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

Mohamed Abdelahi, M.M.; El Bakri, Y.; Benchidmi, M.; Essassi, E.M.; Mague, J.T.

doi:10.1107/S2414314618001517

organic compounds

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ISSN: 2414-3146

Volume 3| Part 1| January 2018| x180151

https://doi.org/10.1107/S2414314618001517

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

Mohamed Mokhtar Mohamed Abdelahi,^a Youness El Bakri,^a Mohammed Benchidmi,^a ^* El Mokhtar Essassi ^a and Joel T. Mague ^b

^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 π–π 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.

Keywords: crystal structure; indazole; hydrogen bond; π–π stacking.

CCDC reference: 1818813

Structure description

Although rare in nature (Liu et al., 2004 ; Ali et al., 2008 ), indazoles exhibit a variety of biological activities such as HIV protease inhibition (Patel et al., 1999 ), antiarrhythmic and analgesic activities (Mosti et al., 2000 ). As a continuation of our studies of indazole derivatives (Mohamed Abdelahi et al., 2017 ), we report the synthesis and structure of the title compound (Fig. 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 π–π-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). The stacks are associated through C7—H7⋯O1, C8—H8B⋯O2 and C10—H10⋯O2 hydrogen bonds (Table 1 and Figs. 2 and 3).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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
Detail of the intermolecular interactions, viewed along the b-axis direction. C—H⋯O hydrogen bonds are shown as black dashed lines, while π–π stacking interactions are shown as orange dashed lines.

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. The crystal used contained a minor twin component (CELL_NOW; Sheldrick, 2008a ), which was considered sufficiently small to be ignored in the final refinement.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₄H₁₁N₃O₂
M_r	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)
V (Å³)	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 )
T_min, T_max	0.96, 0.98
No. of measured, independent and observed [I > 2σ(I)] reflections	22904, 3223, 2210
R_int	0.056
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.54, −0.27
Computer programs: APEX3 and SAINT (Bruker, 2016), SHELXT (Sheldrick, 2015a ), SHELXL2016 (Sheldrick, 2015b ), DIAMOND (Brandenburg & Putz, 2012 ) and SHELXTL (Sheldrick, 2008b ).

Structural data

CCDC reference: 1818813

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314618001517/hb4206sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314618001517/hb4206Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314618001517/hb4206Isup3.cdx

Supporting information file. DOI: https://doi.org/10.1107/S2414314618001517/hb4206Isup4.cml

checkCIF report

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

C₁₄H₁₁N₃O₂	F(000) = 528
M_r = 253.26	D_x = 1.427 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
a = 4.4890 (19) Å	Cell parameters from 9894 reflections
b = 19.770 (8) Å	θ = 2.6–28.9°
c = 13.308 (6) Å	µ = 0.10 mm⁻¹
β = 93.608 (6)°	T = 100 K
V = 1178.6 (9) Å³	Column, colourless
Z = 4	0.40 × 0.20 × 0.17 mm

Data collection top

Bruker SMART APEX CCD diffractometer	3223 independent reflections
Radiation source: fine-focus sealed tube	2210 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.056
Detector resolution: 8.3333 pixels mm^-1	θ_max = 29.5°, θ_min = 1.9°
φ and ω scans	h = −6→6
Absorption correction: multi-scan (SADABS; Bruker, 2016)	k = 0→27
T_min = 0.96, T_max = 0.98	l = −18→18
22904 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.059	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.150	H-atom parameters constrained
S = 0.96	w = 1/[σ²(F_o²) + (0.0959P)²] where P = (F_o² + 2F_c²)/3
3223 reflections	(Δ/σ)_max < 0.001
172 parameters	Δρ_max = 0.54 e Å⁻³
0 restraints	Δρ_min = −0.26 e Å⁻³

