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Acta Crystallogr Sect E Struct Rep Online. 2008 November 1; 64(Pt 11): o2112.
Published online 2008 October 15. doi:  10.1107/S1600536808032583
PMCID: PMC2959642

1-(2-Pyrid­yl)-N,N′-dipyrimidin-2-ylmethane­diamine

Abstract

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 [triangle]); Ponticelli & Spanu (1999 [triangle]). For their uses in coordination chemistry, see: Prince et al. (2003 [triangle]); Lee et al. (2003 [triangle]); Masaki et al. (2002 [triangle]). For studies of the reactions of heterocyclic amines with aromatic aldehyde to prepare new ligands, see: Tabatabaee et al. (2006 [triangle], 2007a [triangle],b [triangle], 2008 [triangle]).

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Object name is e-64-o2112-scheme1.jpg

Experimental

Crystal data

  • C14H13N7
  • M r = 279.31
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o2112-efi1.jpg
  • a = 9.5781 (19) Å
  • b = 9.3543 (16) Å
  • c = 15.975 (4) Å
  • β = 97.521 (17)°
  • V = 1419.0 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.09 mm−1
  • T = 296 K
  • 0.45 × 0.20 × 0.05 mm

Data collection

  • Stoe IPDS-II diffractometer
  • Absorption correction: numerical [shape of crystal determined optically; X-SHAPE and X-RED32 (Stoe & Cie, 2005 [triangle])]T min = 0.970, T max = 0.998
  • 12281 measured reflections
  • 2997 independent reflections
  • 2443 reflections with I > 2σ(I)
  • R int = 0.032

Refinement

  • R[F 2 > 2σ(F 2)] = 0.058
  • wR(F 2) = 0.140
  • S = 1.12
  • 2997 reflections
  • 242 parameters
  • All H-atom parameters refined
  • Δρmax = 0.15 e Å−3
  • Δρmin = −0.16 e Å−3

Data collection: X-AREA (Stoe & Cie, 2005 [triangle]); cell refinement: X-AREA; data reduction: X-RED32 (Stoe & Cie, 2005 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808032583/bq2098sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808032583/bq2098Isup2.hkl

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

supplementary crystallographic information

Comment

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).

Experimental

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%).

Refinement

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.

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···\p interaction between one aromatic pyrimidine ring and adjacent molecule.

Crystal data

C14H13N7F(000) = 584
Mr = 279.31Dx = 1.307 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 2000 reflections
a = 9.5781 (19) Åθ = 2.4–26.8°
b = 9.3543 (16) ŵ = 0.09 mm1
c = 15.975 (4) ÅT = 296 K
β = 97.521 (17)°Plate, colorless
V = 1419.0 (5) Å30.45 × 0.20 × 0.05 mm
Z = 4

Data collection

Stoe IPDS-II diffractometer2997 independent reflections
Radiation source: fine-focus sealed tube2443 reflections with I > 2σ(I)
graphiteRint = 0.032
rotation method scansθmax = 26.8°, θmin = 2.4°
Absorption correction: numerical shape of crystal determined optically (Program? reference?)h = −12→12
Tmin = 0.970, Tmax = 0.998k = −11→11
12281 measured reflectionsl = −20→17

