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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 67| Part 6| June 2011| Page o1431
doi:10.1107/S1600536811017831

N-(2-Chloro­pyrimidin-4-yl)-2-methyl-2H-indazol-6-amine methanol monosolvate

Xiang-Chuan Pang,a Xin-Hua Denga* and Yuan Suna

aCollege of Materials Science and Engineering, Tianjin Polytechnic University, Tianjin 300160, People's Republic of China
*Correspondence e-mail: xh.deng@126.com

(Received 26 April 2011; accepted 11 May 2011; online 14 May 2011)

In the title compound, C12H10ClN5·CH3OH, the indazole ring system and the pyrimidine ring make a dihedral angle of 23.86 (4)°. In the crystal, the components are linked by N—H⋯O and O—H⋯N hydrogen bonds into chains propagated in [010]. Inter­molecular π–π inter­actions [centroid–centroid distances = 3.6404 (9), 3.6725 (9) and 3.4566 (9) Å] between the rings of neighbouring chains also stabilize the crystal packing.

Related literature

The title compound was obtained in a continuation of our studies of derivatives of the anti­tumor agent pazopanib (systematic name 5-[[4-[(2,3-dimethyl-2H-indazol-6-yl)methyl­amino]-2-pyrimidin­yl]amino]-2-methyl­benzolsulfonamide), during which we determined the crystal structure of the related compound N-(2-chloro­pyrimidin-4-yl)-N,2-dimethyl-2H-indazol-6-amine, see: Qi et al. (2010[Qi, H.-F., Liu, B.-N., Liu, M. & Liu, D.-K. (2010). Acta Cryst. E66, o2955.]).

[Scheme 1]

Experimental

Crystal data

  • C12H10ClN5·CH4O

  • Mr = 291.74

  • Monoclinic, P 21 /c

  • a = 6.9327 (8) Å

  • b = 17.613 (2) Å

  • c = 11.4883 (16) Å

  • β = 106.690 (8)°

  • V = 1343.7 (3) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.29 mm−1

  • T = 113 K

  • 0.34 × 0.28 × 0.12 mm
Data collection

  • Rigaku Saturn CCD area-detector diffractometer

  • Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2005[Rigaku/MSC (2005). CrystalClear. Rigaku/MSC Inc., The Woodlands, Texas, USA.]) Tmin = 0.909, Tmax = 0.966

  • 13795 measured reflections

  • 3193 independent reflections

  • 2982 reflections with I > 2σ(I)

  • Rint = 0.057
Refinement

  • R[F2 > 2σ(F2)] = 0.039

  • wR(F2) = 0.102

  • S = 1.11

  • 3193 reflections

  • 191 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.46 e Å−3

  • Δρmin = −0.22 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O1—H1⋯N4i 0.80 (2) 2.04 (2) 2.8394 (15) 176 (2)
N3—H3A⋯O1 0.846 (19) 2.110 (19) 2.9452 (14) 168.8 (16)
Symmetry code: (i) [-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: CrystalClear (Rigaku/MSC, 2005[Rigaku/MSC (2005). CrystalClear. Rigaku/MSC Inc., The Woodlands, Texas, USA.]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811017831/cv5083sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811017831/cv5083Isup3.hkl

Supporting information file. DOI: 10.1107/S1600536811017831/cv5083Isup3.cml

checkCIF report


Comment top

In continuation of our studies of derivatives of antitumor agent pazopanib (Qi et al., 2010), we obtained the title compound (I).

In (I) (Fig. 1), all bond lengths and angles are normal and correspond to those reported by Qi et al. (2010). In N-(2-chloropyrimidin-4-yl)-2-methyl-2H-indazol-6-amine (M) molecule, the indazole and pyrimidin fragments form a dihedral angle of 23.86 (4)°.

In the crystal structure, M and methanol molecules are linked by N—H···O and O—H···N hydrogen bonds (Table 2) into chains propagated in [010]. Intermolecular π—π interactions (Table 1) between the rings from the neighbouring chains stabilize the crystal packing.

