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ISSN: 2414-3146

5-Nitro-1-(prop-2-yn-1-yl)-1H-indazole

aLaboratoire de Chimie Organique Hétérocyclique, URAC 21, Pôle de Compétence Pharmacochimie, Av. Ibn Battouta, BP 1014, Faculté des Sciences, Université Mohammed V, Rabat, Morocco, and bDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA
*Correspondence e-mail: mboulhaoua@gmail.com

Edited by O. Blacque, University of Zürich, Switzerland (Received 15 March 2016; accepted 21 March 2016; online 24 March 2016)

The packing of the title mol­ecule, C10H7N3O2, features the formation of weak dimers via pairwise C—H⋯O inter­actions across centers of symmetry. The prop-2-yn-1-yl moiety is twisted out of the plane of the indazole unit by 78.53 (17)°.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

Recently there has been considerable inter­est in the chemistry of indazoles. This is undoubtedly due to a broad variety of biological functions of indazole derivatives such as anti-inflammatory (Schmidt et al., 2008[Schmidt, A., Beutler, A. & Snovydovych, B. (2008). Eur. J. Org. Chem. pp. 4073-4095.]), anti­bacterial (Shafakat Ali et al., 2012[Shafakat Ali, N. a., Zakir, S., Patel, M. & Farooqui, M. (2012). Eur. J. Med. Chem. 50, 39-43.]) and anti­tumor activities (Abbassi et al., 2014[Abbassi, N., Rakib, E. M., Chicha, H., Bouissane, L., Hannioui, A., Aiello, C., Gangemi, R., Castagnola, P., Rosano, C. & Viale, M. (2014). Arch. Pharm. Chem. Life Sci. 347, 423-431.]). The present work is a continuation of our work on indazole derivatives (El Brahmi et al., 2011[El Brahmi, N., Benchidmi, M., Essassi, E. M., Ladeira, S. & Ng, S. W. (2011). Acta Cryst. E67, o3260.]). In contrast to 1-(5-nitro-1H-indazol-1-yl)ethanone, the nitro group here is within a degree of planarity with the indazole moiety (Fig. 1[link]). However, the prop-2-yn-1-yl moiety is twisted out of the plane of the indazole unit by 78.53 (17)°. In the crystal, mol­ecules are linked by pairs of C3—H3⋯O2 inter­actions, forming inversion dimers (Fig. 2[link] and Table 1[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C3—H3⋯O2i 0.95 2.47 3.298 (2) 146
Symmetry code: (i) -x+2, -y+1, -z+1.
[Figure 1]
Figure 1
The title mol­ecule with the atom-labeling scheme and 50% probability ellipsoids.
[Figure 2]
Figure 2
Packing viewed down the a axis with C—H⋯O inter­actions shown as dotted lines.

Synthesis and crystallization

To a solution of 5-nitro-1H-indazole (1 g, 6.13 mmol) in acetone (30 ml) was added potassium hydroxide (0.38 g, 6.8 mmol). After 15 min of stirring at room temperature, propargyl bromide (1.09 ml, 12.26 mmol) was added dropwise. Upon disappearance of the starting material as indicated by TLC, the resulting mixture was evaporated. The crude material was dissolved with EtOAc (50 ml), washed with water and brine, dried over MgSO4 and the solvent was evaporated in vacuo. The resulting residue was purified by column chromatography (EtOAc/hexane 1/9). The title compound was recrystallized from ethanol at room temperature giving colorless crystals (yield: 57%; m.p. 355–357 K).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. Trial refinements with both the single component reflection file extracted from the full data set by TWINABS and with the full twinned data set indicated that the former refinement gave better results, as judged by lower values for R1, wR2, su's and residual features in the final difference map.

