organic compounds
N,N′-(4-Chlorobenzylidene)dipyrimidin-2-amine
aDepartment of Chemistry, Islamic Azad University, Yazd Branch, Yazd, Iran
*Correspondence e-mail: tabatabaee45m@yahoo.com
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); Ponticelli et al. (1999). For studies of the reactions of heterocyclic with aromatic 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).
Experimental
Crystal data
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Refinement
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Data collection: SMART (Bruker, 1998); cell SAINT-Plus (Bruker, 1998); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.
Supporting information
10.1107/S1600536809045243/ez2187sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809045243/ez2187Isup2.hkl
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%).
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.
Data collection: SMART (Bruker, 1998); cell
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).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) Å3 | 0.17 × 0.15 × 0.14 mm |
Z = 4 |
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 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)] = 0.061 | Hydrogen site location: mixed |
wR(F2) = 0.163 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.01 | w = 1/[σ2(Fo2) + (0.061P)2 + 1.85P] where P = (Fo2 + 2Fc2)/3 |
3924 reflections | (Δ/σ)max = 0.001 |
207 parameters | Δρmax = 0.55 e Å−3 |
0 restraints | Δρmin = −0.28 e Å−3 |
C15H13ClN6 | V = 1477.2 (4) Å3 |
Mr = 312.76 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 9.6030 (14) Å | µ = 0.26 mm−1 |
b = 10.5706 (15) Å | T = 120 K |
c = 14.792 (2) Å | 0.17 × 0.15 × 0.14 mm |
β = 100.331 (3)° |
Bruker SMART 1000 CCD area-detector diffractometer | 3924 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1998) | 2429 reflections with I > 2σ(I) |
Tmin = 0.950, Tmax = 0.964 | Rint = 0.063 |
15899 measured reflections |
R[F2 > 2σ(F2)] = 0.061 | 0 restraints |
wR(F2) = 0.163 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.01 | Δρmax = 0.55 e Å−3 |
3924 reflections | Δρmin = −0.28 e Å−3 |
207 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 | ||
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* |
U11 | U22 | U33 | U12 | U13 | U23 | |
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) |
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) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···N3i | 0.84 (3) | 2.20 (3) | 3.033 (3) | 174 (3) |
N4—H4N···N6ii | 0.83 (3) | 2.24 (3) | 3.057 (3) | 172 (3) |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x, −y, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C15H13ClN6 |
Mr | 312.76 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 120 |
a, b, c (Å) | 9.6030 (14), 10.5706 (15), 14.792 (2) |
β (°) | 100.331 (3) |
V (Å3) | 1477.2 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.26 |
Crystal size (mm) | 0.17 × 0.15 × 0.14 |
Data collection | |
Diffractometer | Bruker SMART 1000 CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1998) |
Tmin, Tmax | 0.950, 0.964 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 15899, 3924, 2429 |
Rint | 0.063 |
(sin θ/λ)max (Å−1) | 0.682 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.061, 0.163, 1.01 |
No. of reflections | 3924 |
No. of parameters | 207 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.55, −0.28 |
Computer programs: SMART (Bruker, 1998), SAINT-Plus (Bruker, 1998), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···N3i | 0.84 (3) | 2.20 (3) | 3.033 (3) | 174 (3) |
N4—H4N···N6ii | 0.83 (3) | 2.24 (3) | 3.057 (3) | 172 (3) |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x, −y, −z+1. |
Acknowledgements
The authors express their appreciation to the Islamic Azad University, Yazd Branch, for financial support of this work.
References
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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.
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).