Related literature top

The title compound was obtained in a continuation of our studies of derivatives of the antitumor agent pazopanib (systematic name 5-[[4-[(2,3-dimethyl-2H-indazol-6-yl)methylamino]-2-pyrimidinyl]amino]-2-methylbenzolsulfonamide). For the crystal structure of the related compound N-(2-chloropyrimidin-4-yl)-N,2-dimethyl-2H-indazol-6-amine, see: Qi et al. (2010).

Experimental top

To a stirred solution of the 2-methyl-2H-indazol-6-amine (10 g, 0.07 mol) and NaHCO3 (12 g, 0.14 mol) in ethanol (250 ml) was added 2,4-dichloropyrimidine (12 g, 0.08 mol) at room temperature. After the reaction was heated for four hours, the suspension was cooled to room temperature, filtered and washed thoroughly with ethyl acetate. The filtrate was concentrated under reduced pressure to get off-white solid as crude product. The solid was dissolved in methanol 40 ml at 293 k, then colourless crystals were generated slowly.

Refinement top

C-bound H atoms were geometrically positioned (C—H 0.95–0.98 Å), and refined as riding with Uiso = 1.2–1.5Ueq(C). The H atoms of N—H and O—H were found from difference map and isotropically refined.

Computing details top

Data collection: CrystalClear (Rigaku/MSC, 2005); cell refinement: CrystalClear (Rigaku/MSC, 2005); data reduction: CrystalClear (Rigaku/MSC, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL(Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I). Displacement ellipsoids are drawn at the 50% probability level.
N-(2-Chloropyrimidin-4-yl)-2-methyl-2H-indazol-6-amine methanol monosolvate top
Crystal data top
C12H10ClN5·CH4OF(000) = 608
Mr = 291.74Dx = 1.442 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 4513 reflections
a = 6.9327 (8) Åθ = 1.9–27.9°
b = 17.613 (2) ŵ = 0.29 mm−1
c = 11.4883 (16) ÅT = 113 K
β = 106.690 (8)°Prism, colorless
V = 1343.7 (3) Å30.34 × 0.28 × 0.12 mm
Z = 4
Data collection top
Rigaku Saturn CCD area-detector
diffractometer		3193 independent reflections
Radiation source: rotating anode2982 reflections with I > 2σ(I)
Multilayer monochromatorRint = 0.057
Detector resolution: 14.63 pixels mm-1θmax = 27.9°, θmin = 2.2°
ω and ϕ scansh = −9→9
Absorption correction: multi-scan
(CrystalClear; Rigaku/MSC, 2005)		k = −23→23
Tmin = 0.909, Tmax = 0.966l = −15→14
13795 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)] = 0.039Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.102H atoms treated by a mixture of independent and constrained refinement
S = 1.11 w = 1/[σ2(Fo2) + (0.0548P)2 + 0.3525P]
where P = (Fo2 + 2Fc2)/3
3193 reflections(Δ/σ)max < 0.001
191 parametersΔρmax = 0.46 e Å−3
0 restraintsΔρmin = −0.22 e Å−3
Crystal data top
C12H10ClN5·CH4OV = 1343.7 (3) Å3
Mr = 291.74Z = 4
Monoclinic, P21/cMo Kα radiation
a = 6.9327 (8) ŵ = 0.29 mm−1
b = 17.613 (2) ÅT = 113 K
c = 11.4883 (16) Å0.34 × 0.28 × 0.12 mm
β = 106.690 (8)°
Data collection top
Rigaku Saturn CCD area-detector
diffractometer		3193 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku/MSC, 2005)		2982 reflections with I > 2σ(I)