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

	x	y	z	U_iso*/U_eq
O1	1.1690 (3)	0.27750 (6)	0.70851 (9)	0.0254 (3)
O2	1.1457 (3)	0.17253 (6)	0.66604 (9)	0.0314 (3)
N1	0.1797 (3)	0.36929 (6)	0.39590 (9)	0.0156 (3)
N2	0.3722 (3)	0.38443 (6)	0.47413 (9)	0.0164 (3)
N3	1.0647 (3)	0.23134 (6)	0.65597 (10)	0.0193 (3)
C1	0.5118 (3)	0.32514 (7)	0.49448 (11)	0.0143 (3)
C2	0.7354 (3)	0.31196 (7)	0.57032 (11)	0.0152 (3)
H2	0.813941	0.346431	0.614108	0.018*
C3	0.8331 (4)	0.24708 (8)	0.57749 (11)	0.0163 (3)
C4	0.7253 (4)	0.19377 (8)	0.51450 (11)	0.0189 (3)
H4	0.800949	0.149231	0.524440	0.023*
C5	0.5123 (4)	0.20657 (8)	0.43946 (11)	0.0194 (3)
H5	0.440036	0.171504	0.395606	0.023*
C6	0.4017 (4)	0.27289 (7)	0.42839 (11)	0.0153 (3)
C7	0.1870 (3)	0.30481 (7)	0.36564 (11)	0.0171 (3)
H7	0.068645	0.284850	0.311847	0.020*
C8	−0.0081 (3)	0.42330 (8)	0.35141 (11)	0.0179 (3)
H8A	−0.088342	0.450603	0.405911	0.021*
H8B	−0.179168	0.402997	0.311612	0.021*
C9	0.1609 (3)	0.46872 (7)	0.28450 (11)	0.0164 (3)
C10	0.1313 (4)	0.46162 (8)	0.18117 (12)	0.0216 (4)
H10	0.006152	0.427191	0.151969	0.026*
C11	0.2830 (4)	0.50439 (9)	0.11997 (13)	0.0275 (4)
H11	0.259724	0.499660	0.048866	0.033*
C12	0.4678 (4)	0.55385 (8)	0.16192 (13)	0.0269 (4)
H12	0.572625	0.583060	0.119773	0.032*
C13	0.5007 (4)	0.56093 (8)	0.26501 (13)	0.0247 (4)
H13	0.628790	0.594894	0.293986	0.030*
C14	0.3475 (4)	0.51870 (7)	0.32611 (12)	0.0201 (3)
H14	0.369781	0.523851	0.397166	0.024*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0261 (7)	0.0325 (7)	0.0165 (6)	−0.0024 (5)	−0.0068 (5)	0.0013 (5)
O2	0.0377 (8)	0.0312 (7)	0.0244 (7)	0.0144 (5)	−0.0048 (6)	0.0036 (5)
N1	0.0136 (7)	0.0232 (7)	0.0099 (6)	−0.0006 (5)	−0.0010 (5)	0.0022 (5)
N2	0.0166 (7)	0.0223 (6)	0.0099 (6)	0.0001 (5)	−0.0024 (5)	−0.0003 (5)
N3	0.0193 (8)	0.0280 (7)	0.0107 (6)	0.0029 (5)	0.0019 (5)	0.0034 (5)
C1	0.0155 (8)	0.0184 (7)	0.0091 (7)	−0.0018 (6)	0.0014 (5)	0.0005 (5)
C2	0.0150 (8)	0.0220 (7)	0.0086 (7)	−0.0019 (6)	0.0005 (5)	−0.0002 (5)
C3	0.0153 (8)	0.0257 (8)	0.0079 (7)	0.0010 (6)	0.0017 (6)	0.0026 (5)
C4	0.0234 (9)	0.0193 (7)	0.0141 (7)	0.0026 (6)	0.0026 (6)	0.0010 (5)
C5	0.0232 (9)	0.0216 (8)	0.0135 (7)	−0.0023 (6)	0.0023 (6)	−0.0035 (6)
C6	0.0158 (8)	0.0222 (8)	0.0081 (7)	−0.0023 (6)	0.0024 (5)	−0.0005 (5)
C7	0.0168 (8)	0.0220 (7)	0.0124 (7)	−0.0034 (6)	0.0011 (6)	−0.0010 (5)
C8	0.0157 (8)	0.0246 (8)	0.0129 (7)	0.0030 (6)	−0.0018 (6)	0.0027 (5)
C9	0.0154 (8)	0.0191 (7)	0.0146 (7)	0.0049 (6)	−0.0006 (6)	0.0007 (5)
C10	0.0224 (9)	0.0268 (8)	0.0154 (8)	0.0000 (6)	−0.0010 (6)	−0.0006 (6)
C11	0.0294 (11)	0.0384 (9)	0.0148 (8)	0.0023 (7)	0.0029 (7)	0.0054 (7)
C12	0.0246 (10)	0.0288 (9)	0.0280 (10)	0.0016 (7)	0.0072 (7)	0.0101 (7)
C13	0.0240 (10)	0.0188 (8)	0.0312 (10)	0.0001 (6)	−0.0004 (7)	0.0008 (6)
C14	0.0203 (9)	0.0225 (8)	0.0172 (8)	0.0037 (6)	−0.0014 (6)	−0.0006 (6)

