organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoIUCrDATA
ISSN: 2414-3146

2-Benzyl-6-nitro-2H-indazole

aLaboratoire de Chimie Organique Hétérocyclique, Centre de Recherche des Sciences des médicaments, 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: jalilmostafa202@gmail.com

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 22 January 2018; accepted 23 January 2018; online 31 January 2018)

In the title compound, C14H11N3O2, the indazole portion is planar to within 0.022 (2) Å and subtends a dihedral angle of 65.87 (7)° with the pendant benzene ring. In the crystal, oblique stacks of mol­ecules extending along the a-axis direction are generated by ππ stacking inter­actions between the five- and six-membered rings [centroid–centroid separation = 3.6743 (19) Å] and the stacks are cross-linked by C—H⋯O hydrogen bonds.

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

Structure description

Although rare in nature (Liu et al., 2004[Liu, Y., Yang, J. & Liu, Q. (2004). Chem. Pharm. Bull. 52, 454-455.]; Ali et al., 2008[Ali, Z., Ferreira, D., Carvalho, P., Avery, M. A. & Khan, I. A. (2008). J. Nat. Prod. 71, 1111-1112.]), indazoles exhibit a variety of biological activities such as HIV protease inhibition (Patel et al., 1999[Patel, M., Rodgers, J. D., McHugh, R. J. Jr, Johnson, B. L., Cordova, B. C., Klabe, R. M., Bacheler, L. T., Erickson-Viitanen, S. & Ko, S. S. (1999). Bioorg. Med. Chem. Lett. 9, 3217-3220.]), anti­arrhythmic and analgesic activities (Mosti et al., 2000[Mosti, L., Menozzi, G., Fossa, P., Filippelli, W., Gessi, S., Rinaldi, B. & Falcone, G. (2000). Arzneim.-Forsch. Drug. Res. 50, 963-972.]). As a continuation of our studies of indazole derivatives (Mohamed Abdelahi et al., 2017[Mohamed Abdelahi, M. M., El Bakri, Y., Minnih, M. S., Benchidmi, M., Essassi, E. M. & Mague, J. T. (2017). IUCrData, 2, x170652.]), we report the synthesis and structure of the title compound (Fig. 1[link]).

[Figure 1]
Figure 1
The title mol­ecule, with the atom-labeling scheme and 50% probability displacement ellipsoids.

The indazole portion is almost planar (r.m.s. deviation 0.017 Å) with the atoms farthest from the mean plane being C6 (0.018 (2) Å) and C5 (−0.022 (2) Å). The dihedral angle between the mean plane of the indazole unit and the benzene ring of the benzyl side chain is 65.87 (7)°. The crystal packing involves oblique stacks of mol­ecules extending along the a-axis direction formed by ππ-stacking inter­actions between the five- and six-membered rings of the indazole units with a centroid–centroid distance of 3.6744 (19) Å and a dihedral angle of 1.63 (8)° (Fig. 2[link]). The stacks are associated through C7—H7⋯O1, C8—H8B⋯O2 and C10—H10⋯O2 hydrogen bonds (Table 1[link] and Figs. 2[link] and 3[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C7—H7⋯O1i 0.95 2.51 3.437 (2) 164
C8—H8B⋯O2i 0.99 2.53 3.407 (2) 147
C10—H10⋯O2i 0.95 2.56 3.431 (3) 152
Symmetry code: (i) [x-{\script{3\over 2}}, -y+{\script{1\over 2}}, z-{\script{1\over 2}}].
[Figure 2]
Figure 2
Detail of the inter­molecular inter­actions, viewed along the b-axis direction. C—H⋯O hydrogen bonds are shown as black dashed lines, while ππ stacking inter­actions are shown as orange dashed lines.
[Figure 3]
Figure 3
Packing, viewed along the a-axis direction, with C—H⋯O hydrogen bonds shown as black dashed lines.