Table 2
Experimental details

Crystal data
Chemical formula C10H7N3O2
Mr 201.19
Crystal system, space group Monoclinic, P21/n
Temperature (K) 150
a, b, c (Å) 4.0105 (1), 21.0705 (7), 10.7451 (4)
β (°) 96.323 (2)
V3) 902.47 (5)
Z 4
Radiation type Cu Kα
μ (mm−1) 0.90
Crystal size (mm) 0.22 × 0.17 × 0.14
 
Data collection
Diffractometer Bruker D8 VENTURE PHOTON 100 CMOS
Absorption correction Multi-scan (TWINABS; Sheldrick, 2009[Sheldrick, G. M. (2009). TWINABS. University of Göttingen, Germany.])
Tmin, Tmax 0.58, 0.88
No. of measured, independent and observed [I > 2σ(I)] reflections 11748, 1747, 1561
Rint 0.045
(sin θ/λ)max−1) 0.618
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.044, 0.124, 1.04
No. of reflections 1747
No. of parameters 141
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.22, −0.21
Computer programs: APEX3 and SAINT (Bruker, 2016[Bruker (2016). APEX3, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), CELL_NOW (Sheldrick, 2008a[Sheldrick, G. M. (2008a). CELL_NOW. University of Göttingen, Germany.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2014 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), DIAMOND (Brandenburg & Putz, 2012[Brandenburg, K. & Putz, H. (2012). DIAMOND. Crystal Impact GbR, Bonn, Germany.]) and SHELXTL (Sheldrick, 2008b[Sheldrick, G. M. (2008b). Acta Cryst. A64, 112-122.]).

Structural data


Experimental top

To a solution of 5-nitro-1H-indazole (1 g, 6.13 mmol) in acetone (30 ml) was added potassium hydroxide (0.38 g, 6.8 mmol). After 15 min of stirring at room temperature, propargyl bromide (1.09 ml, 12.26 mmol) was added dropwise. Upon disappearance of the starting material as indicated by TLC, the resulting mixture was evaporated. The crude material was dissolved with EtOAc (50 ml), washed with water and brine, dried over MgSO4 and the solvent was evaporated in vacuo. The resulting residue was purified by column chromatography (EtOAc/hexane 1/9). The title compound was recrystallized from ethanol at room temperature giving colorless crystals (yield: 57%; m.p. 355–357 K).

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 2. Trial refinements with both the single component reflection file extracted from the full data set by TWINABS and with the full twinned data set indicated that the former refinement gave better results, as judged by lower values for R1, wR2, su's and residual features in the final difference map.

Structure description top

Recently there has been considerable interest in the chemistry of indazoles. This is undoubtedly due to a broad variety of biological functions of indazole derivatives such as anti-inflammatory (Schmidt et al., 2008), antibacterial (Shafakat Ali et al., 2012) and antitumor activities (Abbassi et al., 2014). The present work is a continuation of our work on indazole derivatives (El Brahmi et al., 2011). In contrast to 1-(5-nitro-1H-indazol-1-yl)ethanone, the nitro group here is within a degree of planarity with the indazole moiety (Fig. 1). However, the prop-2-yn-1-yl moiety is twisted out of the plane of the indazole unit by 78.53 (17)°. In the crystal, the molecules form weak dimers via pairwise C3—H3···O2 interactions across centers of symmetry (Fig. 2 and Table 1).

Computing details top

Data collection: APEX3 (Bruker, 2016); cell refinement: SAINT (Bruker, 2016) and CELL_NOW (Sheldrick, 2008a); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008b).

