1-Chloro-3-(6-nitro-1H-indazol-1-yl)propan-2-ol

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

doi:10.1107/S241431461700637X

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 2| Part 5| May 2017| x170637

https://doi.org/10.1107/S241431461700637X

Open

access

1-Chloro-3-(6-nitro-1H-indazol-1-yl)propan-2-ol

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, 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 J. Simpson, University of Otago, New Zealand (Received 20 April 2017; accepted 27 April 2017; online 5 May 2017)

In the title compound, C₁₀H₁₀ClN₃O₃, the side chain is oriented nearly perpendicular to the mean plane of the indazole ring system. In the crystal, complementary sets of O—H⋯N and C—H⋯O hydrogen bonds form chains of molecules stacked along the a-axis direction

Keywords: crystal structure; indazole; hydrogen bond.

CCDC reference: 1546601

Structure description

Indazoles and their derivatives have gained considerable importance in medicinal chemistry in view of their promising pharmacological properties (Caron & Vazquez, 1999 ; Yeu et al., 2001 ). Substituted indazoles are especially important sub-structures and these compounds are present in numerous pharmacophores including antitumor, antiplatelet, anti-viral and anti-microbial agents (Abbassi et al., 2014 ).

In the title compound (Fig. 1), the indazole moiety is planar with an r.m.s. deviation of 0.0046 Å. The C1—N1—C8—C9 torsion angle of −81.0 (2)° indicates that the side chain is close to perpendicular to the indazole plane. In the crystal, inversion-related O3—H3⋯N2ⁱ hydrogen bonds form dimers enclosing R₂²(12) rings (Table 1 and Fig. 2). Non-classical C2—H2⋯Oⁱⁱ hydrogen bonds also form inversion dimers and R₂²(10) rings. These contacts combine to link molecules in a head-to-tail fashion into chains along the c-axis direction. Additional C10—H10A⋯O3ⁱⁱⁱ hydrogen bonds link adjacent chains, stacking molecules along the a-axis direction (Table 1 and Fig. 3).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O3—H3⋯N2ⁱ	1.00	1.88	2.871 (2)	169
C2—H2⋯O1ⁱⁱ	0.93	2.59	3.492 (3)	163
C10—H10A⋯O3ⁱⁱⁱ	0.97	2.49	3.268 (3)	137
Symmetry codes: (i) -x+1, -y+1, -z; (ii) -x+1, -y+1, -z+1; (iii) x-1, y, z.

Figure 1
The title molecule with labeling scheme and 30% probability ellipsoids.

Figure 2
Chains of molecules formed along c by O—H⋯N and C—H⋯O hydrogen bonds shown as red and black dotted lines, respectively.

Figure 3
Molecules stacked along the a-axis direction by O—H⋯N and C—H⋯O hydrogen bonds shown as red and black dashed lines, respectively.

Synthesis and crystallization

To a solution of 6-nitroindazole (0.01 mol, 0.5 g) in tetrahydrofuran (40 ml), was added potassium bicarbonate (0.02 mol, 2.76 g), 2-(chloromethyl)oxirane (0.02 mol, 1.2 ml) and tetra n-butylammonium bromide (0.001 mol, 0.16 g). The reaction mixture was stirred at room temperature for 48 h. The solution was filtered and the the solvent removed under reduced pressure. The residue obtained was chromatographed on a silica-gel column using hexane and ethyl acetate (80/20) as eluents to afford the title compound as yellow plate-like crystals.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₀H₁₀ClN₃O₃
M_r	255.66
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	298
a, b, c (Å)	4.3949 (4), 9.9144 (8), 13.1376 (11)
α, β, γ (°)	98.481 (1), 90.755 (1), 97.377 (1)
V (Å³)	561.19 (8)
Z	2
Radiation type	Mo Kα
μ (mm⁻¹)	0.34
Crystal size (mm)	0.45 × 0.20 × 0.11

Data collection
Diffractometer	Bruker SMART APEX CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2016 )
T_min, T_max	0.87, 0.96
No. of measured, independent and observed [I > 2σ(I)] reflections	10444, 2790, 1874
R_int	0.023
(sin θ/λ)_max (Å⁻¹)	0.668

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.047, 0.151, 1.06
No. of reflections	2790
No. of parameters	156
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.43, −0.19
Computer programs: APEX3 and SAINT (Bruker, 2016), SHELXT (Sheldrick, 2015a ), SHELXL2014 (Sheldrick, 2015b ), DIAMOND (Brandenburg & Putz, 2012 ) and SHELXTL (Sheldrick, 2008 ).

