organic compounds
1-(2-Pyridyl)-N,N′-dipyrimidin-2-ylmethanediamine
aDepartment of Chemistry, Islamic Azad University, Yazd Branch, Yazd, Iran, bDepartment of Chemistry, Islamic Azad University, Mashhad Branch, Mashhad, Iran, cDepartment of Textile Engineering, Yazd, Iran, and dDepartment of Chemistry, Shahid Beheshti University, Tehran, Iran
*Correspondence e-mail: tabatabaee45m@yahoo.com
In the title compound, C14H13N7, intermolecular N—H⋯N and C—H⋯N hydrogen bonds link the molecules into infinite one-dimensional chains along (100). A C—H⋯π interaction also occurs in the crystal.
Related literature
For the biological activity of pyrimidine derivatives, see: Onal & Altral (1999); Ponticelli & Spanu (1999). For their uses in coordination chemistry, see: Prince et al. (2003); Lee et al. (2003); Masaki et al. (2002). For studies of the reactions of heterocyclic with aromatic aldehyde to prepare new ligands, see: Tabatabaee et al. (2006, 2007a,b, 2008).
Experimental
Crystal data
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Refinement
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Data collection: X-AREA (Stoe & Cie, 2005); cell X-AREA; data reduction: X-RED32 (Stoe & Cie, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).
Supporting information
10.1107/S1600536808032583/bq2098sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536808032583/bq2098Isup2.hkl
A solution of 2-aminopyrimidine (0.94 g, 1 mmol) in EtOH (15 ml) was treated with 2-pyridinecarbaldehyde (0.107 g, 1 mmol) and the resulting mixture was acidified with 37% hydrochloric acid (0.2 ml). The reaction mixture was refluxed for 8 h. The solid residue was filtered and the filtrate was kept at 293 K. Colorless crystals of the title compound were obtained after a few days (yield 83%).
All of the H atoms were located in a difference synthesis and refined isotropically [aromatic C—H = 0.82 (2)–1.07 (3) Å, tertiary C—H = 0.97 (2) Å and N—H = 0.79 (2)–0.89 (2) Å] and refined isotropically.
Data collection: X-AREA (Stoe & Cie, 2005); cell
X-AREA (Stoe & Cie, 2005); data reduction: X-RED32 (Stoe & Cie, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).Fig. 1. The molecular structure of (I). Displacement ellipsoids are drawn at the 50% probability level. | |
Fig. 2. Packing diagram of (I), molecules are linked into infinite one dimensional chains by hydrogen-bond interactions (dashed lines). | |
Fig. 3. Intermolecular C—H···\p interaction between one aromatic pyrimidine ring and adjacent molecule. |
C14H13N7 | F(000) = 584 |
Mr = 279.31 | Dx = 1.307 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 2000 reflections |
a = 9.5781 (19) Å | θ = 2.4–26.8° |
b = 9.3543 (16) Å | µ = 0.09 mm−1 |
c = 15.975 (4) Å | T = 296 K |
β = 97.521 (17)° | Plate, colorless |
V = 1419.0 (5) Å3 | 0.45 × 0.20 × 0.05 mm |
Z = 4 |
Stoe IPDS-II diffractometer | 2997 independent reflections |
Radiation source: fine-focus sealed tube | 2443 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.032 |