Figures top
[Figure 1] Fig. 1. The title molecule with the atom-labeling scheme and 50% probability ellipsoids.
[Figure 2] Fig. 2. Packing viewed down the a axis with C—H···O interactions shown as dotted lines.
5-Nitro-1-(prop-2-yn-1-yl)-1H-indazole top
Crystal data top
C10H7N3O2F(000) = 416
Mr = 201.19Dx = 1.481 Mg m3
Monoclinic, P21/nCu Kα radiation, λ = 1.54178 Å
a = 4.0105 (1) ÅCell parameters from 6907 reflections
b = 21.0705 (7) Åθ = 4.2–72.4°
c = 10.7451 (4) ŵ = 0.90 mm1
β = 96.323 (2)°T = 150 K
V = 902.47 (5) Å3Block, colourless
Z = 40.22 × 0.17 × 0.14 mm
Data collection top
Bruker D8 VENTURE PHOTON 100 CMOS
diffractometer
1747 independent reflections
Radiation source: INCOATEC IµS micro–focus source1561 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.045
Detector resolution: 10.4167 pixels mm-1θmax = 72.4°, θmin = 4.2°
ω scansh = 44
Absorption correction: multi-scan
(TWINABS; Sheldrick, 2009)
k = 2626
Tmin = 0.58, Tmax = 0.88l = 122
11748 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.044H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.124 w = 1/[σ2(Fo2) + (0.0769P)2 + 0.2542P]
where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
1747 reflectionsΔρmax = 0.22 e Å3
141 parametersΔρmin = 0.20 e Å3
0 restraintsExtinction correction: SHELXL2014 (Sheldrick, 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0086 (15)
Crystal data top
C10H7N3O2V = 902.47 (5) Å3
Mr = 201.19Z = 4
Monoclinic, P21/nCu Kα radiation
a = 4.0105 (1) ŵ = 0.90 mm1
b = 21.0705 (7) ÅT = 150 K
c = 10.7451 (4) Å0.22 × 0.17 × 0.14 mm
β = 96.323 (2)°
Data collection top
Bruker D8 VENTURE PHOTON 100 CMOS
diffractometer
1747 independent reflections
Absorption correction: multi-scan
(TWINABS; Sheldrick, 2009)
1561 reflections with I > 2σ(I)
Tmin = 0.58, Tmax = 0.88Rint = 0.045
11748 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0440 restraints
wR(F2) = 0.124H atoms treated by a mixture of independent and constrained refinement
S = 1.04Δρmax = 0.22 e Å3
1747 reflectionsΔρmin = 0.20 e Å3
141 parameters
Special details top

Experimental. Analysis of 644 reflections having I/σ(I) > 12 and chosen from the full data set with CELL_NOW (Sheldrick, 2008) showed the crystal to belong to the monoclinic system and to be twinned by a 180° rotation about the a axis. The raw data were processed using the multi-component version of SAINT under control of the two-component orientation file generated by CELL_NOW.