Synthesis and crystallization

To a solution of 6-nitro-1H-indazole (1 g, 5 mmol) in tetra­hydro­furan (30 ml) was added benzyl­chloride (0.8 g, 5 mmol), potassium carbonate (1.24 g, 9 mmol) and a catalytic qu­antity of tetra-n-butyl­ammonium iodide. The mixture was stirred at room temperature for 48 h. The solution was filtered and the solvent removed under reduced pressure. The residue was recrystallized from ethanol solution to afford the title compound as colourless crystals (yield: 86%)

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. The crystal used contained a minor twin component (CELL_NOW; Sheldrick, 2008a[Sheldrick, G. M. (2008a). CELL_NOW. University of Göttingen, Göttingen, Germany.]), which was considered sufficiently small to be ignored in the final refinement.

Table 2
Experimental details

Crystal data
Chemical formula C14H11N3O2
Mr 253.26
Crystal system, space group Monoclinic, P21/n
Temperature (K) 100
a, b, c (Å) 4.4890 (19), 19.770 (8), 13.308 (6)
β (°) 93.608 (6)
V3) 1178.6 (9)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.10
Crystal size (mm) 0.40 × 0.20 × 0.17
 
Data collection
Diffractometer Bruker SMART APEX CCD
Absorption correction Multi-scan (SADABS; Bruker, 2016[Bruker (2016). APEX3, SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.96, 0.98
No. of measured, independent and observed [I > 2σ(I)] reflections 22904, 3223, 2210
Rint 0.056
(sin θ/λ)max−1) 0.693
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.059, 0.150, 0.96
No. of reflections 3223
No. of parameters 172
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.54, −0.27
Computer programs: APEX3 and SAINT (Bruker, 2016[Bruker (2016). APEX3, SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2016 (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


Computing details top

Data collection: APEX3 (Bruker, 2016); cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2016 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008b).

2-Benzyl-6-nitro-2H-indazole top
Crystal data top
C14H11N3O2F(000) = 528
Mr = 253.26Dx = 1.427 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 4.4890 (19) ÅCell parameters from 9894 reflections
b = 19.770 (8) Åθ = 2.6–28.9°
c = 13.308 (6) ŵ = 0.10 mm1
β = 93.608 (6)°T = 100 K
V = 1178.6 (9) Å3Column, colourless
Z = 40.40 × 0.20 × 0.17 mm
Data collection top
Bruker SMART APEX CCD
diffractometer
3223 independent reflections
Radiation source: fine-focus sealed tube2210 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.056
Detector resolution: 8.3333 pixels mm-1θmax = 29.5°, θmin = 1.9°
φ and ω scansh = 66
Absorption correction: multi-scan
(SADABS; Bruker, 2016)
k = 027
Tmin = 0.96, Tmax = 0.98l = 1818
22904 measured reflections
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)] = 0.059Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.150H-atom parameters constrained
S = 0.96 w = 1/[σ2(Fo2) + (0.0959P)2]
where P = (Fo2 + 2Fc2)/3
3223 reflections(Δ/σ)max < 0.001
172 parametersΔρmax = 0.54 e Å3
0 restraintsΔρmin = 0.26 e Å3
Special details top

Experimental. The diffraction data were obtained from 3 sets of 400 frames, each of width 0.5° in ω, colllected at φ = 0.00, 90.00 and 180.00° and 2 sets of 800 frames, each of width 0.45° in φ, collected at ω = –30.00 and 210.00°. The scan time was 20 sec/frame.