Geometric parameters (Å, º) top

O1—N3	1.2245 (17)	C6—C7	1.387 (2)
O2—N3	1.2230 (17)	C7—H7	0.9500
N1—C7	1.3379 (19)	C8—C9	1.503 (2)
N1—N2	1.3441 (17)	C8—H8A	0.9900
N1—C8	1.4623 (19)	C8—H8B	0.9900
N2—C1	1.3487 (19)	C9—C10	1.380 (2)
N3—C3	1.460 (2)	C9—C14	1.388 (2)
C1—C2	1.402 (2)	C10—C11	1.383 (2)
C1—C6	1.425 (2)	C10—H10	0.9500
C2—C3	1.357 (2)	C11—C12	1.378 (3)
C2—H2	0.9500	C11—H11	0.9500
C3—C4	1.413 (2)	C12—C13	1.378 (2)
C4—C5	1.362 (2)	C12—H12	0.9500
C4—H4	0.9500	C13—C14	1.379 (2)
C5—C6	1.406 (2)	C13—H13	0.9500
C5—H5	0.9500	C14—H14	0.9500

C7—N1—N2	114.75 (12)	N1—C7—H7	126.8
C7—N1—C8	126.75 (13)	C6—C7—H7	126.8
N2—N1—C8	118.49 (12)	N1—C8—C9	112.12 (13)
N1—N2—C1	103.29 (12)	N1—C8—H8A	109.2
O2—N3—O1	123.07 (14)	C9—C8—H8A	109.2
O2—N3—C3	118.31 (13)	N1—C8—H8B	109.2
O1—N3—C3	118.61 (13)	C9—C8—H8B	109.2
N2—C1—C2	127.49 (13)	H8A—C8—H8B	107.9
N2—C1—C6	111.56 (14)	C10—C9—C14	119.19 (15)
C2—C1—C6	120.95 (13)	C10—C9—C8	120.59 (14)
C3—C2—C1	116.09 (13)	C14—C9—C8	120.22 (14)
C3—C2—H2	122.0	C9—C10—C11	120.31 (15)
C1—C2—H2	122.0	C9—C10—H10	119.8
C2—C3—C4	124.50 (14)	C11—C10—H10	119.8
C2—C3—N3	117.65 (13)	C12—C11—C10	120.11 (16)
C4—C3—N3	117.85 (14)	C12—C11—H11	119.9
C5—C4—C3	119.65 (14)	C10—C11—H11	119.9
C5—C4—H4	120.2	C13—C12—C11	119.97 (16)
C3—C4—H4	120.2	C13—C12—H12	120.0
C4—C5—C6	118.48 (14)	C11—C12—H12	120.0
C4—C5—H5	120.8	C12—C13—C14	119.98 (16)
C6—C5—H5	120.8	C12—C13—H13	120.0
C7—C6—C5	135.61 (14)	C14—C13—H13	120.0
C7—C6—C1	104.05 (13)	C13—C14—C9	120.44 (15)
C5—C6—C1	120.32 (14)	C13—C14—H14	119.8
N1—C7—C6	106.36 (13)	C9—C14—H14	119.8

