1-(6-Nitro-1H-indazol-1-yl)ethanone

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

doi:10.1107/S2414314617008318

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 2| Part 6| June 2017| x170831

https://doi.org/10.1107/S2414314617008318

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access

1-(6-Nitro-1H-indazol-1-yl)ethanone

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

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

Edited by A. J. Lough, University of Toronto, Canada (Received 14 May 2017; accepted 5 June 2017; online 13 June 2017)

In the title molecule, C₉H₇N₃O₃, the indazole moiety is essentially planar and the mean plane of the acetyl substituent is twisted by 5.3 (1)° from its plane. In the crystal, weak C—H⋯O and C—H⋯N hydrogen bonds form layers parallel to (102), which are associated through π-stacking interactions to form a three-dimensional network. The structure was refined as a two-component twin.

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

CCDC reference: 1554341

Structure description

The diverse pharmacological properties exhibited by 1H-indazoles have sparked the emergence of novel methods toward their synthesis. Indazole is a frequently found motif in drug substances with important biological activities such as antimicrobial (Li et al., 2003 ), anti-inflammatory (Lin et al., 2008 ) and anticancer effects (Zhu et al., 2007 ). The crystal structure study of the title compound constitutes a continuation of our previous work on indazole derivatives (Mohamed Abdelahi et al., 2017 ; El Brahmi et al., 2012 ).

The indazole moiety is planar to within 0.0093 (16) Å for (C6) with an r.m.s. deviation from the mean plane of 0.005 Å. The acetyl group is slightly twisted out of the indazole plane, as indicated by the dihedral angle of 5.3 (1)° between it and the N2/C8/C9/O1 plane. This orientation may be due in part to the intramolecular C2—H2⋯O1 hydrogen bond (Table 1 and Fig. 1).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C2—H2⋯O1	0.94 (2)	2.46 (2)	2.929 (2)	111.3 (16)
C4—H4⋯O1ⁱ	0.95 (3)	2.37 (3)	3.213 (2)	148 (2)
C7—H7⋯N1ⁱⁱ	0.95 (2)	2.65 (2)	3.328 (2)	129.2 (18)
Symmetry codes: (i) $[x-1, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]$ ; (ii) -x+1, -y+1, -z+1.

Figure 1
The title molecule with labeling scheme and 50% probability ellipsoids. The intramolecular C—H⋯O interaction is shown by a dashed line.

In the crystal, the molecules form dimers through pairwise C7—H7⋯N1 hydrogen bonds which are linked into sheets parallel to (102) by C4—H4⋯O1 hydrogen bonds (Table 1 and Fig. 2). The sheets stack along the a-axis direction and are associated through head-to-head π-stacking interactions (Fig. 3) with centroid⋯centroid distances of 3.892 (1) Å.

Figure 2
Packing viewed along the a-axis direction with C—H⋯O and C—H⋯N hydrogen bonds shown as dashed lines.

Figure 3
Details of the π-stacking interactions (orange dashed lines) and the intermolecular C—H⋯O and C—H⋯N hydrogen bonds (black dashed lines).

Synthesis and crystallization

A mixture of 6-nitro-1H-indazole (0.6 g, 3 mmol), acetic acid (2 ml) and acetic anhydride (10 ml) were heated under reflux for 24 h. After completion of the reaction (monitored by TLC), the solvent was removed under vacuum. The residue obtained was recrystallized from ethanol to afford the title compound as colorless crystals (yield: 70%).

Refinement

Crystal and refinement details are presented in Table 2. The structure was refined as a two-component twin.

Table 2
Experimental details

Crystal data
Chemical formula	C₉H₇N₃O₃
M_r	205.18
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	150
a, b, c (Å)	3.8919 (1), 20.4831 (6), 11.2580 (4)
β (°)	92.757 (1)
V (Å³)	896.43 (5)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	1.00
Crystal size (mm)	0.25 × 0.18 × 0.07

Data collection
Diffractometer	Bruker D8 VENTURE PHOTON 100 CMOS
Absorption correction	Multi-scan (TWINABS; Sheldrick, 2009 )
T_min, T_max	0.79, 0.93
No. of measured, independent and observed [I > 2σ(I)] reflections	12167, 11998, 9449
R_int	0.038
(sin θ/λ)_max (Å⁻¹)	0.618

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.050, 0.140, 1.03
No. of reflections	11998
No. of parameters	165
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.27, −0.29
Computer programs: APEX3 and SAINT (Bruker, 2016 ), SHELXT (Sheldrick, 2015a ), SHELXL2014/7 (Sheldrick, 2015b ), DIAMOND (Brandenburg & Putz, 2012 ) and SHELXTL (Sheldrick, 2008 ).

