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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 68| Part 7| July 2012| Page o1977
https://doi.org/10.1107/S1600536812024166

2-Methyl-3-(1H-pyrazol-3-yl)imidazo[1,2-a]pyrimidine

Guo-Rui Gaoa and Wen-Hu Duana,b*

aSchool of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China, and bDepartment of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
*Correspondence e-mail: whduan@mail.shcnc.ac.cn

(Received 9 May 2012; accepted 27 May 2012; online 2 June 2012)

In the title compound, C10H9N5, the fused 2-methyl­imidazo[1,2-a]pyrimidine ring system is approximately planar [dihedral angle of 1.14 (9)° between the two fused rings] and the 1H-pyrazole ring is rotated by 28.16 (11)° out of that plane. In the crystal, the mol­ecules are linked into linear chains along the [100] direction by classical inter­molecular N—H⋯N hydrogen bonds.

Related literature

For the medical properties of imidazo[1,2-a]pyrimidine derivatives, see: An et al. (2009[An, H.-Y., Xi, B., Abassi, Y., Wang, X.-B. & Xu, X. (2009). WO Patent No. 2009023402.]); Kim et al. (2011[Kim, J.-H., Hong, S.-H. & Hong, S.-W. (2011). Bioorg. Med. Chem. Lett. 21, 6977-6981.]); Linton et al. (2011[Linton, A., Kang, P., Ornelas, M., Kephart, S., Hu, Q.-Y., Pairish, M., Jiang, Y. & Guo, C.-X. (2011). J. Med. Chem. 54, 7705-7712.]). For related structures, see: Yang et al. (2008[Yang, F.-L., Li, G.-C. & Yao, C.-S. (2008). Acta Cryst. E64, o2469.]); Anaflous et al. (2004[Anaflous, A., Benchat, N.-E., Ben-Hadda, T., El Bali, B. & Bolte, M. (2004). Acta Cryst. E60, o1131-o1132.]).

[Scheme 1]

Experimental

Crystal data

  • C10H9N5

  • Mr = 199.22

  • Monoclinic, P 21 /n

  • a = 8.962 (2) Å

  • b = 8.851 (2) Å

  • c = 12.481 (3) Å

  • β = 101.751 (3)°

  • V = 969.3 (4) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 173 K

  • 0.50 × 0.10 × 0.08 mm
Data collection

  • Bruker SMART APEX CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2000[Bruker (2000). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.956, Tmax = 0.993

  • 5121 measured reflections

  • 1907 independent reflections

  • 1552 reflections with I > 2σ(I)

  • Rint = 0.024
Refinement

  • R[F2 > 2σ(F2)] = 0.051

  • wR(F2) = 0.128

  • S = 1.09

  • 1907 reflections

  • 152 parameters

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

  • Δρmax = 0.20 e Å−3

  • Δρmin = −0.14 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N12—H30A⋯N6i 0.89 (2) 2.08 (2) 2.966 (2) 175 (2)
Symmetry code: (i) x-1, y, z.

Data collection: SMART (Bruker, 2000[Bruker (2000). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SMART; data reduction: SAINT (Bruker, 2000[Bruker (2000). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); 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: https://doi.org/10.1107/S1600536812024166/rk2359sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812024166/rk2359Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536812024166/rk2359Isup3.cml

checkCIF report


Comment top

Imidazo[1,2-a]pyrimidine derivatives have been used for treatment of cancers (An et al., 2009; Kim et al., 2011; Linton et al., 2011), and some analogues were reported (Anaflous et al., 2004; Yang et al., 2008). The title compound was synthesized by the reaction of 1-(2-methylimidazo[1,2-a]pyrimidin-3-yl)ethanone with 1,1-dimethoxy-N,N-dimethylmethanamine, and its crystal structure was confirmed by single crystal X-ray analysis (Fig. 1). In this compound, the fused 2-methylimidazo[1,2-a]pyrimidine ring system are approximately coplanar with a tiny dihedral angle being 1.14 (9)°, but the 1H-pyrazole ring is rotated 28.16 (11)° out of the the fused 2-methylimidazo[1,2-a]pyrimidine ring system plane. Further analysis showed that each molecule is associated with two neighbors to generate an infinite one-dimensional chain extending along the [1 0 0] direction with the formation classical intermolecular N12—H30A···N6i hydrogen bond (Fig. 2). Symmetry code: (i) x - 1, y, z. The relevant parameters are listed in Table 1.

Related literature top

For the medical properties of imidazo[1,2-a]pyrimidine derivatives, see: An et al. (2009); Kim et al. (2011); Linton et al. (2011). For related structures, see: Yang et al. (2008); Anaflous et al. (2004).

Experimental top

A mixture of 1-(2-methylimidazo[1,2-a]pyrimidin-3-yl)ethanone (500 mg, 2.86 mmol) and 1,1-dimethoxy-N,N-dimethylmethanamine (3.8 ml, 28.6 mmol) was heated at 373 K for 6 h. After cooling to room temperature, EtOH (10 ml) and hydrazine hydrate (0.28 ml, 5.72 mmol) were added and the reaction mixture was refluxed for 3 h. The mixture was diluted with water and extracted with CH2Cl2. The organic layer was dried over MgSO4 and evaporated. The crude product was chromatographed on silica gel eluting with DCM–MeOH (10/1) to give the title compound as a pale-yellow solid (300 mg, yield: 52%).

Refinement top

H atoms attached to NH group and methyl C atoms were located in a difference Fourier map and refined isotropically. The other H atoms attached to C atoms were positioned with idealized geometry (C—H = 0.95Å) using a riding model with Uiso(H) = 1.2Ueq(C).

Structure description top

Imidazo[1,2-a]pyrimidine derivatives have been used for treatment of cancers (An et al., 2009; Kim et al., 2011; Linton et al., 2011), and some analogues were reported (Anaflous et al., 2004; Yang et al., 2008). The title compound was synthesized by the reaction of 1-(2-methylimidazo[1,2-a]pyrimidin-3-yl)ethanone with 1,1-dimethoxy-N,N-dimethylmethanamine, and its crystal structure was confirmed by single crystal X-ray analysis (Fig. 1). In this compound, the fused 2-methylimidazo[1,2-a]pyrimidine ring system are approximately coplanar with a tiny dihedral angle being 1.14 (9)°, but the 1H-pyrazole ring is rotated 28.16 (11)° out of the the fused 2-methylimidazo[1,2-a]pyrimidine ring system plane. Further analysis showed that each molecule is associated with two neighbors to generate an infinite one-dimensional chain extending along the [1 0 0] direction with the formation classical intermolecular N12—H30A···N6i hydrogen bond (Fig. 2). Symmetry code: (i) x - 1, y, z. The relevant parameters are listed in Table 1.

For the medical properties of imidazo[1,2-a]pyrimidine derivatives, see: An et al. (2009); Kim et al. (2011); Linton et al. (2011). For related structures, see: Yang et al. (2008); Anaflous et al. (2004).

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SMART (Bruker, 2000); data reduction: SAINT (Bruker, 2000); 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. Molecular structure of the title compound, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are presented as a small spheres of arbitrary radius.
[Figure 2] Fig. 2. The one-dimensional chain structure extending along [100], with hydrogen bonds shown as dashed lines. Symmetry codes: (i) x - 1, y, z; (ii) x + 1, y, z.
2-Methyl-3-(1H-pyrazol-3-yl)imidazo[1,2-a]pyrimidine top
Crystal data top
C10H9N5F(000) = 416
Mr = 199.22Dx = 1.365 Mg m−3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 1511 reflections
a = 8.962 (2) Åθ = 2.6–24.0°
b = 8.851 (2) ŵ = 0.09 mm−1
c = 12.481 (3) ÅT = 173 K
β = 101.751 (3)°Bar, pale yellow
V = 969.3 (4) Å30.50 × 0.10 × 0.08 mm
Z = 4
Data collection top
Bruker SMART APEX CCD
diffractometer		1907 independent reflections
Radiation source: fine-focus sealed tube1552 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.024
φ and ω scansθmax = 26.0°, θmin = 2.6°
Absorption correction: multi-scan
(SADABS; Bruker, 2000)		h = −10→11
Tmin = 0.956, Tmax = 0.993k = −10→10
5121 measured reflectionsl = −15→8
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)] = 0.051Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.128H atoms treated by a mixture of independent and constrained refinement
S = 1.09 w = 1/[σ2(Fo2) + (0.0572P)2 + 0.2361P]
where P = (Fo2 + 2Fc2)/3
1907 reflections(Δ/σ)max < 0.001
152 parametersΔρmax = 0.20 e Å−3
0 restraintsΔρmin = −0.14 e Å−3
Crystal data top
C10H9N5V = 969.3 (4) Å3
Mr = 199.22Z = 4
Monoclinic, P21/nMo Kα radiation
a = 8.962 (2) ŵ = 0.09 mm−1
b = 8.851 (2) ÅT = 173 K
c = 12.481 (3) Å0.50 × 0.10 × 0.08 mm
β = 101.751 (3)°
Data collection top
Bruker SMART APEX CCD
diffractometer		1907 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2000)		1552 reflections with I > 2σ(I)
Tmin = 0.956, Tmax = 0.993Rint = 0.024
5121 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0510 restraints
wR(F2) = 0.128H atoms treated by a mixture of independent and constrained refinement
S = 1.09Δρmax = 0.20 e Å−3
1907 reflectionsΔρmin = −0.14 e Å−3
152 parameters
Special details top

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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
N40.44313 (15)0.15343 (16)0.08173 (12)0.0371 (4)
N10.65249 (16)0.11695 (18)0.21150 (13)0.0455 (4)
N60.68599 (17)0.2102 (2)0.03899 (14)0.0495 (4)
C30.39442 (19)0.0960 (2)0.17190 (15)0.0376 (4)
N12−0.00496 (19)0.0927 (2)0.13228 (16)0.0531 (5)
C50.60176 (19)0.1626 (2)0.11018 (15)0.0401 (4)
C90.3688 (2)0.1977 (2)−0.01970 (16)0.0475 (5)
H9A0.26090.1930−0.03990.057*
C100.23463 (19)0.0676 (2)0.17285 (15)0.0399 (4)
N110.12533 (17)0.14869 (19)0.10998 (14)0.0492 (5)
C20.5255 (2)0.0765 (2)0.24983 (15)0.0431 (5)
C130.0186 (2)−0.0174 (2)0.2049 (2)0.0565 (6)
H13A−0.0573−0.07190.23190.068*
C80.4521 (2)0.2482 (3)−0.09045 (17)0.0560 (6)
H8A0.40380.2812−0.16150.067*
C140.1724 (2)−0.0382 (2)0.23391 (19)0.0536 (5)
H14A0.2255−0.10940.28470.064*
C70.6118 (2)0.2516 (3)−0.05784 (18)0.0560 (6)
H7A0.66920.2859−0.10920.067*
C150.5385 (3)0.0238 (4)0.3649 (2)0.0648 (7)
H30A−0.095 (3)0.129 (3)0.1009 (18)0.061 (7)*
H15C0.478 (4)−0.057 (4)0.372 (3)0.130 (13)*
H15B0.639 (4)−0.005 (4)0.396 (3)0.119 (12)*
H15A0.512 (5)0.106 (6)0.410 (4)0.184 (19)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N40.0254 (7)0.0391 (8)0.0440 (9)0.0020 (6)0.0003 (6)−0.0010 (6)
N10.0289 (8)0.0517 (10)0.0521 (10)−0.0001 (7)−0.0008 (7)0.0043 (7)
N60.0318 (9)0.0591 (10)0.0575 (11)−0.0004 (7)0.0089 (7)0.0040 (8)
C30.0303 (9)0.0368 (9)0.0446 (10)0.0011 (7)0.0051 (7)−0.0007 (8)
N120.0259 (9)0.0593 (11)0.0735 (12)0.0001 (7)0.0086 (8)0.0012 (9)
C50.0259 (9)0.0429 (10)0.0492 (11)0.0010 (7)0.0026 (7)−0.0013 (8)
C90.0325 (10)0.0550 (12)0.0504 (11)0.0036 (8)−0.0024 (8)0.0025 (9)
C100.0305 (9)0.0376 (10)0.0506 (11)0.0012 (7)0.0060 (8)−0.0044 (8)
N110.0265 (8)0.0531 (10)0.0666 (11)0.0001 (7)0.0063 (7)0.0046 (8)
C20.0344 (10)0.0436 (11)0.0485 (11)−0.0003 (8)0.0019 (8)0.0015 (8)
C130.0412 (11)0.0518 (12)0.0803 (16)−0.0067 (9)0.0212 (10)0.0038 (11)
C80.0467 (12)0.0715 (14)0.0474 (12)0.0043 (10)0.0040 (9)0.0095 (10)
C140.0393 (11)0.0500 (12)0.0720 (14)0.0008 (9)0.0124 (10)0.0112 (10)
C70.0455 (12)0.0683 (14)0.0565 (13)−0.0008 (10)0.0156 (10)0.0093 (11)
C150.0530 (15)0.0809 (18)0.0544 (14)−0.0088 (13)−0.0037 (11)0.0185 (13)
Geometric parameters (Å, º) top
N4—C91.362 (2)C9—H9A0.9500
N4—C31.384 (2)C10—N111.333 (2)
N4—C51.396 (2)C10—C141.394 (3)
N1—C51.317 (2)C2—C151.492 (3)
N1—C21.369 (2)C13—C141.364 (3)
N6—C71.307 (3)C13—H13A0.9500
N6—C51.345 (2)C8—C71.406 (3)
C3—C21.375 (2)C8—H8A0.9500
C3—C101.456 (2)C14—H14A0.9500
N12—C131.318 (3)C7—H7A0.9500
N12—N111.349 (2)C15—H15C0.92 (4)
N12—H30A0.89 (2)C15—H15B0.94 (4)
C9—C81.343 (3)C15—H15A0.98 (5)
C9—N4—C3133.30 (15)N1—C2—C3111.79 (17)
C9—N4—C5119.96 (16)N1—C2—C15120.70 (18)
C3—N4—C5106.74 (14)C3—C2—C15127.5 (2)
C5—N1—C2105.47 (14)N12—C13—C14107.10 (18)
C7—N6—C5116.74 (17)N12—C13—H13A126.4
C2—C3—N4104.82 (16)C14—C13—H13A126.4
C2—C3—C10132.26 (18)C9—C8—C7119.0 (2)
N4—C3—C10122.92 (15)C9—C8—H8A120.5
C13—N12—N11112.94 (17)C7—C8—H8A120.5
C13—N12—H30A125.4 (15)C13—C14—C10105.02 (19)
N11—N12—H30A121.7 (15)C13—C14—H14A127.5
N1—C5—N6126.85 (16)C10—C14—H14A127.5
N1—C5—N4111.16 (16)N6—C7—C8123.9 (2)
N6—C5—N4121.98 (17)N6—C7—H7A118.0
C8—C9—N4118.35 (17)C8—C7—H7A118.0
C8—C9—H9A120.8C2—C15—H15C114 (2)
N4—C9—H9A120.8C2—C15—H15B111 (2)
N11—C10—C14110.84 (17)H15C—C15—H15B106 (3)
N11—C10—C3120.54 (17)C2—C15—H15A110 (3)
C14—C10—C3128.62 (17)H15C—C15—H15A108 (3)
C10—N11—N12104.10 (16)H15B—C15—H15A107 (3)
C9—N4—C3—C2−178.99 (18)N4—C3—C10—C14152.1 (2)
C5—N4—C3—C21.06 (19)C14—C10—N11—N120.0 (2)
C9—N4—C3—C101.0 (3)C3—C10—N11—N12−179.70 (16)
C5—N4—C3—C10−178.91 (16)C13—N12—N11—C100.0 (2)
C2—N1—C5—N6−178.49 (18)C5—N1—C2—C30.3 (2)
C2—N1—C5—N40.4 (2)C5—N1—C2—C15−177.7 (2)
C7—N6—C5—N1−179.55 (19)N4—C3—C2—N1−0.9 (2)
C7—N6—C5—N41.7 (3)C10—C3—C2—N1179.06 (18)
C9—N4—C5—N1179.12 (16)N4—C3—C2—C15177.0 (2)
C3—N4—C5—N1−0.9 (2)C10—C3—C2—C15−3.0 (4)
C9—N4—C5—N6−2.0 (3)N11—N12—C13—C14−0.1 (3)
C3—N4—C5—N6177.99 (17)N4—C9—C8—C70.8 (3)
C3—N4—C9—C8−179.3 (2)N12—C13—C14—C100.0 (3)
C5—N4—C9—C80.6 (3)N11—C10—C14—C130.0 (2)
C2—C3—C10—N11151.8 (2)C3—C10—C14—C13179.63 (19)
N4—C3—C10—N11−28.2 (3)C5—N6—C7—C8−0.2 (3)
C2—C3—C10—C14−27.8 (3)C9—C8—C7—N6−1.1 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N12—H30A···N6i0.89 (2)2.08 (2)2.966 (2)175 (2)
Symmetry code: (i) x−1, y, z.