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. H-atoms attached to aromatic and carbon atoms were placed in calculated positions (C—H = 0.95 − 0.99 Å) and included as riding contributions with isotropic displacement parameters 1.2 times those of the attached atoms. Trial refinements with both the single component reflection file extracted from the full data set by TWINABS and with the full twinned data set indicated that the former refinement gave better results as judged by lower values for R1, wR2, su's and residual features in the final difference map.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.6905 (4)0.49477 (6)0.13174 (12)0.0456 (4)
O20.9003 (3)0.52591 (5)0.31507 (11)0.0416 (4)
N10.2066 (3)0.28236 (6)0.47196 (12)0.0268 (3)
N20.3207 (4)0.29212 (6)0.59556 (12)0.0315 (3)
N30.7330 (3)0.48851 (6)0.24594 (13)0.0299 (3)
C10.4940 (4)0.34546 (7)0.59953 (15)0.0318 (4)
H10.60220.36380.67400.038*
C20.4980 (4)0.37187 (7)0.47786 (14)0.0255 (3)
C30.6386 (4)0.42590 (7)0.42929 (14)0.0261 (4)
H30.76580.45560.48150.031*
C40.5824 (4)0.43369 (6)0.30145 (14)0.0251 (4)
C50.3948 (4)0.39102 (7)0.22039 (14)0.0272 (4)
H50.36510.39900.13290.033*
C60.2552 (4)0.33801 (7)0.26761 (14)0.0262 (4)
H60.12800.30870.21460.031*
C70.3087 (4)0.32901 (6)0.39784 (15)0.0241 (3)
C80.0010 (4)0.22729 (7)0.43653 (16)0.0305 (4)
H8A0.12520.23490.35300.037*
H8B0.16770.22210.49720.037*
C90.1934 (4)0.16838 (7)0.43243 (14)0.0276 (4)
C100.3423 (4)0.12015 (7)0.42753 (16)0.0327 (4)
H100.462 (5)0.0839 (10)0.4232 (18)0.043 (6)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0688 (10)0.0379 (7)0.0298 (6)0.0131 (6)0.0035 (6)0.0046 (5)
O20.0524 (8)0.0313 (6)0.0400 (7)0.0131 (5)0.0002 (6)0.0025 (5)
N10.0272 (7)0.0240 (6)0.0296 (7)0.0018 (5)0.0058 (5)0.0004 (5)
N20.0380 (8)0.0301 (7)0.0269 (7)0.0044 (5)0.0055 (6)0.0007 (5)
N30.0340 (7)0.0247 (7)0.0312 (7)0.0007 (5)0.0046 (5)0.0007 (5)
C10.0400 (9)0.0278 (8)0.0276 (8)0.0028 (6)0.0039 (7)0.0011 (6)
C20.0273 (7)0.0225 (7)0.0268 (8)0.0043 (5)0.0040 (6)0.0036 (6)
C30.0284 (8)0.0221 (7)0.0274 (8)0.0030 (5)0.0017 (6)0.0048 (6)
C40.0252 (8)0.0209 (7)0.0296 (8)0.0029 (5)0.0052 (6)0.0011 (6)
C50.0287 (8)0.0282 (8)0.0251 (7)0.0028 (5)0.0042 (6)0.0026 (6)
C60.0246 (8)0.0267 (7)0.0274 (8)0.0007 (5)0.0033 (6)0.0055 (6)
C70.0233 (7)0.0208 (7)0.0291 (8)0.0043 (5)0.0066 (6)0.0018 (5)
C80.0258 (8)0.0265 (7)0.0402 (9)0.0016 (6)0.0082 (6)0.0001 (6)
C90.0299 (8)0.0266 (8)0.0268 (8)0.0042 (6)0.0058 (6)0.0014 (6)
C100.0374 (9)0.0265 (8)0.0342 (9)0.0022 (6)0.0031 (7)0.0020 (6)
Geometric parameters (Å, º) top
O1—N31.2272 (18)C3—H30.9500
O2—N31.2302 (18)C4—C51.410 (2)
N1—C71.3564 (19)C5—C61.372 (2)
N1—N21.3718 (18)C5—H50.9500
N1—C81.4542 (19)C6—C71.405 (2)
N2—C11.320 (2)C6—H60.9500
N3—C41.4608 (19)C8—C91.469 (2)
C1—C21.423 (2)C8—H8A0.9900
C1—H10.9500C8—H8B0.9900
C2—C31.397 (2)C9—C101.183 (2)
C2—C71.410 (2)C10—H100.91 (2)
C3—C41.377 (2)
C7—N1—N2111.70 (12)C5—C4—N3117.93 (13)
C7—N1—C8128.73 (14)C6—C5—C4120.17 (14)
N2—N1—C8119.56 (13)C6—C5—H5119.9
C1—N2—N1106.10 (13)C4—C5—H5119.9
O1—N3—O2122.77 (13)C5—C6—C7117.03 (14)
O1—N3—C4118.37 (13)C5—C6—H6121.5
O2—N3—C4118.85 (13)C7—C6—H6121.5
N2—C1—C2111.26 (14)N1—C7—C6131.27 (14)
N2—C1—H1124.4N1—C7—C2106.46 (14)
C2—C1—H1124.4C6—C7—C2122.28 (14)
C3—C2—C7120.44 (14)N1—C8—C9113.07 (13)
C3—C2—C1135.07 (14)N1—C8—H8A109.0
C7—C2—C1104.48 (14)C9—C8—H8A109.0
C4—C3—C2116.19 (14)N1—C8—H8B109.0
C4—C3—H3121.9C9—C8—H8B109.0
C2—C3—H3121.9H8A—C8—H8B107.8
C3—C4—C5123.89 (14)C10—C9—C8178.21 (17)
C3—C4—N3118.16 (13)C9—C10—H10178.1 (14)
C7—N1—N2—C10.38 (17)N3—C4—C5—C6178.43 (13)
C8—N1—N2—C1178.83 (13)C4—C5—C6—C70.0 (2)
N1—N2—C1—C20.14 (18)N2—N1—C7—C6179.25 (14)
N2—C1—C2—C3179.98 (16)C8—N1—C7—C61.6 (3)
N2—C1—C2—C70.13 (18)N2—N1—C7—C20.47 (16)
C7—C2—C3—C40.4 (2)C8—N1—C7—C2178.66 (13)
C1—C2—C3—C4179.45 (16)C5—C6—C7—N1179.96 (14)
C2—C3—C4—C50.2 (2)C5—C6—C7—C20.3 (2)
C2—C3—C4—N3178.21 (12)C3—C2—C7—N1179.74 (13)
O1—N3—C4—C3178.20 (14)C1—C2—C7—N10.35 (16)
O2—N3—C4—C30.8 (2)C3—C2—C7—C60.5 (2)
O1—N3—C4—C50.3 (2)C1—C2—C7—C6179.39 (14)
O2—N3—C4—C5179.27 (14)C7—N1—C8—C9102.40 (18)
C3—C4—C5—C60.1 (2)N2—N1—C8—C978.53 (17)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C3—H3···O2i0.952.473.298 (2)146
Symmetry code: (i) x+2, y+1, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C3—H3···O2i0.952.473.298 (2)146
Symmetry code: (i) x+2, y+1, z+1.

