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Acta Crystallogr Sect E Struct Rep Online. 2009 December 1; 65(Pt 12): o2979.
Published online 2009 November 4. doi:  10.1107/S1600536809045243
PMCID: PMC2971878

N,N′-(4-Chloro­benzyl­idene)dipyrimidin-2-amine

Abstract

The title compound, C15H13ClN6, contains two pyrimidine rings and one benzene ring, where the dihedral angle between the planes through the pyrimidine rings is 81.57 (10)°, and those between the pyrimidine rings and the benzene ring are 84.02 (8) and 89.46 (7)°, indicating that the three rings are almost perpendicular. In the crystal, inter­molecular N—H(...)N hydrogen bonds link the mol­ecules into infinite chains along (100).

Related literature

For the biological activity of pyrimidine derivatives, see: Onal & Altral (1999 [triangle]); Ponticelli et al. (1999 [triangle]). For studies of the reactions of heterocyclic amines with aromatic aldehydes to prepare new ligands, see: Tabatabaee et al. (2006 [triangle]); Tabatabaee, Ghassemzadeh, Dehghan et al. (2007 [triangle]); Tabatabaee, Ghassemzadeh, Zarabi et al. (2007 [triangle]); Tabatabaee, Ghassemzadeh et al. (2008 [triangle]); Tabatabaee, Hakimi et al. (2008 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2979-scheme1.jpg

Experimental

Crystal data

  • C15H13ClN6
  • M r = 312.76
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2979-efi1.jpg
  • a = 9.6030 (14) Å
  • b = 10.5706 (15) Å
  • c = 14.792 (2) Å
  • β = 100.331 (3)°
  • V = 1477.2 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.26 mm−1
  • T = 120 K
  • 0.17 × 0.15 × 0.14 mm

Data collection

  • Bruker SMART 1000 CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1998 [triangle]) T min = 0.950, T max = 0.964
  • 15899 measured reflections
  • 3924 independent reflections
  • 2429 reflections with I > 2σ(I)
  • R int = 0.063

Refinement

  • R[F 2 > 2σ(F 2)] = 0.061
  • wR(F 2) = 0.163
  • S = 1.01
  • 3924 reflections
  • 207 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.55 e Å−3
  • Δρmin = −0.28 e Å−3

Data collection: SMART (Bruker, 1998 [triangle]); cell refinement: SAINT-Plus (Bruker, 1998 [triangle]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809045243/ez2187sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809045243/ez2187Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors express their appreciation to the Islamic Azad University, Yazd Branch, for financial support of this work.

supplementary crystallographic information

Comment

Pyrimidine derivatives represent a class of heterocycles of great importance. Many pyrimidines, or their derivatives, possess remarkable biological activity and have been widely used in medicinal and industrial applications (Onal & Altral, 1999; Ponticelli et al., 1999). In the continuation of our recent work on the reactions of heterocyclic amines with aromatic aldehydes to prepare new ligands (Tabatabaee et al., 2006; Tabatabaee, Ghassemzadeh, Dehghan et al., 2007; Tabatabaee, Ghassemzadeh, Zarabi et al., 2007; Tabatabaee, Ghassemzadeh et al., 2008; Tabatabaee, Hakimi et al., 2008) we report our results on the reaction of 2-aminopyrimidine and 4-chlorobenzaldehyde in this communication.

The crystal structure of (I) (Fig. 1) shows that one molecule of 4-chlorobenzaldehyde reacted with two molecules of 2-aminopyrimidine to form (I). Bond lengths and angles are unexceptional. The compound contains two pyrimidine (A:N2/C8/N3/C11/C10/C9 and B: N5/C12/N6/C15/C14/C13) and one benzene (C: C2/C3/C4/C5/C6/C7) rings, The dihedral angles formed by the planes through A and B is 81.57 (10)°, through A and C is 84.02 (8)° and through B and C is 89.49 (7)°, indicating that the three rings are almost perpendicular.

Intermolecular N—H···N hydrogen bonds link the molecules into infinite one-dimensional chains along (100) (Table 1 and Fig 2). An interesting feature of compound (I) is the presence of C—H···π stacking interactions between C—H groups from one molecule and aromatic rings on adjacent molecules. The C—H···π distance is 2.89 Å for C9—H9A···Cg3 (Cg3: C2/C3—C7), with an angle of 133.21° and 2.99 Å for C4—H4A···Cg1 (Cg1: N2/C8 — C9) with an angle of 132.27° (Fig. 3).