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. H-atoms attached to carbon were placed in calculated positions (C—H = 0.95 - 0.99 Å). All were included as riding contributions with isotropic displacement parameters 1.2 times those of the attached atoms.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O11.1690 (3)0.27750 (6)0.70851 (9)0.0254 (3)
O21.1457 (3)0.17253 (6)0.66604 (9)0.0314 (3)
N10.1797 (3)0.36929 (6)0.39590 (9)0.0156 (3)
N20.3722 (3)0.38443 (6)0.47413 (9)0.0164 (3)
N31.0647 (3)0.23134 (6)0.65597 (10)0.0193 (3)
C10.5118 (3)0.32514 (7)0.49448 (11)0.0143 (3)
C20.7354 (3)0.31196 (7)0.57032 (11)0.0152 (3)
H20.8139410.3464310.6141080.018*
C30.8331 (4)0.24708 (8)0.57749 (11)0.0163 (3)
C40.7253 (4)0.19377 (8)0.51450 (11)0.0189 (3)
H40.8009490.1492310.5244400.023*
C50.5123 (4)0.20657 (8)0.43946 (11)0.0194 (3)
H50.4400360.1715040.3956060.023*
C60.4017 (4)0.27289 (7)0.42839 (11)0.0153 (3)
C70.1870 (3)0.30481 (7)0.36564 (11)0.0171 (3)
H70.0686450.2848500.3118470.020*
C80.0081 (3)0.42330 (8)0.35141 (11)0.0179 (3)
H8A0.0883420.4506030.4059110.021*
H8B0.1791680.4029970.3116120.021*
C90.1609 (3)0.46872 (7)0.28450 (11)0.0164 (3)
C100.1313 (4)0.46162 (8)0.18117 (12)0.0216 (4)
H100.0061520.4271910.1519690.026*
C110.2830 (4)0.50439 (9)0.11997 (13)0.0275 (4)
H110.2597240.4996600.0488660.033*
C120.4678 (4)0.55385 (8)0.16192 (13)0.0269 (4)
H120.5726250.5830600.1197730.032*
C130.5007 (4)0.56093 (8)0.26501 (13)0.0247 (4)
H130.6287900.5948940.2939860.030*
C140.3475 (4)0.51870 (7)0.32611 (12)0.0201 (3)
H140.3697810.5238510.3971660.024*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0261 (7)0.0325 (7)0.0165 (6)0.0024 (5)0.0068 (5)0.0013 (5)
O20.0377 (8)0.0312 (7)0.0244 (7)0.0144 (5)0.0048 (6)0.0036 (5)
N10.0136 (7)0.0232 (7)0.0099 (6)0.0006 (5)0.0010 (5)0.0022 (5)
N20.0166 (7)0.0223 (6)0.0099 (6)0.0001 (5)0.0024 (5)0.0003 (5)
N30.0193 (8)0.0280 (7)0.0107 (6)0.0029 (5)0.0019 (5)0.0034 (5)
C10.0155 (8)0.0184 (7)0.0091 (7)0.0018 (6)0.0014 (5)0.0005 (5)
C20.0150 (8)0.0220 (7)0.0086 (7)0.0019 (6)0.0005 (5)0.0002 (5)
C30.0153 (8)0.0257 (8)0.0079 (7)0.0010 (6)0.0017 (6)0.0026 (5)
C40.0234 (9)0.0193 (7)0.0141 (7)0.0026 (6)0.0026 (6)0.0010 (5)
C50.0232 (9)0.0216 (8)0.0135 (7)0.0023 (6)0.0023 (6)0.0035 (6)
C60.0158 (8)0.0222 (8)0.0081 (7)0.0023 (6)0.0024 (5)0.0005 (5)
C70.0168 (8)0.0220 (7)0.0124 (7)0.0034 (6)0.0011 (6)0.0010 (5)
C80.0157 (8)0.0246 (8)0.0129 (7)0.0030 (6)0.0018 (6)0.0027 (5)
C90.0154 (8)0.0191 (7)0.0146 (7)0.0049 (6)0.0006 (6)0.0007 (5)
C100.0224 (9)0.0268 (8)0.0154 (8)0.0000 (6)0.0010 (6)0.0006 (6)
C110.0294 (11)0.0384 (9)0.0148 (8)0.0023 (7)0.0029 (7)0.0054 (7)
C120.0246 (10)0.0288 (9)0.0280 (10)0.0016 (7)0.0072 (7)0.0101 (7)