Structural data

CCDC reference: 1546601

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S241431461700637X/sj4104sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S241431461700637X/sj4104Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S241431461700637X/sj4104Isup3.cdx

Supporting information file. DOI: https://doi.org/10.1107/S241431461700637X/sj4104Isup4.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 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

1-Chloro-3-(6-nitro-1H-indazol-1-yl)propan-2-ol top

Crystal data top

C₁₀H₁₀ClN₃O₃	Z = 2
M_r = 255.66	F(000) = 264
Triclinic, P1	D_x = 1.513 Mg m⁻³
a = 4.3949 (4) Å	Mo Kα radiation, λ = 0.71073 Å
b = 9.9144 (8) Å	Cell parameters from 3584 reflections
c = 13.1376 (11) Å	θ = 2.4–27.0°
α = 98.481 (1)°	µ = 0.34 mm⁻¹
β = 90.755 (1)°	T = 298 K
γ = 97.377 (1)°	Plate, pale yellow
V = 561.19 (8) Å³	0.45 × 0.20 × 0.11 mm

Data collection top

Bruker SMART APEX CCD diffractometer	2790 independent reflections
Radiation source: fine-focus sealed tube	1874 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.023
Detector resolution: 8.3333 pixels mm^-1	θ_max = 28.4°, θ_min = 1.6°
φ and ω scans	h = −5→5
Absorption correction: multi-scan (SADABS; Bruker, 2016)	k = −13→13
T_min = 0.87, T_max = 0.96	l = −17→17
10444 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)] = 0.047	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.151	H-atom parameters constrained
S = 1.06	w = 1/[σ²(F_o²) + (0.0916P)²] where P = (F_o² + 2F_c²)/3
2790 reflections	(Δ/σ)_max < 0.001
156 parameters	Δρ_max = 0.43 e Å⁻³
0 restraints	Δρ_min = −0.19 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 - 0.98 Å) while that attached to oxygen was placed in a location derived from a difference map and its coordinates adjusted to give O—H = 1.00 %A. All were included as riding contributions with isotropic displacement parameters 1.2 - 1.5 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
Cl1	0.46205 (13)	0.09914 (5)	0.12647 (5)	0.0763 (2)
O1	0.8217 (5)	0.6041 (2)	0.57705 (12)	0.0975 (6)
O2	1.1879 (6)	0.7675 (3)	0.61324 (14)	0.1311 (9)
O3	0.7011 (3)	0.38489 (14)	0.07195 (10)	0.0562 (4)
H3	0.562	0.362	0.0091	0.084*
N1	0.5788 (3)	0.63286 (15)	0.19817 (10)	0.0462 (4)
N2	0.6434 (4)	0.70386 (16)	0.11859 (11)	0.0544 (4)
N3	0.9933 (5)	0.6999 (2)	0.55419 (13)	0.0732 (5)
C1	0.7535 (4)	0.69161 (17)	0.28323 (12)	0.0428 (4)
C2	0.7652 (4)	0.65277 (18)	0.38148 (13)	0.0480 (4)