Tmin = 0.909, Tmax = 0.966Rint = 0.057
13795 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0390 restraints
wR(F2) = 0.102H atoms treated by a mixture of independent and constrained refinement
S = 1.11Δρmax = 0.46 e Å−3
3193 reflectionsΔρmin = −0.22 e Å−3
191 parameters
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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 > σ(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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl1−0.00948 (5)0.910378 (17)−0.00877 (3)0.02682 (12)
N1−0.00275 (16)0.77456 (6)−0.09446 (10)0.0196 (2)
N20.16759 (15)0.79520 (6)0.11655 (9)0.0171 (2)
N30.34415 (16)0.69626 (6)0.23692 (9)0.0169 (2)
N40.65827 (16)0.92220 (6)0.46761 (9)0.0182 (2)
N50.75805 (16)0.92466 (6)0.58823 (9)0.0182 (2)
C10.05934 (19)0.81451 (7)0.00587 (11)0.0183 (2)
C20.05172 (19)0.70044 (7)−0.07866 (11)0.0196 (3)
H20.01100.6673−0.14660.023*
C30.16207 (18)0.67115 (7)0.02996 (11)0.0181 (2)
H30.19530.61870.03880.022*
C40.22490 (17)0.72195 (7)0.12872 (11)0.0158 (2)
C50.45085 (18)0.73798 (7)0.33979 (11)0.0163 (2)
C60.52216 (18)0.69442 (7)0.44890 (11)0.0180 (2)
H60.49420.64160.44690.022*
C70.62928 (18)0.72683 (7)0.55577 (11)0.0184 (2)
H70.67500.69730.62760.022*
C80.67065 (18)0.80541 (7)0.55709 (11)0.0163 (2)
C90.60301 (17)0.84828 (7)0.44820 (11)0.0158 (2)
C100.49085 (18)0.81456 (7)0.33800 (11)0.0166 (2)
H100.44480.84350.26550.020*
C110.76954 (18)0.85771 (7)0.64502 (11)0.0185 (2)
H110.83260.84780.72860.022*
C120.8408 (2)0.99639 (7)0.64371 (12)0.0229 (3)
H12A0.88570.99070.73230.034*
H12B0.73701.03580.62150.034*
H12C0.95541.01090.61470.034*
H3A0.369 (2)0.6491 (11)0.2405 (15)0.026 (4)*
C130.3829 (3)0.48388 (8)0.32210 (13)0.0322 (3)
H13A0.52080.46620.35970.048*
H13B0.29420.44000.29530.048*
H13C0.33670.51320.38140.048*
O10.37868 (17)0.53015 (5)0.22112 (9)0.0274 (2)
H10.372 (3)0.5011 (11)0.1665 (19)0.039 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0307 (2)0.01501 (17)0.02887 (19)0.00241 (11)−0.00087 (14)0.00305 (11)
N10.0193 (5)0.0211 (5)0.0176 (5)0.0000 (4)0.0040 (4)0.0018 (4)
N20.0163 (5)0.0168 (5)0.0171 (5)0.0008 (4)0.0029 (4)0.0008 (4)
N30.0198 (5)0.0133 (5)0.0163 (5)0.0013 (4)0.0032 (4)0.0005 (4)
N40.0197 (5)0.0192 (5)0.0134 (5)0.0006 (4)0.0008 (4)0.0003 (4)
N50.0189 (5)0.0195 (5)0.0136 (5)0.0005 (4)0.0007 (4)−0.0001 (4)
C10.0171 (6)0.0160 (5)0.0212 (6)0.0000 (4)0.0048 (5)0.0021 (4)
C20.0195 (6)0.0213 (6)0.0178 (6)−0.0015 (5)0.0051 (5)−0.0022 (4)
C30.0189 (6)0.0170 (5)0.0189 (6)−0.0001 (4)0.0059 (5)−0.0009 (4)
C40.0142 (5)0.0174 (5)0.0169 (6)−0.0011 (4)0.0063 (5)0.0009 (4)
C50.0156 (5)0.0182 (6)0.0155 (6)0.0013 (4)0.0050 (4)0.0006 (4)
C60.0190 (6)0.0161 (5)0.0191 (6)0.0005 (4)0.0058 (5)0.0033 (4)
C70.0191 (6)0.0195 (6)0.0167 (6)0.0029 (4)0.0052 (5)0.0057 (4)
C80.0152 (5)0.0200 (6)0.0140 (5)0.0022 (4)0.0044 (4)0.0028 (4)
C90.0146 (5)0.0172 (5)0.0156 (6)0.0021 (4)0.0042 (4)0.0021 (4)
C100.0173 (6)0.0181 (5)0.0140 (6)0.0015 (4)0.0038 (4)0.0021 (4)
