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

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).

Key indicators

• Single-crystal X-ray study
• T = 120 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.061
• wR factor = 0.163
• Data-to-parameter ratio = 19.0

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT431_ALERT_2_C Short Inter HL..A Contact  Cl1    ..  N3      ..       3.15 Ang.
PLAT927_ALERT_1_C Reported and Calculated  wR2 * 100.0 Differ by .      -0.11

Alert level G
PLAT960_ALERT_3_G Number of Intensities with I .LT. - 2*sig(I) ..           2
PLAT128_ALERT_4_G Non-standard setting of Space-group P21/c   ....      P21/n

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   2 ALERT level G = General alerts; check

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. 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).

Related literature

For the biological activity of pyrimidine derivatives, see: Onal & Altral (1999); Ponticelli et al. (1999). For studies of the reactions of heterocyclic amines with aromatic aldehyde to prepare new ligands, see: 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).

S2. 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%).

S3. 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 U_iso(H) parameters equal to 1.2 U_eq(Ci), where U(Ci) are the equivalent thermal parameters of the CH and CH₂ carbon atoms to which the corresponding H atoms are bonded.

Computing details

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

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.

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

Crystal data

C15H13ClN6	F(000) = 648
Mr = 312.76	Dx = 1.406 Mg m^−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 697 reflections
a = 9.6030 (14) Å	θ = 3–30°
b = 10.5706 (15) Å	µ = 0.26 mm^−1
c = 14.792 (2) Å	T = 120 K
β = 100.331 (3)°	Prism, colorless
V = 1477.2 (4) Å^3	0.17 × 0.15 × 0.14 mm
Z = 4

Data collection

Bruker SMART 1000 CCD area-detector diffractometer	3924 independent reflections
Radiation source: fine-focus sealed tube	2429 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.063
ω scans	θmax = 29.0°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Sheldrick, 1998)	h = −13→13
Tmin = 0.950, Tmax = 0.964	k = −14→14
15899 measured reflections	l = −20→20

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.061	Hydrogen site location: mixed
wR(F^2) = 0.163	H atoms treated by a mixture of independent and constrained refinement
S = 1.01	w = 1/[σ^2(Fo^2) + (0.061P)^2 + 1.85P] where P = (Fo^2 + 2Fc^2)/3
3924 reflections	(Δ/σ)max = 0.001
207 parameters	Δρmax = 0.55 e Å^−3
0 restraints	Δρmin = −0.28 e Å^−3

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 (Ų)

	x	y	z	Uiso*/Ueq
Cl1	−0.02192 (8)	0.53784 (7)	0.18886 (5)	0.0355 (2)
N1	0.3768 (2)	0.1522 (2)	0.49990 (15)	0.0255 (5)
H1N	0.372 (3)	0.073 (3)	0.4970 (19)	0.026 (7)*
N2	0.5083 (2)	0.3334 (2)	0.53797 (15)	0.0288 (5)
N3	0.6177 (2)	0.13385 (19)	0.51466 (14)	0.0252 (5)
N4	0.1456 (2)	0.1274 (2)	0.53239 (15)	0.0271 (5)
H4N	0.100 (3)	0.085 (3)	0.490 (2)	0.026 (7)*
N5	0.1916 (2)	0.1776 (2)	0.68744 (15)	0.0297 (5)
N6	0.0426 (2)	0.0032 (2)	0.62930 (15)	0.0324 (5)
C1	0.2469 (3)	0.2170 (2)	0.51066 (17)	0.0236 (5)
H1A	0.2701	0.2771	0.5635	0.028*
C2	0.1814 (3)	0.2927 (2)	0.42613 (17)	0.0231 (5)
C3	0.2361 (3)	0.2959 (2)	0.34541 (18)	0.0281 (6)
H3A	0.3172	0.2468	0.3403	0.034*
C4	0.1729 (3)	0.3708 (3)	0.27187 (17)	0.0305 (6)
H4A	0.2106	0.3727	0.2168	0.037*
C5	0.0551 (3)	0.4423 (2)	0.27932 (17)	0.0257 (5)
C6	−0.0013 (3)	0.4405 (2)	0.35850 (18)	0.0274 (5)
H6A	−0.0824	0.4898	0.3633	0.033*
C7	0.0623 (3)	0.3653 (2)	0.43127 (17)	0.0263 (5)
H7A	0.0235	0.3635	0.4860	0.032*
C8	0.5041 (3)	0.2088 (2)	0.51871 (16)	0.0227 (5)
C9	0.6373 (3)	0.3841 (3)	0.5586 (2)	0.0346 (6)
H9A	0.6452	0.4713	0.5741	0.041*
C10	0.7596 (3)	0.3161 (3)	0.5585 (2)	0.0353 (7)
H10A	0.8505	0.3537	0.5745	0.042*
C11	0.7431 (3)	0.1905 (3)	0.53381 (18)	0.0295 (6)
H11A	0.8254	0.1421	0.5303	0.035*
C12	0.1273 (3)	0.1023 (3)	0.61980 (17)	0.0266 (5)
C13	0.1706 (3)	0.1484 (3)	0.77168 (19)	0.0346 (6)
H13A	0.2127	0.2005	0.8215	0.041*
C14	0.0906 (3)	0.0461 (3)	0.7899 (2)	0.0406 (7)
H14A	0.0802	0.0247	0.8507	0.049*
C15	0.0269 (3)	−0.0232 (3)	0.7149 (2)	0.0406 (7)
H15A	−0.0309	−0.0929	0.7247	0.049*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.0406 (4)	0.0320 (4)	0.0312 (4)	0.0008 (3)	−0.0014 (3)	0.0066 (3)
N1	0.0227 (11)	0.0213 (11)	0.0316 (12)	−0.0002 (9)	0.0021 (9)	0.0004 (9)
N2	0.0303 (12)	0.0236 (11)	0.0335 (12)	−0.0039 (9)	0.0081 (9)	−0.0030 (9)
N3	0.0245 (11)	0.0236 (11)	0.0263 (11)	−0.0021 (9)	0.0016 (8)	−0.0015 (9)
N4	0.0272 (11)	0.0300 (12)	0.0229 (11)	−0.0074 (9)	0.0016 (9)	−0.0006 (9)
N5	0.0288 (12)	0.0333 (12)	0.0267 (11)	−0.0018 (10)	0.0043 (9)	−0.0002 (9)
N6	0.0310 (12)	0.0394 (13)	0.0256 (11)	−0.0081 (10)	0.0021 (9)	0.0041 (10)
C1	0.0227 (12)	0.0234 (12)	0.0238 (12)	−0.0010 (10)	0.0021 (9)	−0.0017 (10)
C2	0.0237 (12)	0.0221 (12)	0.0235 (12)	−0.0048 (10)	0.0042 (9)	0.0003 (10)
C3	0.0300 (14)	0.0268 (13)	0.0287 (13)	0.0029 (11)	0.0082 (11)	−0.0007 (11)
C4	0.0366 (15)	0.0345 (15)	0.0220 (12)	−0.0018 (12)	0.0098 (11)	−0.0007 (11)
C5	0.0288 (13)	0.0235 (12)	0.0230 (12)	−0.0030 (10)	−0.0001 (10)	−0.0001 (10)
C6	0.0238 (12)	0.0273 (13)	0.0300 (13)	0.0005 (10)	0.0023 (10)	−0.0025 (10)
C7	0.0246 (13)	0.0306 (13)	0.0245 (12)	−0.0010 (11)	0.0065 (10)	−0.0003 (10)
C8	0.0261 (13)	0.0221 (12)	0.0199 (12)	−0.0036 (10)	0.0039 (10)	0.0014 (10)
C9	0.0353 (15)	0.0254 (13)	0.0458 (16)	−0.0095 (12)	0.0147 (13)	−0.0094 (12)
C10	0.0306 (14)	0.0339 (15)	0.0437 (16)	−0.0109 (12)	0.0128 (12)	−0.0118 (13)
C11	0.0267 (13)	0.0306 (14)	0.0316 (14)	−0.0019 (11)	0.0065 (11)	−0.0009 (11)
C12	0.0225 (12)	0.0311 (14)	0.0256 (13)	0.0013 (11)	0.0028 (10)	0.0023 (11)
C13	0.0317 (15)	0.0410 (16)	0.0291 (14)	0.0026 (12)	0.0004 (11)	−0.0044 (12)
C14	0.0368 (16)	0.059 (2)	0.0258 (14)	−0.0061 (15)	0.0058 (12)	0.0057 (14)
C15	0.0346 (16)	0.0541 (19)	0.0330 (15)	−0.0126 (14)	0.0059 (12)	0.0119 (14)

Geometric parameters (Å, º)

Cl1—C5	1.732 (3)	C3—C4	1.394 (4)
N1—C8	1.345 (3)	C3—H3A	0.9500
N1—C1	1.456 (3)	C4—C5	1.381 (4)
N1—H1N	0.84 (3)	C4—H4A	0.9500
N2—C9	1.334 (3)	C5—C6	1.376 (4)
N2—C8	1.347 (3)	C6—C7	1.388 (4)
N3—C11	1.329 (3)	C6—H6A	0.9500
N3—C8	1.358 (3)	C7—H7A	0.9500
N4—C12	1.362 (3)	C9—C10	1.377 (4)
N4—C1	1.435 (3)	C9—H9A	0.9500
N4—H4N	0.83 (3)	C10—C11	1.378 (4)
N5—C13	1.334 (4)	C10—H10A	0.9500
N5—C12	1.339 (3)	C11—H11A	0.9500
N6—C15	1.331 (4)	C13—C14	1.381 (4)
N6—C12	1.349 (3)	C13—H13A	0.9500
C1—C2	1.523 (3)	C14—C15	1.378 (4)
C1—H1A	1.0000	C14—H14A	0.9500
C2—C3	1.389 (3)	C15—H15A	0.9500
C2—C7	1.390 (3)
C8—N1—C1	122.2 (2)	C5—C6—H6A	120.6
C8—N1—H1N	120 (2)	C7—C6—H6A	120.6
C1—N1—H1N	116 (2)	C6—C7—C2	121.7 (2)
C9—N2—C8	115.6 (2)	C6—C7—H7A	119.2
C11—N3—C8	115.6 (2)	C2—C7—H7A	119.2
C12—N4—C1	123.3 (2)	N1—C8—N2	118.0 (2)
C12—N4—H4N	118 (2)	N1—C8—N3	116.1 (2)
C1—N4—H4N	119 (2)	N2—C8—N3	125.9 (2)
C13—N5—C12	115.7 (2)	N2—C9—C10	123.2 (3)
C15—N6—C12	115.8 (2)	N2—C9—H9A	118.4
N4—C1—N1	110.0 (2)	C10—C9—H9A	118.4
N4—C1—C2	109.5 (2)	C9—C10—C11	116.5 (3)
N1—C1—C2	113.2 (2)	C9—C10—H10A	121.8
N4—C1—H1A	108.0	C11—C10—H10A	121.8
N1—C1—H1A	108.0	N3—C11—C10	123.1 (3)
C2—C1—H1A	108.0	N3—C11—H11A	118.4
C3—C2—C7	118.4 (2)	C10—C11—H11A	118.4
C3—C2—C1	123.7 (2)	N5—C12—N6	126.1 (2)
C7—C2—C1	117.9 (2)	N5—C12—N4	118.2 (2)
C2—C3—C4	120.4 (2)	N6—C12—N4	115.7 (2)
C2—C3—H3A	119.8	N5—C13—C14	123.1 (3)
C4—C3—H3A	119.8	N5—C13—H13A	118.5
C5—C4—C3	119.8 (2)	C14—C13—H13A	118.5
C5—C4—H4A	120.1	C15—C14—C13	116.2 (3)
C3—C4—H4A	120.1	C15—C14—H14A	121.9
C6—C5—C4	120.9 (2)	C13—C14—H14A	121.9
C6—C5—Cl1	119.1 (2)	N6—C15—C14	123.0 (3)
C4—C5—Cl1	120.0 (2)	N6—C15—H15A	118.5
C5—C6—C7	118.8 (2)	C14—C15—H15A	118.5
C12—N4—C1—N1	96.1 (3)	C1—N1—C8—N3	173.6 (2)
C12—N4—C1—C2	−139.0 (2)	C9—N2—C8—N1	178.2 (2)
C8—N1—C1—N4	−150.6 (2)	C9—N2—C8—N3	−3.1 (4)
C8—N1—C1—C2	86.6 (3)	C11—N3—C8—N1	−179.7 (2)
N4—C1—C2—C3	−120.7 (3)	C11—N3—C8—N2	1.6 (4)
N1—C1—C2—C3	2.5 (3)	C8—N2—C9—C10	1.5 (4)
N4—C1—C2—C7	61.2 (3)	N2—C9—C10—C11	1.2 (4)
N1—C1—C2—C7	−175.7 (2)	C8—N3—C11—C10	1.5 (4)
C7—C2—C3—C4	0.3 (4)	C9—C10—C11—N3	−2.8 (4)
C1—C2—C3—C4	−177.9 (2)	C13—N5—C12—N6	1.4 (4)
C2—C3—C4—C5	0.0 (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—Cl1	178.8 (2)	C15—N6—C12—N4	178.6 (3)
C4—C5—C6—C7	0.1 (4)	C1—N4—C12—N5	10.1 (4)
Cl1—C5—C6—C7	−179.0 (2)	C1—N4—C12—N6	−170.9 (2)
C5—C6—C7—C2	0.3 (4)	C12—N5—C13—C14	1.4 (4)
C3—C2—C7—C6	−0.4 (4)	N5—C13—C14—C15	−2.8 (5)
C1—C2—C7—C6	177.8 (2)	C12—N6—C15—C14	0.8 (5)
C1—N1—C8—N2	−7.6 (3)	C13—C14—C15—N6	1.6 (5)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···N3^i	0.84 (3)	2.20 (3)	3.033 (3)	174 (3)
N4—H4N···N6^ii	0.83 (3)	2.24 (3)	3.057 (3)	172 (3)

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