Experimental

A solution of 2-aminopyrimidine (0.951 g, 10 mmol) in EtOH (10 ml) was treated with 4- chlorobenzaldehyde (0.7 g, 5 mmol) and the resulting mixture was acidified with 37% hydrochloric acid (0.2 ml). The reaction mixture was refluxed for 12 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 92%).

Refinement

The hydrogen atoms of NH groups were found in difference Fourier syntheses and refined isotropically. The H(C) atom positions were calculated and refined in isotropic approximation using a riding model with the Uiso(H) parameters equal to 1.2 Ueq(Ci), where U(Ci) are the equivalent thermal parameters of the CH and CH2 carbon atoms to which the corresponding H atoms are bonded.

Figures

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···π interactions (dashed lines) between aromatic rings of adjacent molecules.

Crystal data

C15H13ClN6F(000) = 648
Mr = 312.76Dx = 1.406 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 697 reflections
a = 9.6030 (14) Åθ = 3–30°
b = 10.5706 (15) ŵ = 0.26 mm1
c = 14.792 (2) ÅT = 120 K
β = 100.331 (3)°Prism, colorless
V = 1477.2 (4) Å30.17 × 0.15 × 0.14 mm
Z = 4

Data collection

Bruker SMART 1000 CCD area-detector diffractometer3924 independent reflections
Radiation source: fine-focus sealed tube2429 reflections with I > 2σ(I)
graphiteRint = 0.063
ω scansθmax = 29.0°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Sheldrick, 1998)h = −13→13
Tmin = 0.950, Tmax = 0.964k = −14→14
15899 measured reflectionsl = −20→20

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.061Hydrogen site location: mixed
wR(F2) = 0.163H atoms treated by a mixture of independent and constrained refinement
S = 1.01w = 1/[σ2(Fo2) + (0.061P)2 + 1.85P] where P = (Fo2 + 2Fc2)/3
3924 reflections(Δ/σ)max = 0.001
207 parametersΔρmax = 0.55 e Å3
0 restraintsΔρmin = −0.28 e Å3

Special details

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)

xyzUiso*/Ueq
Cl1−0.02192 (8)0.53784 (7)0.18886 (5)0.0355 (2)
N10.3768 (2)0.1522 (2)0.49990 (15)0.0255 (5)
H1N0.372 (3)0.073 (3)0.4970 (19)0.026 (7)*
N20.5083 (2)0.3334 (2)0.53797 (15)0.0288 (5)
N30.6177 (2)0.13385 (19)0.51466 (14)0.0252 (5)
N40.1456 (2)0.1274 (2)0.53239 (15)0.0271 (5)
H4N0.100 (3)0.085 (3)0.490 (2)0.026 (7)*
N50.1916 (2)0.1776 (2)0.68744 (15)0.0297 (5)
N60.0426 (2)0.0032 (2)0.62930 (15)0.0324 (5)
C10.2469 (3)0.2170 (2)0.51066 (17)0.0236 (5)
H1A0.27010.27710.56350.028*
C20.1814 (3)0.2927 (2)0.42613 (17)0.0231 (5)
C30.2361 (3)0.2959 (2)0.34541 (18)0.0281 (6)
H3A0.31720.24680.34030.034*
C40.1729 (3)0.3708 (3)0.27187 (17)0.0305 (6)
H4A0.21060.37270.21680.037*
C50.0551 (3)0.4423 (2)0.27932 (17)0.0257 (5)
C6−0.0013 (3)0.4405 (2)0.35850 (18)0.0274 (5)
H6A−0.08240.48980.36330.033*
C70.0623 (3)0.3653 (2)0.43127 (17)0.0263 (5)
H7A0.02350.36350.48600.032*
C80.5041 (3)0.2088 (2)0.51871 (16)0.0227 (5)
C90.6373 (3)0.3841 (3)0.5586 (2)0.0346 (6)
H9A0.64520.47130.57410.041*
C100.7596 (3)0.3161 (3)0.5585 (2)0.0353 (7)
H10A0.85050.35370.57450.042*
C110.7431 (3)0.1905 (3)0.53381 (18)0.0295 (6)
H11A0.82540.14210.53030.035*
C120.1273 (3)0.1023 (3)0.61980 (17)0.0266 (5)
C130.1706 (3)0.1484 (3)0.77168 (19)0.0346 (6)
H13A0.21270.20050.82150.041*
C140.0906 (3)0.0461 (3)0.7899 (2)0.0406 (7)
H14A0.08020.02470.85070.049*
C150.0269 (3)−0.0232 (3)0.7149 (2)0.0406 (7)
H15A−0.0309−0.09290.72470.049*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0406 (4)0.0320 (4)0.0312 (4)0.0008 (3)−0.0014 (3)0.0066 (3)
N10.0227 (11)0.0213 (11)0.0316 (12)−0.0002 (9)0.0021 (9)0.0004 (9)
N20.0303 (12)0.0236 (11)0.0335 (12)−0.0039 (9)0.0081 (9)−0.0030 (9)
N30.0245 (11)0.0236 (11)0.0263 (11)−0.0021 (9)0.0016 (8)−0.0015 (9)
N40.0272 (11)0.0300 (12)0.0229 (11)−0.0074 (9)0.0016 (9)−0.0006 (9)
N50.0288 (12)0.0333 (12)0.0267 (11)−0.0018 (10)0.0043 (9)−0.0002 (9)
N60.0310 (12)0.0394 (13)0.0256 (11)−0.0081 (10)0.0021 (9)0.0041 (10)
C10.0227 (12)0.0234 (12)0.0238 (12)−0.0010 (10)0.0021 (9)−0.0017 (10)
C20.0237 (12)0.0221 (12)0.0235 (12)−0.0048 (10)0.0042 (9)0.0003 (10)
C30.0300 (14)0.0268 (13)0.0287 (13)0.0029 (11)0.0082 (11)−0.0007 (11)
C40.0366 (15)0.0345 (15)0.0220 (12)−0.0018 (12)0.0098 (11)−0.0007 (11)
C50.0288 (13)0.0235 (12)0.0230 (12)−0.0030 (10)−0.0001 (10)−0.0001 (10)
C60.0238 (12)0.0273 (13)0.0300 (13)0.0005 (10)0.0023 (10)−0.0025 (10)
C70.0246 (13)0.0306 (13)0.0245 (12)−0.0010 (11)0.0065 (10)−0.0003 (10)
C80.0261 (13)0.0221 (12)0.0199 (12)−0.0036 (10)0.0039 (10)0.0014 (10)
C90.0353 (15)0.0254 (13)0.0458 (16)−0.0095 (12)0.0147 (13)−0.0094 (12)
C100.0306 (14)0.0339 (15)0.0437 (16)−0.0109 (12)0.0128 (12)−0.0118 (13)
C110.0267 (13)0.0306 (14)0.0316 (14)−0.0019 (11)0.0065 (11)−0.0009 (11)
C120.0225 (12)0.0311 (14)0.0256 (13)0.0013 (11)0.0028 (10)0.0023 (11)
C130.0317 (15)0.0410 (16)0.0291 (14)0.0026 (12)0.0004 (11)−0.0044 (12)
C140.0368 (16)0.059 (2)0.0258 (14)−0.0061 (15)0.0058 (12)0.0057 (14)
C150.0346 (16)0.0541 (19)0.0330 (15)−0.0126 (14)0.0059 (12)0.0119 (14)

Geometric parameters (Å, °)

Cl1—C51.732 (3)C3—C41.394 (4)
N1—C81.345 (3)C3—H3A0.9500
N1—C11.456 (3)C4—C51.381 (4)
N1—H1N0.84 (3)C4—H4A0.9500
N2—C91.334 (3)C5—C61.376 (4)
N2—C81.347 (3)C6—C71.388 (4)
N3—C111.329 (3)C6—H6A0.9500
N3—C81.358 (3)C7—H7A0.9500
N4—C121.362 (3)C9—C101.377 (4)
N4—C11.435 (3)C9—H9A0.9500
N4—H4N0.83 (3)C10—C111.378 (4)
N5—C131.334 (4)C10—H10A0.9500
N5—C121.339 (3)C11—H11A0.9500
N6—C151.331 (4)C13—C141.381 (4)
N6—C121.349 (3)C13—H13A0.9500
C1—C21.523 (3)C14—C151.378 (4)
C1—H1A1.0000C14—H14A0.9500
C2—C31.389 (3)C15—H15A0.9500
C2—C71.390 (3)
C8—N1—C1122.2 (2)C5—C6—H6A120.6
C8—N1—H1N120 (2)C7—C6—H6A120.6
C1—N1—H1N116 (2)C6—C7—C2121.7 (2)
C9—N2—C8115.6 (2)C6—C7—H7A119.2
C11—N3—C8115.6 (2)C2—C7—H7A119.2
C12—N4—C1123.3 (2)N1—C8—N2118.0 (2)
C12—N4—H4N118 (2)N1—C8—N3116.1 (2)
C1—N4—H4N119 (2)N2—C8—N3125.9 (2)
C13—N5—C12115.7 (2)N2—C9—C10123.2 (3)
C15—N6—C12115.8 (2)N2—C9—H9A118.4
N4—C1—N1110.0 (2)C10—C9—H9A118.4
N4—C1—C2109.5 (2)C9—C10—C11116.5 (3)
N1—C1—C2113.2 (2)C9—C10—H10A121.8
N4—C1—H1A108.0C11—C10—H10A121.8
N1—C1—H1A108.0N3—C11—C10123.1 (3)
C2—C1—H1A108.0N3—C11—H11A118.4
C3—C2—C7118.4 (2)C10—C11—H11A118.4
C3—C2—C1123.7 (2)N5—C12—N6126.1 (2)
C7—C2—C1117.9 (2)N5—C12—N4118.2 (2)
C2—C3—C4120.4 (2)N6—C12—N4115.7 (2)
C2—C3—H3A119.8N5—C13—C14123.1 (3)
C4—C3—H3A119.8N5—C13—H13A118.5
C5—C4—C3119.8 (2)C14—C13—H13A118.5
C5—C4—H4A120.1C15—C14—C13116.2 (3)
C3—C4—H4A120.1C15—C14—H14A121.9
C6—C5—C4120.9 (2)C13—C14—H14A121.9
C6—C5—Cl1119.1 (2)N6—C15—C14123.0 (3)
C4—C5—Cl1120.0 (2)N6—C15—H15A118.5
C5—C6—C7118.8 (2)C14—C15—H15A118.5
C12—N4—C1—N196.1 (3)C1—N1—C8—N3173.6 (2)
C12—N4—C1—C2−139.0 (2)C9—N2—C8—N1178.2 (2)
C8—N1—C1—N4−150.6 (2)C9—N2—C8—N3−3.1 (4)
C8—N1—C1—C286.6 (3)C11—N3—C8—N1−179.7 (2)
N4—C1—C2—C3−120.7 (3)C11—N3—C8—N21.6 (4)
N1—C1—C2—C32.5 (3)C8—N2—C9—C101.5 (4)
N4—C1—C2—C761.2 (3)N2—C9—C10—C111.2 (4)
N1—C1—C2—C7−175.7 (2)C8—N3—C11—C101.5 (4)
C7—C2—C3—C40.3 (4)C9—C10—C11—N3−2.8 (4)
C1—C2—C3—C4−177.9 (2)C13—N5—C12—N61.4 (4)
C2—C3—C4—C50.0 (4)C13—N5—C12—N4−179.7 (2)
C3—C4—C5—C6−0.2 (4)C15—N6—C12—N5−2.5 (4)
C3—C4—C5—Cl1178.8 (2)C15—N6—C12—N4178.6 (3)
C4—C5—C6—C70.1 (4)C1—N4—C12—N510.1 (4)
Cl1—C5—C6—C7−179.0 (2)C1—N4—C12—N6−170.9 (2)
C5—C6—C7—C20.3 (4)C12—N5—C13—C141.4 (4)
C3—C2—C7—C6−0.4 (4)N5—C13—C14—C15−2.8 (5)
C1—C2—C7—C6177.8 (2)C12—N6—C15—C140.8 (5)
C1—N1—C8—N2−7.6 (3)C13—C14—C15—N61.6 (5)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N···N3i0.84 (3)2.20 (3)3.033 (3)174 (3)
N4—H4N···N6ii0.83 (3)2.24 (3)3.057 (3)172 (3)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: EZ2187).

References

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  • Tabatabaee, M., Hakimi, F., Roshani, M., Mirjalili, M. & Kavasi, H. R. (2008). Acta Cryst. E64, o2112. [PMC free article] [PubMed]

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