Experimental details

Crystal data
Chemical formulaC10H9N5
Mr199.22
Crystal system, space groupMonoclinic, P21/n
Temperature (K)173
a, b, c (Å)8.962 (2), 8.851 (2), 12.481 (3)
β (°) 101.751 (3)
V (Å3)969.3 (4)
Z4
Radiation typeMo Kα
µ (mm−1)0.09
Crystal size (mm)0.50 × 0.10 × 0.08
Data collection
DiffractometerBruker SMART APEX CCD
Absorption correctionMulti-scan
(SADABS; Bruker, 2000)
Tmin, Tmax0.956, 0.993
No. of measured, independent and
observed [I > 2σ(I)] reflections		5121, 1907, 1552
Rint0.024
(sin θ/λ)max (Å−1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.051, 0.128, 1.09
No. of reflections1907
No. of parameters152
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.20, −0.14

Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N12—H30A···N6i0.89 (2)2.08 (2)2.966 (2)175 (2)
Symmetry code: (i) x−1, y, z.
 

Acknowledgements

The authors thank the National Natural Science Foundation (grant Nos. 81102461, 81021062 and 90813034) and the National Science and Technology Major Project `Key New Drug Creation and Manufacturing Program' (grant Nos. 2012ZX09301-001-007 and 2012ZX09103101-024) of the People's Republic of China, and the Shanghai Science and Technology Commission (grant No. 11431921100).

References

First citationAn, H.-Y., Xi, B., Abassi, Y., Wang, X.-B. & Xu, X. (2009). WO Patent No. 2009023402.  Google Scholar
 First citationAnaflous, A., Benchat, N.-E., Ben-Hadda, T., El Bali, B. & Bolte, M. (2004). Acta Cryst. E60, o1131–o1132.  Web of Science CSD CrossRef IUCr Journals Google Scholar
 First citationBruker (2000). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationKim, J.-H., Hong, S.-H. & Hong, S.-W. (2011). Bioorg. Med. Chem. Lett. 21, 6977–6981.  Web of Science CrossRef CAS PubMed Google Scholar
 First citationLinton, A., Kang, P., Ornelas, M., Kephart, S., Hu, Q.-Y., Pairish, M., Jiang, Y. & Guo, C.-X. (2011). J. Med. Chem. 54, 7705–7712.  Web of Science CrossRef CAS PubMed Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationYang, F.-L., Li, G.-C. & Yao, C.-S. (2008). Acta Cryst. E64, o2469.  Web of Science CSD CrossRef 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 68| Part 7| July 2012| Page o1977
https://doi.org/10.1107/S1600536812024166
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