0028 (9)0.0031 (9)0.0043 (8)
C30.0489 (14)0.0417 (13)0.0375 (12)−0.0020 (10)0.0084 (10)0.0051 (9)
C40.0503 (14)0.0439 (13)0.0290 (11)0.0011 (10)0.0091 (10)0.0018 (8)
C50.0385 (12)0.0340 (11)0.0331 (11)0.0060 (9)0.0029 (8)0.0005 (8)
C60.0363 (12)0.0334 (11)0.0364 (11)0.0055 (9)−0.0002 (8)0.0019 (8)
C70.0346 (12)0.0323 (11)0.0289 (10)0.0054 (9)0.0038 (8)0.0016 (8)
C80.0384 (12)0.0312 (11)0.0303 (10)0.0083 (9)0.0011 (8)0.0007 (8)

Geometric parameters (Å, °)

S1—C71.734 (2)C1—C21.418 (3)
S1—C61.760 (2)C1—H10.9300
N1—C11.319 (3)C2—C81.405 (3)
N1—N21.370 (3)C2—C31.411 (3)
N2—C81.354 (3)C3—C41.371 (3)
N2—H20.9500C3—H30.9300
N3—C61.307 (3)C4—C51.419 (3)
N3—C51.391 (3)C4—H40.9300
N4—C61.343 (3)C5—C71.392 (3)
N4—H60.9529C7—C81.400 (3)
N4—H50.9822
C7—S1—C688.59 (10)C2—C3—H3120.4
C1—N1—N2105.85 (18)C3—C4—C5120.3 (2)
C8—N2—N1111.39 (18)C3—C4—H4119.9
C8—N2—H2132.7C5—C4—H4119.9
N1—N2—H2115.8N3—C5—C7115.03 (19)
C6—N3—C5110.62 (18)N3—C5—C4123.89 (19)
C6—N4—H6121.6C7—C5—C4121.1 (2)
C6—N4—H5117.1N3—C6—N4124.3 (2)
H6—N4—H5121.2N3—C6—S1115.53 (17)
N1—C1—C2111.8 (2)N4—C6—S1120.12 (16)
N1—C1—H1124.1C5—C7—C8118.54 (19)
C2—C1—H1124.1C5—C7—S1110.22 (16)
C8—C2—C3120.5 (2)C8—C7—S1131.23 (16)
C8—C2—C1103.94 (19)N2—C8—C7132.6 (2)
C3—C2—C1135.5 (2)N2—C8—C2107.05 (19)
C4—C3—C2119.2 (2)C7—C8—C2120.32 (19)
C4—C3—H3120.4

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2···N3i0.951.922.864 (3)170
N4—H5···N1ii0.982.193.123 (3)158
N4—H6···N1iii0.952.093.019 (3)164

Symmetry codes: (i) x, −y+1/2, z−1/2; (ii) x+1, −y+1/2, z+1/2; (iii) −x+2, y+1/2, −z+3/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HB2931).

References

  • Brandenburg, K. (1999). DIAMOND Crystal Impact GbR, Bonn,Germany.
  • Cagnoli, N., Martani, A. & Fravolini, A. (1968). Ann. Chim pp. 823–837.
  • Chakrabarty, M., Kundu, T., Arima, S. & Harigaya, Y. (2008). Tetrahedron, 64, 6711–6723.
  • Jacobson, R. (1998). Private communication to the Rigaku Corporation, Tokyo, Japan.
  • Martínez, R. & Chacón-García, L. (2005). Curr. Med. Chem 12, 127–151. [PubMed]
  • Rigaku (2002). CrystalClear Rigaku Corporation, Tokyo, Japan.
  • Rigaku/MSC (2004). CrystalStructure Rigaku/MSC, The Woodlands, Texas, USA.
  • Salazar, J. & Dorta, R. (2004). Synlett 7, 1318–1320.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst D65, 148–155. [PMC free article] [PubMed]

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography