organic compounds
1-Chloro-3-(6-nitro-1H-indazol-1-yl)propan-2-ol
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
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).
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 .
details are summarized in Table 2Structural data
CCDC reference: 1546601
https://doi.org/10.1107/S241431461700637X/sj4104sup1.cif
contains datablocks global, I. DOI: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
Data collection: APEX3 (Bruker, 2016); cell
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).C10H10ClN3O3 | Z = 2 |
Mr = 255.66 | F(000) = 264 |
Triclinic, P1 | Dx = 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 |
Bruker SMART APEX CCD diffractometer | 2790 independent reflections |
Radiation source: fine-focus sealed tube | 1874 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.023 |
Detector resolution: 8.3333 pixels mm-1 | θmax = 28.4°, θmin = 1.6° |
φ and ω scans | h = −5→5 |
Absorption correction: multi-scan (SADABS; Bruker, 2016) | k = −13→13 |
Tmin = 0.87, Tmax = 0.96 | l = −17→17 |
10444 measured reflections |
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(Fo2) + (0.0916P)2] where P = (Fo2 + 2Fc2)/3 |
2790 reflections | (Δ/σ)max < 0.001 |
156 parameters | Δρmax = 0.43 e Å−3 |
0 restraints | Δρmin = −0.19 e Å−3 |
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. |
x | y | z | Uiso*/Ueq | ||
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* |
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) |
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) |
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
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