Structural data

CCDC reference: 1554341

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314617008318/lh4020sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314617008318/lh4020Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314617008318/lh4020Isup3.cdx

Supporting information file. DOI: https://doi.org/10.1107/S2414314617008318/lh4020Isup4.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: SHELXL2014/7 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

1-(6-Nitro-1H-indazol-1-yl)ethanone top

Crystal data top

C₉H₇N₃O₃	F(000) = 424
M_r = 205.18	D_x = 1.520 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.54178 Å
a = 3.8919 (1) Å	Cell parameters from 7750 reflections
b = 20.4831 (6) Å	θ = 4.3–72.2°
c = 11.2580 (4) Å	µ = 1.00 mm⁻¹
β = 92.757 (1)°	T = 150 K
V = 896.43 (5) Å³	Plate, colourless
Z = 4	0.25 × 0.18 × 0.07 mm

Data collection top

Bruker D8 VENTURE PHOTON 100 CMOS diffractometer	11998 independent reflections
Radiation source: INCOATEC IµS micro-focus source	9449 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.038
Detector resolution: 10.4167 pixels mm^-1	θ_max = 72.2°, θ_min = 4.3°
ω scans	h = −4→4
Absorption correction: multi-scan (TWINABS; Sheldrick, 2009)	k = −25→24
T_min = 0.79, T_max = 0.93	l = −13→13
12167 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)] = 0.050	Hydrogen site location: difference Fourier map
wR(F²) = 0.140	All H-atom parameters refined
S = 1.03	w = 1/[σ²(F_o²) + (0.0691P)² + 0.0964P] where P = (F_o² + 2F_c²)/3
11998 reflections	(Δ/σ)_max < 0.001
165 parameters	Δρ_max = 0.27 e Å⁻³
0 restraints	Δρ_min = −0.29 e Å⁻³