C7—N1—N2—C1	0.19 (16)	N2—C1—C6—C5	−177.95 (14)
C8—N1—N2—C1	−178.47 (12)	C2—C1—C6—C5	1.2 (2)
N1—N2—C1—C2	−179.58 (14)	N2—N1—C7—C6	0.16 (17)
N1—N2—C1—C6	−0.48 (16)	C8—N1—C7—C6	178.70 (14)
N2—C1—C2—C3	177.76 (15)	C5—C6—C7—N1	177.76 (17)
C6—C1—C2—C3	−1.3 (2)	C1—C6—C7—N1	−0.43 (16)
C1—C2—C3—C4	0.1 (2)	C7—N1—C8—C9	−101.09 (17)
C1—C2—C3—N3	−179.67 (13)	N2—N1—C8—C9	77.40 (16)
O2—N3—C3—C2	176.93 (14)	N1—C8—C9—C10	101.16 (16)
O1—N3—C3—C2	−3.1 (2)	N1—C8—C9—C14	−79.25 (17)
O2—N3—C3—C4	−2.9 (2)	C14—C9—C10—C11	−0.8 (2)
O1—N3—C3—C4	177.09 (14)	C8—C9—C10—C11	178.78 (15)
C2—C3—C4—C5	1.2 (2)	C9—C10—C11—C12	0.8 (3)
N3—C3—C4—C5	−179.05 (14)	C10—C11—C12—C13	−0.3 (3)
C3—C4—C5—C6	−1.2 (2)	C11—C12—C13—C14	−0.3 (3)
C4—C5—C6—C7	−177.89 (17)	C12—C13—C14—C9	0.3 (2)
C4—C5—C6—C1	0.1 (2)	C10—C9—C14—C13	0.2 (2)
N2—C1—C6—C7	0.58 (17)	C8—C9—C14—C13	−179.36 (14)
C2—C1—C6—C7	179.75 (14)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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−3/2, −y+1/2, z−1/2.

Acknowledgements

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

References

Ali, Z., Ferreira, D., Carvalho, P., Avery, M. A. & Khan, I. A. (2008). J. Nat. Prod. 71, 1111–1112. Web of Science CSD CrossRef PubMed CAS Google Scholar
Brandenburg, K. & Putz, H. (2012). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Bruker (2016). APEX3, SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Liu, Y., Yang, J. & Liu, Q. (2004). Chem. Pharm. Bull. 52, 454–455. Web of Science CrossRef PubMed CAS Google Scholar
Mohamed Abdelahi, M. M., El Bakri, Y., Minnih, M. S., Benchidmi, M., Essassi, E. M. & Mague, J. T. (2017). IUCrData, 2, x170652. Google Scholar
Mosti, L., Menozzi, G., Fossa, P., Filippelli, W., Gessi, S., Rinaldi, B. & Falcone, G. (2000). Arzneim.-Forsch. Drug. Res. 50, 963–972. CAS Google Scholar
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. Web of Science CrossRef PubMed CAS Google Scholar
Sheldrick, G. M. (2008a). CELL_NOW. University of Göttingen, Göttingen, Germany. Google Scholar
Sheldrick, G. M. (2008b). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar

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

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

Structure description

Synthesis and crystallization

Refinement

Structural data

Acknowledgements

References

organic compounds