rotation method scans | θmax = 26.8°, θmin = 2.4° |
Absorption correction: numerical shape of crystal determined optically (Program? reference?) | h = −12→12 |
Tmin = 0.970, Tmax = 0.998 | k = −11→11 |
12281 measured reflections | l = −20→17 |
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)] = 0.058 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.140 | All H-atom parameters refined |
S = 1.12 | w = 1/[σ2(Fo2) + (0.0555P)2 + 0.3988P] where P = (Fo2 + 2Fc2)/3 |
2997 reflections | (Δ/σ)max = 0.002 |
242 parameters | Δρmax = 0.15 e Å−3 |
0 restraints | Δρmin = −0.16 e Å−3 |
C14H13N7 | V = 1419.0 (5) Å3 |
Mr = 279.31 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 9.5781 (19) Å | µ = 0.09 mm−1 |
b = 9.3543 (16) Å | T = 296 K |
c = 15.975 (4) Å | 0.45 × 0.20 × 0.05 mm |
β = 97.521 (17)° |
Stoe IPDS-II diffractometer | 2997 independent reflections |
Absorption correction: numerical shape of crystal determined optically (Program? reference?) | 2443 reflections with I > 2σ(I) |
Tmin = 0.970, Tmax = 0.998 | Rint = 0.032 |
12281 measured reflections |
R[F2 > 2σ(F2)] = 0.058 | 0 restraints |
wR(F2) = 0.140 | All H-atom parameters refined |
S = 1.12 | Δρmax = 0.15 e Å−3 |
2997 reflections | Δρmin = −0.16 e Å−3 |
242 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.9822 (4) | 0.8397 (4) | 0.2536 (3) | 0.1170 (12) | |
H1 | 1.065 (4) | 0.909 (5) | 0.265 (3) | 0.172 (17)* | |
C2 | 0.9364 (4) | 0.7672 (5) | 0.3161 (2) | 0.1087 (12) | |
H2 | 0.973 (4) | 0.786 (4) | 0.372 (3) | 0.149 (14)* | |
C3 | 0.8303 (4) | 0.6738 (5) | 0.2982 (2) | 0.1054 (12) | |
H3 | 0.783 (4) | 0.619 (4) | 0.328 (3) | 0.141 (14)* | |
C4 | 0.7696 (3) | 0.6561 (3) | 0.21369 (16) | 0.0746 (7) | |
H4 | 0.702 (3) | 0.604 (3) | 0.2000 (16) | 0.074 (8)* | |
C5 | 0.82060 (18) | 0.7345 (2) | 0.15391 (11) | 0.0488 (4) | |
C6 | 0.76338 (17) | 0.7253 (2) | 0.06118 (11) | 0.0458 (4) | |
H6 | 0.7549 (19) | 0.821 (2) | 0.0380 (12) | 0.048 (5)* | |
C7 | 0.87637 (17) | 0.6815 (2) | −0.06540 (11) | 0.0464 (4) | |
C8 | 0.8208 (3) | 0.8159 (3) | −0.18238 (15) | 0.0816 (8) | |
H8 | 0.753 (3) | 0.896 (3) | −0.2127 (17) | 0.098 (8)* | |
C9 | 0.9149 (3) | 0.7437 (3) | −0.22277 (16) | 0.0859 (8) | |
H9 | 0.928 (3) | 0.768 (3) | −0.2817 (19) | 0.106 (9)* | |
C10 | 0.9855 (3) | 0.6351 (3) | −0.17964 (14) | 0.0745 (7) | |
H10 | 1.054 (3) | 0.577 (3) | −0.2047 (16) | 0.086 (7)* | |
C11 | 0.50462 (17) | 0.72192 (19) | 0.05133 (10) | 0.0441 (4) | |
C12 | 0.3865 (2) | 0.9233 (2) | 0.07540 (14) | 0.0599 (5) | |
H12 | 0.394 (2) | 1.026 (3) | 0.0921 (14) | 0.074 (7)* | |
C13 | 0.2605 (2) | 0.8541 (3) | 0.05806 (16) | 0.0698 (6) | |
H13 | 0.170 (3) | 0.897 (3) | 0.0602 (16) | 0.091 (8)* | |
C14 | 0.2664 (2) | 0.7119 (3) | 0.03806 (16) | 0.0681 (6) | |
H14 | 0.180 (3) | 0.652 (3) | 0.0280 (15) | 0.078 (7)* | |
N1 | 0.9275 (2) | 0.8262 (3) | 0.17169 (15) | 0.0913 (7) | |
N2 | 0.86343 (15) | 0.65215 (18) | 0.01597 (9) | 0.0504 (4) | |
H2B | 0.915 (2) | 0.583 (2) | 0.0422 (13) | 0.058 (6)* | |
N3 | 0.7991 (2) | 0.7869 (2) | −0.10338 (11) | 0.0681 (5) | |
N4 | 0.96897 (16) | 0.59970 (18) | −0.10065 (10) | 0.0565 (4) | |
N5 | 0.62782 (15) | 0.65417 (19) | 0.04528 (11) | 0.0523 (4) | |
H5B | 0.623 (2) | 0.575 (2) | 0.0285 (13) | 0.055 (6)* | |
N6 | 0.51088 (15) | 0.85980 (16) | 0.07449 (10) | 0.0505 (4) | |
N7 | 0.38702 (15) | 0.64257 (18) | 0.03335 (11) | 0.0569 (4) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.116 (3) | 0.121 (3) | 0.100 (3) | −0.013 (2) | −0.041 (2) | −0.015 (2) |
C2 | 0.116 (3) | 0.145 (3) | 0.0593 (18) | 0.041 (2) | −0.0115 (17) | −0.023 (2) |
C3 | 0.108 (2) | 0.148 (3) | 0.0659 (18) | 0.040 (2) | 0.0316 (17) | 0.026 (2) |
C4 | 0.0699 (15) | 0.0954 (18) | 0.0600 (14) | 0.0035 (14) | 0.0142 (11) | 0.0109 (12) |
C5 | 0.0422 (9) | 0.0545 (10) | 0.0499 (10) | 0.0134 (8) | 0.0070 (7) | −0.0050 (8) |
C6 | 0.0405 (8) | 0.0518 (10) | 0.0466 (9) | 0.0107 (7) | 0.0112 (7) | −0.0019 (8) |
C7 | 0.0407 (8) | 0.0538 (10) | 0.0455 (9) | 0.0083 (7) | 0.0090 (7) | −0.0013 (7) |
C8 | 0.1015 (18) | 0.0871 (17) | 0.0587 (13) | 0.0359 (15) | 0.0206 (12) | 0.0189 (12) |
C9 | 0.112 (2) | 0.0959 (19) | 0.0560 (13) | 0.0323 (16) | 0.0355 (13) | 0.0144 (12) |
C10 | 0.0840 (15) | 0.0874 (16) | 0.0574 (13) | 0.0288 (13) | 0.0289 (11) | −0.0031 (11) |
C11 | 0.0417 (9) | 0.0548 (10) | 0.0366 (8) | 0.0108 (7) | 0.0072 (6) | −0.0032 (7) |
C12 | 0.0564 (11) | 0.0512 (11) | 0.0751 (14) | 0.0147 (9) | 0.0204 (10) | −0.0017 (10) |
C13 | 0.0472 (11) | 0.0715 (14) | 0.0916 (16) | 0.0217 (10) | 0.0126 (10) | −0.0089 (12) |
C14 | 0.0410 (10) | 0.0758 (15) | 0.0865 (16) | 0.0063 (10) | 0.0041 (9) | −0.0215 (12) |
N1 | 0.0819 (14) | 0.0997 (16) | 0.0858 (15) | −0.0169 (13) | −0.0136 (11) | 0.0007 (12) |
N2 | 0.0471 (8) | 0.0599 (10) | 0.0458 (8) | 0.0211 (7) | 0.0127 (6) | 0.0045 (7) |
N3 | 0.0792 (12) | 0.0745 (12) | 0.0535 (10) | 0.0336 (10) | 0.0197 (8) | 0.0095 (8) |
N4 | 0.0549 (9) | 0.0641 (10) | 0.0533 (9) | 0.0174 (8) | 0.0173 (7) | −0.0023 (7) |
N5 | 0.0394 (8) | 0.0528 (10) | 0.0648 (10) | 0.0093 (7) | 0.0066 (6) | −0.0165 (8) |
N6 | 0.0480 (8) | 0.0486 (8) | 0.0575 (9) | 0.0088 (7) | 0.0162 (7) | −0.0010 (7) |
N7 | 0.0406 (8) | 0.0603 (10) | 0.0690 (11) | 0.0080 (7) | 0.0041 (7) | −0.0189 (8) |
C1—C2 | 1.327 (6) | C8—C9 | 1.355 (3) |
C1—N1 | 1.350 (4) | C8—H8 | 1.07 (3) |
C1—H1 | 1.03 (4) | C9—C10 | 1.357 (4) |
C2—C3 | 1.343 (6) | C9—H9 | 0.99 (3) |
C2—H2 | 0.93 (4) | C10—N4 | 1.334 (3) |
C3—C4 | 1.408 (4) | C10—H10 | 0.98 (3) |
C3—H3 | 0.87 (4) | C11—N6 | 1.341 (2) |
C4—C5 | 1.346 (3) | C11—N7 | 1.348 (2) |
C4—H4 | 0.82 (2) | C11—N5 | 1.354 (2) |
C5—N1 | 1.338 (3) | C12—N6 | 1.333 (2) |
C5—C6 | 1.513 (3) | C12—C13 | 1.366 (3) |
C6—N2 | 1.446 (2) | C12—H12 | 1.00 (2) |
C6—N5 | 1.452 (2) | C13—C14 | 1.371 (3) |
C6—H6 | 0.97 (2) | C13—H13 | 0.96 (3) |
C7—N3 | 1.331 (2) | C14—N7 | 1.335 (2) |
C7—N4 | 1.349 (2) | C14—H14 | 1.00 (2) |