Special details top

Experimental. Analysis of 1886 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 b 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 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. Refined as a 2-component twin.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	1.0289 (4)	0.63313 (7)	0.16899 (13)	0.0386 (4)
O2	0.8908 (5)	0.85449 (7)	0.26601 (14)	0.0455 (5)
O3	0.6050 (5)	0.89484 (7)	0.40880 (16)	0.0489 (5)
N1	0.6127 (4)	0.55971 (8)	0.40377 (15)	0.0325 (4)
N2	0.7342 (4)	0.60698 (7)	0.32890 (14)	0.0267 (4)
N3	0.7188 (4)	0.84860 (7)	0.35434 (15)	0.0324 (4)
C1	0.6747 (5)	0.66903 (8)	0.37279 (16)	0.0243 (4)
C2	0.7481 (5)	0.73060 (8)	0.32808 (16)	0.0252 (4)
H2	0.861 (6)	0.7372 (11)	0.257 (2)	0.032 (6)*
C3	0.6468 (5)	0.78218 (8)	0.39653 (17)	0.0265 (4)
C4	0.4795 (5)	0.77587 (9)	0.50369 (17)	0.0285 (5)
H4	0.420 (6)	0.8142 (13)	0.545 (2)	0.040 (6)*
C5	0.4104 (5)	0.71433 (9)	0.54587 (17)	0.0295 (4)
H5	0.293 (6)	0.7092 (11)	0.621 (2)	0.034 (6)*
C6	0.5103 (5)	0.66033 (9)	0.47964 (16)	0.0262 (4)
C7	0.4820 (5)	0.59099 (10)	0.49217 (18)	0.0323 (5)
H7	0.378 (6)	0.5673 (11)	0.553 (2)	0.038 (6)*
C8	0.9034 (5)	0.59016 (9)	0.22604 (18)	0.0302 (5)
C9	0.9149 (7)	0.51924 (11)	0.1962 (3)	0.0448 (6)
H9A	1.039 (9)	0.4957 (16)	0.261 (3)	0.069 (9)*
H9B	0.693 (11)	0.5004 (16)	0.191 (3)	0.082 (11)*
H9C	1.034 (8)	0.5145 (14)	0.126 (3)	0.060 (8)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0437 (9)	0.0361 (8)	0.0371 (8)	−0.0018 (6)	0.0129 (6)	−0.0027 (6)
O2	0.0670 (11)	0.0297 (8)	0.0409 (9)	−0.0095 (7)	0.0128 (8)	0.0042 (6)
O3	0.0630 (12)	0.0241 (8)	0.0602 (11)	0.0065 (6)	0.0101 (8)	−0.0024 (7)
N1	0.0365 (10)	0.0245 (8)	0.0366 (9)	−0.0034 (6)	0.0023 (7)	0.0061 (6)
N2	0.0303 (9)	0.0209 (7)	0.0289 (8)	−0.0003 (6)	0.0022 (6)	0.0015 (6)
N3	0.0377 (10)	0.0239 (8)	0.0350 (9)	−0.0012 (6)	−0.0043 (7)	−0.0001 (7)
C1	0.0240 (9)	0.0242 (9)	0.0245 (9)	0.0001 (6)	−0.0024 (7)	−0.0002 (7)
C2	0.0262 (10)	0.0253 (9)	0.0240 (9)	−0.0011 (6)	0.0001 (7)	0.0019 (7)
C3	0.0278 (10)	0.0239 (9)	0.0273 (10)	−0.0012 (6)	−0.0035 (8)	0.0019 (7)
C4	0.0285 (10)	0.0292 (10)	0.0276 (10)	0.0026 (7)	−0.0010 (8)	−0.0053 (7)
C5	0.0288 (10)	0.0359 (10)	0.0238 (9)	0.0006 (7)	0.0010 (8)	−0.0006 (7)
C6	0.0249 (10)	0.0288 (9)	0.0248 (9)	−0.0016 (7)	−0.0004 (7)	0.0038 (7)
C7	0.0352 (11)	0.0295 (10)	0.0322 (10)	−0.0035 (7)	0.0029 (8)	0.0064 (8)
C8	0.0273 (10)	0.0303 (10)	0.0328 (10)	0.0018 (7)	0.0007 (8)	−0.0046 (8)
C9	0.0441 (14)	0.0339 (11)	0.0573 (16)	0.0001 (9)	0.0103 (12)	−0.0146 (10)

Geometric parameters (Å, º) top

O1—C8	1.207 (2)	C3—C4	1.404 (3)
O2—N3	1.231 (2)	C4—C5	1.378 (3)
O3—N3	1.223 (2)	C4—H4	0.95 (3)
N1—C7	1.307 (3)	C5—C6	1.399 (3)
N1—N2	1.382 (2)	C5—H5	0.99 (2)
N2—C1	1.387 (2)	C6—C7	1.432 (3)
N2—C8	1.402 (3)	C7—H7	0.95 (2)
N3—C3	1.472 (2)	C8—C9	1.492 (3)
C1—C2	1.393 (2)	C9—H9A	0.98 (3)
C1—C6	1.401 (3)	C9—H9B	0.95 (4)
C2—C3	1.377 (3)	C9—H9C	0.94 (3)
C2—H2	0.94 (2)

C7—N1—N2	106.15 (15)	C4—C5—C6	118.39 (18)
N1—N2—C1	110.90 (15)	C4—C5—H5	119.9 (13)
N1—N2—C8	121.30 (15)	C6—C5—H5	121.7 (13)
C1—N2—C8	127.76 (16)	C5—C6—C1	120.47 (17)
O3—N3—O2	123.58 (17)	C5—C6—C7	134.97 (18)
O3—N3—C3	118.35 (17)	C1—C6—C7	104.55 (16)
O2—N3—C3	118.07 (16)	N1—C7—C6	112.12 (17)
N2—C1—C2	131.33 (18)	N1—C7—H7	119.9 (14)
N2—C1—C6	106.28 (15)	C6—C7—H7	128.0 (14)
C2—C1—C6	122.39 (17)	O1—C8—N2	118.59 (17)
C3—C2—C1	115.06 (18)	O1—C8—C9	125.0 (2)
C3—C2—H2	121.5 (14)	N2—C8—C9	116.44 (18)
C1—C2—H2	123.4 (14)	C8—C9—H9A	109.4 (19)
C2—C3—C4	124.57 (17)	C8—C9—H9B	112 (2)
C2—C3—N3	117.68 (17)	H9A—C9—H9B	105 (3)
C4—C3—N3	117.76 (16)	C8—C9—H9C	108.1 (18)
C5—C4—C3	119.12 (17)	H9A—C9—H9C	109 (3)
C5—C4—H4	122.0 (15)	H9B—C9—H9C	113 (3)
C3—C4—H4	118.8 (15)