C110.0182 (6)0.0217 (6)0.0149 (5)0.0019 (4)0.0035 (4)0.0020 (4)
C120.0260 (7)0.0199 (6)0.0191 (6)−0.0017 (5)0.0004 (5)−0.0024 (4)
C130.0489 (9)0.0241 (7)0.0239 (7)0.0045 (6)0.0109 (6)0.0023 (5)
O10.0438 (6)0.0168 (5)0.0215 (5)0.0015 (4)0.0095 (4)−0.0006 (4)
Geometric parameters (Å, º) top
Cl1—C11.7495 (13)C6—C71.3641 (18)
N1—C11.3130 (16)C6—H60.9500
N1—C21.3566 (16)C7—C81.4125 (17)
N2—C11.3219 (16)C7—H70.9500
N2—C41.3454 (15)C8—C111.3933 (17)
N3—C41.3576 (15)C8—C91.4205 (16)
N3—C51.4077 (15)C9—C101.4124 (17)
N3—H3A0.846 (19)C10—H100.9500
N4—C91.3574 (16)C11—H110.9500
N4—N51.3601 (14)C12—H12A0.9800
N5—C111.3389 (16)C12—H12B0.9800
N5—C121.4565 (16)C12—H12C0.9800
C2—C31.3638 (17)C13—O11.4111 (17)
C2—H20.9500C13—H13A0.9800
C3—C41.4120 (16)C13—H13B0.9800
C3—H30.9500C13—H13C0.9800
C5—C101.3783 (16)O1—H10.80 (2)
C5—C61.4312 (16)
Cg1···Cg2i3.6404 (9)Cg2···Cg3iii3.4566 (9)
Cg2···Cg3ii3.6725 (9)
C1—N1—C2112.94 (11)C6—C7—H7120.8
C1—N2—C4114.57 (10)C8—C7—H7120.8
C4—N3—C5129.02 (10)C11—C8—C7135.37 (11)
C4—N3—H3A115.7 (11)C11—C8—C9104.85 (10)
C5—N3—H3A114.9 (11)C7—C8—C9119.78 (11)
C9—N4—N5103.58 (9)N4—C9—C10127.40 (11)
C11—N5—N4114.21 (10)N4—C9—C8111.04 (10)
C11—N5—C12126.14 (11)C10—C9—C8121.56 (11)
N4—N5—C12119.65 (10)C5—C10—C9117.36 (11)
N1—C1—N2131.22 (11)C5—C10—H10121.3
N1—C1—Cl1114.91 (9)C9—C10—H10121.3
N2—C1—Cl1113.87 (9)N5—C11—C8106.32 (11)
N1—C2—C3123.22 (11)N5—C11—H11126.8
N1—C2—H2118.4C8—C11—H11126.8
C3—C2—H2118.4N5—C12—H12A109.5
C2—C3—C4117.26 (11)N5—C12—H12B109.5
C2—C3—H3121.4H12A—C12—H12B109.5
C4—C3—H3121.4N5—C12—H12C109.5
N2—C4—N3119.92 (11)H12A—C12—H12C109.5
N2—C4—C3120.69 (11)H12B—C12—H12C109.5
N3—C4—C3119.39 (11)O1—C13—H13A109.5
C10—C5—N3123.90 (11)O1—C13—H13B109.5
C10—C5—C6121.15 (11)H13A—C13—H13B109.5
N3—C5—C6114.93 (10)O1—C13—H13C109.5
C7—C6—C5121.72 (11)H13A—C13—H13C109.5
C7—C6—H6119.1H13B—C13—H13C109.5
C5—C6—H6119.1C13—O1—H1104.9 (14)
C6—C7—C8118.43 (11)
C9—N4—N5—C110.26 (13)C5—C6—C7—C8−0.37 (18)
C9—N4—N5—C12−179.77 (11)C6—C7—C8—C11179.08 (13)
C2—N1—C1—N21.7 (2)C6—C7—C8—C9−0.80 (17)
C2—N1—C1—Cl1−179.22 (9)N5—N4—C9—C10178.57 (11)
C4—N2—C1—N10.2 (2)N5—N4—C9—C8−0.47 (13)
C4—N2—C1—Cl1−178.82 (8)C11—C8—C9—N40.50 (14)
C1—N1—C2—C3−0.94 (18)C7—C8—C9—N4−179.58 (10)
N1—C2—C3—C4−1.52 (18)C11—C8—C9—C10−178.60 (11)
C1—N2—C4—N3177.11 (10)C7—C8—C9—C101.31 (18)
C1—N2—C4—C3−2.98 (16)N3—C5—C10—C9−178.85 (11)
C5—N3—C4—N2−11.79 (18)C6—C5—C10—C9−0.61 (17)
C5—N3—C4—C3168.30 (11)N4—C9—C10—C5−179.53 (11)
C2—C3—C4—N23.61 (17)C8—C9—C10—C5−0.58 (17)
C2—C3—C4—N3−176.48 (11)N4—N5—C11—C80.04 (14)
C4—N3—C5—C10−16.33 (19)C12—N5—C11—C8−179.92 (12)
C4—N3—C5—C6165.33 (11)C7—C8—C11—N5179.79 (13)
C10—C5—C6—C71.12 (18)C9—C8—C11—N5−0.32 (13)
N3—C5—C6—C7179.51 (11)
Symmetry codes: (i) x+1, −y+3/2, z+1/2; (ii) x−1, −y+3/2, z−1/2; (iii) x, −y+3/2, z−1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···N4iv0.80 (2)2.04 (2)2.8394 (15)176 (2)
N3—H3A···O10.846 (19)2.110 (19)2.9452 (14)168.8 (16)
Symmetry code: (iv) −x+1, y−1/2, −z+1/2.