C130.0240 (10)0.0188 (8)0.0312 (10)0.0001 (6)0.0004 (7)0.0008 (6)
C140.0203 (9)0.0225 (8)0.0172 (8)0.0037 (6)0.0014 (6)0.0006 (6)
Geometric parameters (Å, º) top
O1—N31.2245 (17)C6—C71.387 (2)
O2—N31.2230 (17)C7—H70.9500
N1—C71.3379 (19)C8—C91.503 (2)
N1—N21.3441 (17)C8—H8A0.9900
N1—C81.4623 (19)C8—H8B0.9900
N2—C11.3487 (19)C9—C101.380 (2)
N3—C31.460 (2)C9—C141.388 (2)
C1—C21.402 (2)C10—C111.383 (2)
C1—C61.425 (2)C10—H100.9500
C2—C31.357 (2)C11—C121.378 (3)
C2—H20.9500C11—H110.9500
C3—C41.413 (2)C12—C131.378 (2)
C4—C51.362 (2)C12—H120.9500
C4—H40.9500C13—C141.379 (2)
C5—C61.406 (2)C13—H130.9500
C5—H50.9500C14—H140.9500
C7—N1—N2114.75 (12)N1—C7—H7126.8
C7—N1—C8126.75 (13)C6—C7—H7126.8
N2—N1—C8118.49 (12)N1—C8—C9112.12 (13)
N1—N2—C1103.29 (12)N1—C8—H8A109.2
O2—N3—O1123.07 (14)C9—C8—H8A109.2
O2—N3—C3118.31 (13)N1—C8—H8B109.2
O1—N3—C3118.61 (13)C9—C8—H8B109.2
N2—C1—C2127.49 (13)H8A—C8—H8B107.9
N2—C1—C6111.56 (14)C10—C9—C14119.19 (15)
C2—C1—C6120.95 (13)C10—C9—C8120.59 (14)
C3—C2—C1116.09 (13)C14—C9—C8120.22 (14)
C3—C2—H2122.0C9—C10—C11120.31 (15)
C1—C2—H2122.0C9—C10—H10119.8
C2—C3—C4124.50 (14)C11—C10—H10119.8
C2—C3—N3117.65 (13)C12—C11—C10120.11 (16)
C4—C3—N3117.85 (14)C12—C11—H11119.9
C5—C4—C3119.65 (14)C10—C11—H11119.9
C5—C4—H4120.2C13—C12—C11119.97 (16)
C3—C4—H4120.2C13—C12—H12120.0
C4—C5—C6118.48 (14)C11—C12—H12120.0
C4—C5—H5120.8C12—C13—C14119.98 (16)
C6—C5—H5120.8C12—C13—H13120.0
C7—C6—C5135.61 (14)C14—C13—H13120.0
C7—C6—C1104.05 (13)C13—C14—C9120.44 (15)
C5—C6—C1120.32 (14)C13—C14—H14119.8
N1—C7—C6106.36 (13)C9—C14—H14119.8
C7—N1—N2—C10.19 (16)N2—C1—C6—C5177.95 (14)
C8—N1—N2—C1178.47 (12)C2—C1—C6—C51.2 (2)
N1—N2—C1—C2179.58 (14)N2—N1—C7—C60.16 (17)
N1—N2—C1—C60.48 (16)C8—N1—C7—C6178.70 (14)
N2—C1—C2—C3177.76 (15)C5—C6—C7—N1177.76 (17)
C6—C1—C2—C31.3 (2)C1—C6—C7—N10.43 (16)
C1—C2—C3—C40.1 (2)C7—N1—C8—C9101.09 (17)
C1—C2—C3—N3179.67 (13)N2—N1—C8—C977.40 (16)
O2—N3—C3—C2176.93 (14)N1—C8—C9—C10101.16 (16)
O1—N3—C3—C23.1 (2)N1—C8—C9—C1479.25 (17)
O2—N3—C3—C42.9 (2)C14—C9—C10—C110.8 (2)
O1—N3—C3—C4177.09 (14)C8—C9—C10—C11178.78 (15)
C2—C3—C4—C51.2 (2)C9—C10—C11—C120.8 (3)
N3—C3—C4—C5179.05 (14)C10—C11—C12—C130.3 (3)
C3—C4—C5—C61.2 (2)C11—C12—C13—C140.3 (3)
C4—C5—C6—C7177.89 (17)C12—C13—C14—C90.3 (2)
C4—C5—C6—C10.1 (2)C10—C9—C14—C130.2 (2)
N2—C1—C6—C70.58 (17)C8—C9—C14—C13179.36 (14)
C2—C1—C6—C7179.75 (14)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C7—H7···O1i0.952.513.437 (2)164
C8—H8B···O2i0.992.533.407 (2)147
C10—H10···O2i0.952.563.431 (3)152
Symmetry code: (i) x3/2, y+1/2, z1/2.
 

Acknowledgements

JTM thanks Tulane University for support of the Tulane Crystallography Laboratory.

References

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