C7—N1—N2—C1	−0.2 (2)	N3—C3—C4—C5	−179.61 (16)
C7—N1—N2—C8	177.70 (17)	C3—C4—C5—C6	0.0 (3)
N1—N2—C1—C2	−179.35 (18)	C4—C5—C6—C1	−0.4 (3)
C8—N2—C1—C2	2.9 (3)	C4—C5—C6—C7	−179.1 (2)
N1—N2—C1—C6	0.2 (2)	N2—C1—C6—C5	−179.16 (16)
C8—N2—C1—C6	−177.56 (17)	C2—C1—C6—C5	0.4 (3)
N2—C1—C2—C3	179.40 (18)	N2—C1—C6—C7	−0.1 (2)
C6—C1—C2—C3	−0.1 (3)	C2—C1—C6—C7	179.50 (17)
C1—C2—C3—C4	−0.3 (3)	N2—N1—C7—C6	0.2 (2)
C1—C2—C3—N3	179.68 (15)	C5—C6—C7—N1	178.8 (2)
O3—N3—C3—C2	173.97 (17)	C1—C6—C7—N1	0.0 (2)
O2—N3—C3—C2	−6.0 (3)	N1—N2—C8—O1	−174.05 (18)
O3—N3—C3—C4	−6.0 (3)	C1—N2—C8—O1	3.5 (3)
O2—N3—C3—C4	173.97 (17)	N1—N2—C8—C9	5.6 (3)
C2—C3—C4—C5	0.4 (3)	C1—N2—C8—C9	−176.86 (19)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···O1	0.94 (2)	2.46 (2)	2.929 (2)	111.3 (16)
C4—H4···O1ⁱ	0.95 (3)	2.37 (3)	3.213 (2)	148 (2)
C7—H7···N1ⁱⁱ	0.95 (2)	2.65 (2)	3.328 (2)	129.2 (18)

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

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

Brandenburg, K. & Putz, H. (2012). DIAMOND, Crystal Impact GbR, Bonn, Germany. Google Scholar
Bruker (2016). APEX3, SAINT and SADABS. Bruker AXS, Inc., Madison, Wisconsin, USA. Google Scholar
El Brahmi, N., Benchidmi, M., Essassi, E. M., Ladeira, S. & El Ammari, L. (2012). Acta Cryst. E68, o3368. CSD CrossRef IUCr Journals Google Scholar
Li, X., Chu, S., Feher, V. A., Khalili, M., Nie, Z., Margosiak, S., Nikulin, V., Levin, J., Sprankle, K. G., Tedder, M. E., Almassy, R., Appelt, K. & Yager, K. M. (2003). J. Med. Chem. 46, 5663–5673. Web of Science CrossRef PubMed CAS Google Scholar
Lin, X., Busch-Petersen, V., Deng, J., Edwards, V., Zhang, V. & Kerns, J. K. (2008). Synlett, pp. 3216–3220. Web of Science CrossRef Google Scholar
Mohamed Abdelahi, M. M., El Bakri, Y., Benchidmi, M., Essassi, E. M. & Mague, J. T. (2017). IUCrData, 2, x170432. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sheldrick, G. M. (2009). TWINABS, University of Göttingen, Göttingen, Germany. 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
Zhu, G. D., Gong, J., Gandhi, V. B., Woods, K., Luo, Y., Liu, X., Guan, R., Klinghofer, V., Johnson, E. F., Stoll, V. S., Mamo, M., Li, Q., Rosenberg, S. H. & Giranda, V. L. (2007). Bioorg. Med. Chem. 15, 2441–2452. Web of Science CrossRef PubMed CAS Google Scholar

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

1-(6-Nitro-1H-indazol-1-yl)ethanone

Structure description

Synthesis and crystallization

Refinement

Structural data

Acknowledgements

References

organic compounds