Experimental details

Crystal data
Chemical formulaC12H10ClN5·CH4O
Mr291.74
Crystal system, space groupMonoclinic, P21/c
Temperature (K)113
a, b, c (Å)6.9327 (8), 17.613 (2), 11.4883 (16)
β (°) 106.690 (8)
V (Å3)1343.7 (3)
Z4
Radiation typeMo Kα
µ (mm−1)0.29
Crystal size (mm)0.34 × 0.28 × 0.12
Data collection
DiffractometerRigaku Saturn CCD area-detector
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku/MSC, 2005)
Tmin, Tmax0.909, 0.966
No. of measured, independent and
observed [I > 2σ(I)] reflections		13795, 3193, 2982
Rint0.057
(sin θ/λ)max (Å−1)0.658
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.039, 0.102, 1.11
No. of reflections3193
No. of parameters191
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.46, −0.22

Computer programs: CrystalClear (Rigaku/MSC, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), SHELXTL(Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···N4i0.80 (2)2.04 (2)2.8394 (15)176 (2)
N3—H3A···O10.846 (19)2.110 (19)2.9452 (14)168.8 (16)
Symmetry code: (i) −x+1, y−1/2, −z+1/2.
 

Acknowledgements

The authors thank Mr Hai-Bin Song of Nankai University for his helpful suggestions.

References

First citationQi, H.-F., Liu, B.-N., Liu, M. & Liu, D.-K. (2010). Acta Cryst. E66, o2955.  Web of Science CSD CrossRef IUCr Journals Google Scholar
 First citationRigaku/MSC (2005). CrystalClear. Rigaku/MSC Inc., The Woodlands, Texas, USA.  Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals 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.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 67| Part 6| June 2011| Page o1431
doi:10.1107/S1600536811017831
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