Experimental details

Crystal data
Chemical formulaC10H7N3O2
Mr201.19
Crystal system, space groupMonoclinic, P21/n
Temperature (K)150
a, b, c (Å)4.0105 (1), 21.0705 (7), 10.7451 (4)
β (°) 96.323 (2)
V3)902.47 (5)
Z4
Radiation typeCu Kα
µ (mm1)0.90
Crystal size (mm)0.22 × 0.17 × 0.14
Data collection
DiffractometerBruker D8 VENTURE PHOTON 100 CMOS
Absorption correctionMulti-scan
(TWINABS; Sheldrick, 2009)
Tmin, Tmax0.58, 0.88
No. of measured, independent and
observed [I > 2σ(I)] reflections
11748, 1747, 1561
Rint0.045
(sin θ/λ)max1)0.618
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.044, 0.124, 1.04
No. of reflections1747
No. of parameters141
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.22, 0.20

Computer programs: APEX3 (Bruker, 2016), SAINT (Bruker, 2016) and CELL_NOW (Sheldrick, 2008a), SAINT (Bruker, 2016), SHELXT (Sheldrick, 2015a), SHELXL2014 (Sheldrick, 2015b), DIAMOND (Brandenburg & Putz, 2012), SHELXTL (Sheldrick, 2008b).

 

Acknowledgements

The support of NSF-MRI Grant No. 1228232 for the purchase of the diffractometer and Tulane University for support of the Tulane Crystallography Laboratory are gratefully acknowledged.

References

First citationAbbassi, N., Rakib, E. M., Chicha, H., Bouissane, L., Hannioui, A., Aiello, C., Gangemi, R., Castagnola, P., Rosano, C. & Viale, M. (2014). Arch. Pharm. Chem. Life Sci. 347, 423–431.  Web of Science CrossRef CAS Google Scholar
First citationBrandenburg, K. & Putz, H. (2012). DIAMOND. Crystal Impact GbR, Bonn, Germany.  Google Scholar
First citationBruker (2016). APEX3, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationEl Brahmi, N., Benchidmi, M., Essassi, E. M., Ladeira, S. & Ng, S. W. (2011). Acta Cryst. E67, o3260.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationShafakat Ali, N. a., Zakir, S., Patel, M. & Farooqui, M. (2012). Eur. J. Med. Chem. 50, 39–43.  PubMed Google Scholar
First citationSchmidt, A., Beutler, A. & Snovydovych, B. (2008). Eur. J. Org. Chem. pp. 4073–4095.  Web of Science CrossRef Google Scholar
First citationSheldrick, G. M. (2008a). CELL_NOW. University of Göttingen, Germany.  Google Scholar
First citationSheldrick, G. M. (2008b). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSheldrick, G. M. (2009). TWINABS. University of Göttingen, Germany.  Google Scholar
First citationSheldrick, G. M. (2015a). Acta Cryst. A71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar

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