C7—N2 | 1.350 (2) | N2—H2B | 0.89 (2) |
C8—N3 | 1.334 (3) | N5—H5B | 0.79 (2) |
C2—C1—N1 | 123.8 (4) | C8—C9—H9 | 120.8 (17) |
C2—C1—H1 | 121 (2) | C10—C9—H9 | 122.4 (17) |
N1—C1—H1 | 115 (2) | N4—C10—C9 | 123.6 (2) |
C1—C2—C3 | 119.2 (3) | N4—C10—H10 | 114.7 (15) |
C1—C2—H2 | 120 (3) | C9—C10—H10 | 121.8 (15) |
C3—C2—H2 | 120 (2) | N6—C11—N7 | 126.46 (15) |
C2—C3—C4 | 119.1 (3) | N6—C11—N5 | 117.52 (16) |
C2—C3—H3 | 135 (3) | N7—C11—N5 | 116.02 (16) |
C4—C3—H3 | 106 (3) | N6—C12—C13 | 123.62 (19) |
C5—C4—C3 | 118.3 (3) | N6—C12—H12 | 113.6 (13) |
C5—C4—H4 | 118.9 (18) | C13—C12—H12 | 122.7 (13) |
C3—C4—H4 | 122.7 (18) | C12—C13—C14 | 116.41 (18) |
N1—C5—C4 | 122.5 (2) | C12—C13—H13 | 124.8 (16) |
N1—C5—C6 | 114.40 (18) | C14—C13—H13 | 118.7 (16) |
C4—C5—C6 | 123.1 (2) | N7—C14—C13 | 123.1 (2) |
N2—C6—N5 | 109.37 (15) | N7—C14—H14 | 115.2 (14) |
N2—C6—C5 | 109.70 (14) | C13—C14—H14 | 121.6 (14) |
N5—C6—C5 | 113.47 (15) | C5—N1—C1 | 117.0 (3) |
N2—C6—H6 | 105.9 (11) | C7—N2—C6 | 122.37 (15) |
N5—C6—H6 | 109.2 (11) | C7—N2—H2B | 119.2 (13) |
C5—C6—H6 | 108.9 (11) | C6—N2—H2B | 118.4 (13) |
N3—C7—N4 | 125.93 (16) | C7—N3—C8 | 115.86 (17) |
N3—C7—N2 | 118.29 (15) | C10—N4—C7 | 114.85 (17) |
N4—C7—N2 | 115.78 (16) | C11—N5—C6 | 122.74 (16) |
N3—C8—C9 | 123.0 (2) | C11—N5—H5B | 117.0 (15) |
N3—C8—H8 | 114.3 (15) | C6—N5—H5B | 120.0 (15) |
C9—C8—H8 | 122.5 (15) | C12—N6—C11 | 115.09 (17) |
C8—C9—C10 | 116.7 (2) | C14—N7—C11 | 115.17 (17) |
N1—C1—C2—C3 | 0.4 (6) | N5—C6—N2—C7 | 85.7 (2) |
C1—C2—C3—C4 | −0.5 (5) | C5—C6—N2—C7 | −149.27 (18) |
C2—C3—C4—C5 | −0.3 (5) | N4—C7—N3—C8 | −2.7 (3) |
C3—C4—C5—N1 | 1.1 (4) | N2—C7—N3—C8 | 176.9 (2) |
C3—C4—C5—C6 | −179.6 (2) | C9—C8—N3—C7 | 0.2 (4) |
N1—C5—C6—N2 | 71.8 (2) | C9—C10—N4—C7 | −0.6 (4) |
C4—C5—C6—N2 | −107.6 (2) | N3—C7—N4—C10 | 2.9 (3) |
N1—C5—C6—N5 | −165.58 (18) | N2—C7—N4—C10 | −176.74 (19) |
C4—C5—C6—N5 | 15.0 (3) | N6—C11—N5—C6 | −1.2 (3) |
N3—C8—C9—C10 | 1.8 (5) | N7—C11—N5—C6 | 178.94 (16) |
C8—C9—C10—N4 | −1.6 (5) | N2—C6—N5—C11 | −154.94 (16) |
N6—C12—C13—C14 | −0.7 (4) | C5—C6—N5—C11 | 82.2 (2) |
C12—C13—C14—N7 | −1.5 (4) | C13—C12—N6—C11 | 2.9 (3) |
C4—C5—N1—C1 | −1.1 (4) | N7—C11—N6—C12 | −3.3 (3) |
C6—C5—N1—C1 | 179.5 (3) | N5—C11—N6—C12 | 176.80 (17) |
C2—C1—N1—C5 | 0.4 (5) | C13—C14—N7—C11 | 1.2 (3) |
N3—C7—N2—C6 | 3.6 (3) | N6—C11—N7—C14 | 1.4 (3) |
N4—C7—N2—C6 | −176.73 (17) | N5—C11—N7—C14 | −178.76 (18) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2B···N4i | 0.885 (19) | 2.181 (19) | 3.064 (2) | 175.3 (19) |
N5—H5B···N7ii | 0.787 (19) | 2.259 (19) | 3.042 (3) | 174 (2) |
C4—H4···N5 | 0.82 (3) | 2.53 (3) | 2.851 (3) | 105 (2) |
C6—H6···N3 | 0.968 (19) | 2.373 (19) | 2.756 (3) | 102.9 (13) |
C12—H12···N3iii | 1.00 (3) | 2.57 (2) | 3.304 (3) | 130.4 (15) |
C9—H9···Cg1iv | 0.99 (3) | 2.62 (3) | 3.532 (3) | 154 (3) |
Symmetry codes: (i) −x+2, −y+1, −z; (ii) −x+1, −y+1, −z; (iii) −x+1, −y+2, −z; (iv) x+1/2, −y+3/2, z−1/2. |
Experimental details
Crystal data | |
Chemical formula | C14H13N7 |
Mr | 279.31 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 296 |
a, b, c (Å) | 9.5781 (19), 9.3543 (16), 15.975 (4) |
β (°) | 97.521 (17) |
V (Å3) | 1419.0 (5) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.45 × 0.20 × 0.05 |
Data collection | |
Diffractometer | Stoe IPDS-II diffractometer |
Absorption correction | Numerical shape of crystal determined optically (Program? reference?) |
Tmin, Tmax | 0.970, 0.998 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 12281, 2997, 2443 |
Rint | 0.032 |
(sin θ/λ)max (Å−1) | 0.634 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.058, 0.140, 1.12 |
No. of reflections | 2997 |
No. of parameters | 242 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.15, −0.16 |
Computer programs: X-AREA (Stoe & Cie, 2005), X-RED32 (Stoe & Cie, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2B···N4i | 0.885 (19) | 2.181 (19) | 3.064 (2) | 175.3 (19) |
N5—H5B···N7ii | 0.787 (19) | 2.259 (19) | 3.042 (3) | 174 (2) |
C4—H4···N5 | 0.82 (3) | 2.53 (3) | 2.851 (3) | 105 (2) |
C6—H6···N3 | 0.968 (19) | 2.373 (19) | 2.756 (3) | 102.9 (13) |
C12—H12···N3iii | 1.00 (3) | 2.57 (2) | 3.304 (3) | 130.4 (15) |
C9—H9···Cg1iv | 0.99 (3) | 2.62 (3) | 3.532 (3) | 154 (3) |
Symmetry codes: (i) −x+2, −y+1, −z; (ii) −x+1, −y+1, −z; (iii) −x+1, −y+2, −z; (iv) x+1/2, −y+3/2, z−1/2. |
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Pyrimidines derivatives possess remarkable biological activity and have been widely used in medicinal and industrial applications (Onal & Altral, 1999; Ponticelli et al. 1999). Moreover amino pyrimidine derivatives find use in coordination chemistry (Prince et al. 2003; Masaki et al. 2002; Lee et al. 2003). In continuation of our recent work on the reactions of heterocyclic amines with aromatic aldehyde to prepare of new ligands (Tabatabaee et al. 2006; Tabatabaee et al. 2007a,b; Tabatabaee et al. 2008) in this communication, we report, our results on the reaction of 2-aminopyrimidine and 2-pyridinecarbaldehyde. The title compound, C14H13N7, (I), is a new aminoacetal compound obtained from condensation of 2-aminopyrimidine with 2-pyridinecarbaldehyde. The crystal structure of (I) (Fig. 1) shows that one molecule of 2-pyridinecarbaldehyde was reacted with two molecules of 2-aminopyrimidine to form (I). Bond lengths and angles are unexceptional and the molecular structure is stabilized by some intermolecular N—H···N and C—H···N hydrogen-bonds (Table I). In the crystal packing (Fig. 2), molecules are linked into infinite one dimensional chains by hydrogen-bond interactions. A considerable feature of the compound (I) is the presence of C—H···π stacking interactions between C—H groups from one molecule and aromatic pyrimidine ring of adjacent molecule.The C—H···π distance is 2.62 (3) Å for C9—H9···Cg1 (Cg1 is the center of pyrimidine ring), with the angle of 154 (3)° (Fig.3).