H2	0.6441	0.5758	0.3985	0.058*
C3	0.9679 (5)	0.7365 (2)	0.45025 (13)	0.0530 (5)
C4	1.1529 (5)	0.8533 (2)	0.42777 (15)	0.0617 (5)
H4	1.2851	0.9064	0.4784	0.074*
C5	1.1401 (5)	0.8896 (2)	0.33168 (15)	0.0590 (5)
H5	1.2633	0.9666	0.3157	0.071*
C6	0.9353 (4)	0.80712 (18)	0.25730 (13)	0.0479 (4)
C7	0.8535 (5)	0.80725 (19)	0.15292 (14)	0.0573 (5)
H7	0.9381	0.8724	0.1136	0.069*
C8	0.3623 (4)	0.50762 (18)	0.18429 (13)	0.0472 (4)
H8A	0.2181	0.5100	0.1283	0.057*
H8B	0.2472	0.5025	0.2464	0.057*
C9	0.5248 (4)	0.37983 (17)	0.16051 (12)	0.0454 (4)
H9	0.6651	0.3783	0.2188	0.054*
C10	0.2891 (4)	0.25374 (19)	0.15235 (15)	0.0558 (5)
H10A	0.1403	0.2559	0.0976	0.067*
H10B	0.1810	0.2545	0.2163	0.067*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0755 (4)	0.0445 (3)	0.1061 (5)	0.0009 (2)	0.0158 (3)	0.0074 (3)
O1	0.1276 (16)	0.1079 (15)	0.0554 (9)	−0.0111 (12)	0.0029 (9)	0.0302 (9)
O2	0.155 (2)	0.160 (2)	0.0647 (11)	−0.0362 (17)	−0.0454 (12)	0.0256 (12)
O3	0.0470 (7)	0.0696 (9)	0.0496 (7)	−0.0046 (6)	0.0041 (6)	0.0116 (6)
N1	0.0480 (8)	0.0474 (8)	0.0427 (7)	0.0006 (6)	−0.0045 (6)	0.0104 (6)
N2	0.0634 (10)	0.0521 (9)	0.0482 (8)	−0.0007 (7)	−0.0047 (7)	0.0170 (7)
N3	0.0903 (14)	0.0835 (14)	0.0437 (9)	0.0053 (11)	−0.0071 (9)	0.0086 (9)
C1	0.0427 (9)	0.0418 (8)	0.0436 (9)	0.0066 (7)	0.0001 (7)	0.0048 (7)
C2	0.0517 (10)	0.0478 (9)	0.0445 (9)	0.0037 (8)	0.0037 (7)	0.0088 (7)
C3	0.0599 (11)	0.0582 (11)	0.0402 (9)	0.0097 (9)	−0.0023 (8)	0.0034 (8)
C4	0.0656 (13)	0.0588 (12)	0.0537 (11)	−0.0032 (9)	−0.0113 (9)	−0.0031 (9)
C5	0.0633 (12)	0.0480 (10)	0.0610 (11)	−0.0078 (9)	−0.0014 (9)	0.0060 (9)
C6	0.0517 (10)	0.0420 (9)	0.0497 (9)	0.0027 (7)	0.0008 (8)	0.0090 (7)
C7	0.0695 (13)	0.0491 (10)	0.0534 (10)	−0.0038 (9)	−0.0020 (9)	0.0176 (8)
C8	0.0400 (9)	0.0514 (10)	0.0482 (9)	−0.0030 (7)	−0.0009 (7)	0.0090 (7)
C9	0.0427 (9)	0.0503 (9)	0.0421 (8)	−0.0029 (7)	0.0003 (7)	0.0115 (7)
C10	0.0515 (11)	0.0519 (10)	0.0613 (11)	−0.0042 (8)	0.0070 (9)	0.0092 (8)

Geometric parameters (Å, º) top

Cl1—C10	1.787 (2)	C3—C4	1.398 (3)
O1—N3	1.211 (3)	C4—C5	1.365 (3)
O2—N3	1.210 (3)	C4—H4	0.9300
O3—C9	1.4098 (19)	C5—C6	1.409 (3)
O3—H3	1.0000	C5—H5	0.9300
N1—N2	1.357 (2)	C6—C7	1.413 (2)
N1—C1	1.360 (2)	C7—H7	0.9300
N1—C8	1.451 (2)	C8—C9	1.528 (3)
N2—C7	1.310 (2)	C8—H8A	0.9700
N3—C3	1.470 (3)	C8—H8B	0.9700
C1—C6	1.398 (2)	C9—C10	1.507 (2)
C1—C2	1.403 (2)	C9—H9	0.9800
C2—C3	1.366 (3)	C10—H10A	0.9700
C2—H2	0.9300	C10—H10B	0.9700

C9—O3—H3	109.5	C1—C6—C7	104.02 (15)
N2—N1—C1	110.65 (14)	C5—C6—C7	136.27 (17)
N2—N1—C8	120.76 (13)	N2—C7—C6	111.41 (15)
C1—N1—C8	128.49 (14)	N2—C7—H7	124.3
C7—N2—N1	106.79 (14)	C6—C7—H7	124.3
O2—N3—O1	122.9 (2)	N1—C8—C9	111.61 (14)
O2—N3—C3	117.9 (2)	N1—C8—H8A	109.3
O1—N3—C3	119.21 (19)	C9—C8—H8A	109.3
N1—C1—C6	107.13 (14)	N1—C8—H8B	109.3
N1—C1—C2	130.19 (16)	C9—C8—H8B	109.3
C6—C1—C2	122.68 (16)	H8A—C8—H8B	108.0
C3—C2—C1	114.95 (17)	O3—C9—C10	113.23 (14)
C3—C2—H2	122.5	O3—C9—C8	111.05 (13)
C1—C2—H2	122.5	C10—C9—C8	108.81 (15)
C2—C3—C4	124.27 (17)	O3—C9—H9	107.9
C2—C3—N3	117.44 (18)	C10—C9—H9	107.9
C4—C3—N3	118.29 (17)	C8—C9—H9	107.9
C5—C4—C3	120.15 (17)	C9—C10—Cl1	111.62 (14)
C5—C4—H4	119.9	C9—C10—H10A	109.3
C3—C4—H4	119.9	Cl1—C10—H10A	109.3
C4—C5—C6	118.24 (18)	C9—C10—H10B	109.3
C4—C5—H5	120.9	Cl1—C10—H10B	109.3
C6—C5—H5	120.9	H10A—C10—H10B	108.0
C1—C6—C5	119.71 (16)

C1—N1—N2—C7	−0.7 (2)	C3—C4—C5—C6	0.5 (3)
C8—N1—N2—C7	−177.30 (17)	N1—C1—C6—C5	179.55 (16)
N2—N1—C1—C6	1.0 (2)	C2—C1—C6—C5	−0.1 (3)
C8—N1—C1—C6	177.20 (16)	N1—C1—C6—C7	−0.8 (2)
N2—N1—C1—C2	−179.43 (17)	C2—C1—C6—C7	179.58 (16)
C8—N1—C1—C2	−3.2 (3)	C4—C5—C6—C1	−0.2 (3)
N1—C1—C2—C3	−179.49 (18)	C4—C5—C6—C7	−179.7 (2)
C6—C1—C2—C3	0.0 (3)	N1—N2—C7—C6	0.2 (2)
C1—C2—C3—C4	0.3 (3)	C1—C6—C7—N2	0.4 (2)
C1—C2—C3—N3	−179.21 (16)	C5—C6—C7—N2	179.9 (2)
O2—N3—C3—C2	174.7 (2)	N2—N1—C8—C9	94.92 (18)
O1—N3—C3—C2	−5.0 (3)	C1—N1—C8—C9	−81.0 (2)
O2—N3—C3—C4	−4.8 (3)	N1—C8—C9—O3	−57.54 (17)
O1—N3—C3—C4	175.5 (2)	N1—C8—C9—C10	177.18 (13)
C2—C3—C4—C5	−0.6 (3)	O3—C9—C10—Cl1	56.88 (18)
N3—C3—C4—C5	178.9 (2)	C8—C9—C10—Cl1	−179.12 (11)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3···N2ⁱ	1.00	1.88	2.871 (2)	169
C2—H2···O1ⁱⁱ	0.93	2.59	3.492 (3)	163
C10—H10A···O3ⁱⁱⁱ	0.97	2.49	3.268 (3)	137

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

Acknowledgements

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

References

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. Web of Science CrossRef 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
Caron, S. & Vazquez, E. (1999). Synthesis, pp. 588–592. CrossRef Google Scholar
Sheldrick, G. M. (2008). 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
Yeu, J.-P., Yeh, J.-T., Chen, T.-Y. & Uang, B. (2001). Synthesis, pp. 1775–1777. CrossRef Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

IUCrDATA

ISSN: 2414-3146

Volume 2| Part 5| May 2017| x170637

https://doi.org/10.1107/S241431461700637X

Open

access

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Plain Text
		Text

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Plain Text
		Text

Search IUCr Journals		doi		Advanced search
Author		volume	page

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

1-Chloro-3-(6-nitro-1H-indazol-1-yl)propan-2-ol

Structure description

Synthesis and crystallization

Refinement

Structural data

Acknowledgements

References

organic compounds