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)] = 0.058Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.140All H-atom parameters refined
S = 1.12w = 1/[σ2(Fo2) + (0.0555P)2 + 0.3988P] where P = (Fo2 + 2Fc2)/3
2997 reflections(Δ/σ)max = 0.002
242 parametersΔρmax = 0.15 e Å3
0 restraintsΔρmin = −0.16 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
C10.9822 (4)0.8397 (4)0.2536 (3)0.1170 (12)
H11.065 (4)0.909 (5)0.265 (3)0.172 (17)*
C20.9364 (4)0.7672 (5)0.3161 (2)0.1087 (12)
H20.973 (4)0.786 (4)0.372 (3)0.149 (14)*
C30.8303 (4)0.6738 (5)0.2982 (2)0.1054 (12)
H30.783 (4)0.619 (4)0.328 (3)0.141 (14)*
C40.7696 (3)0.6561 (3)0.21369 (16)0.0746 (7)
H40.702 (3)0.604 (3)0.2000 (16)0.074 (8)*
C50.82060 (18)0.7345 (2)0.15391 (11)0.0488 (4)
C60.76338 (17)0.7253 (2)0.06118 (11)0.0458 (4)
H60.7549 (19)0.821 (2)0.0380 (12)0.048 (5)*
C70.87637 (17)0.6815 (2)−0.06540 (11)0.0464 (4)
C80.8208 (3)0.8159 (3)−0.18238 (15)0.0816 (8)
H80.753 (3)0.896 (3)−0.2127 (17)0.098 (8)*
C90.9149 (3)0.7437 (3)−0.22277 (16)0.0859 (8)
H90.928 (3)0.768 (3)−0.2817 (19)0.106 (9)*
C100.9855 (3)0.6351 (3)−0.17964 (14)0.0745 (7)
H101.054 (3)0.577 (3)−0.2047 (16)0.086 (7)*
C110.50462 (17)0.72192 (19)0.05133 (10)0.0441 (4)
C120.3865 (2)0.9233 (2)0.07540 (14)0.0599 (5)
H120.394 (2)1.026 (3)0.0921 (14)0.074 (7)*
C130.2605 (2)0.8541 (3)0.05806 (16)0.0698 (6)
H130.170 (3)0.897 (3)0.0602 (16)0.091 (8)*
C140.2664 (2)0.7119 (3)0.03806 (16)0.0681 (6)
H140.180 (3)0.652 (3)0.0280 (15)0.078 (7)*
N10.9275 (2)0.8262 (3)0.17169 (15)0.0913 (7)
N20.86343 (15)0.65215 (18)0.01597 (9)0.0504 (4)
H2B0.915 (2)0.583 (2)0.0422 (13)0.058 (6)*
N30.7991 (2)0.7869 (2)−0.10338 (11)0.0681 (5)
N40.96897 (16)0.59970 (18)−0.10065 (10)0.0565 (4)
N50.62782 (15)0.65417 (19)0.04528 (11)0.0523 (4)
H5B0.623 (2)0.575 (2)0.0285 (13)0.055 (6)*
N60.51088 (15)0.85980 (16)0.07449 (10)0.0505 (4)
N70.38702 (15)0.64257 (18)0.03335 (11)0.0569 (4)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.116 (3)0.121 (3)0.100 (3)−0.013 (2)−0.041 (2)−0.015 (2)
C20.116 (3)0.145 (3)0.0593 (18)0.041 (2)−0.0115 (17)−0.023 (2)
C30.108 (2)0.148 (3)0.0659 (18)0.040 (2)0.0316 (17)0.026 (2)
C40.0699 (15)0.0954 (18)0.0600 (14)0.0035 (14)0.0142 (11)0.0109 (12)
C50.0422 (9)0.0545 (10)0.0499 (10)0.0134 (8)0.0070 (7)−0.0050 (8)
C60.0405 (8)0.0518 (10)0.0466 (9)0.0107 (7)0.0112 (7)−0.0019 (8)
C70.0407 (8)0.0538 (10)0.0455 (9)0.0083 (7)0.0090 (7)−0.0013 (7)
C80.1015 (18)0.0871 (17)0.0587 (13)0.0359 (15)0.0206 (12)0.0189 (12)
C90.112 (2)0.0959 (19)0.0560 (13)0.0323 (16)0.0355 (13)0.0144 (12)
C100.0840 (15)0.0874 (16)0.0574 (13)0.0288 (13)0.0289 (11)−0.0031 (11)
C110.0417 (9)0.0548 (10)0.0366 (8)0.0108 (7)0.0072 (6)−0.0032 (7)
C120.0564 (11)0.0512 (11)0.0751 (14)0.0147 (9)0.0204 (10)−0.0017 (10)
C130.0472 (11)0.0715 (14)0.0916 (16)0.0217 (10)0.0126 (10)−0.0089 (12)
C140.0410 (10)0.0758 (15)0.0865 (16)0.0063 (10)0.0041 (9)−0.0215 (12)
N10.0819 (14)0.0997 (16)0.0858 (15)−0.0169 (13)−0.0136 (11)0.0007 (12)
N20.0471 (8)0.0599 (10)0.0458 (8)0.0211 (7)0.0127 (6)0.0045 (7)
N30.0792 (12)0.0745 (12)0.0535 (10)0.0336 (10)0.0197 (8)0.0095 (8)
N40.0549 (9)0.0641 (10)0.0533 (9)0.0174 (8)0.0173 (7)−0.0023 (7)
N50.0394 (8)0.0528 (10)0.0648 (10)0.0093 (7)0.0066 (6)−0.0165 (8)
N60.0480 (8)0.0486 (8)0.0575 (9)0.0088 (7)0.0162 (7)−0.0010 (7)
N70.0406 (8)0.0603 (10)0.0690 (11)0.0080 (7)0.0041 (7)−0.0189 (8)

Geometric parameters (Å, °)

C1—C21.327 (6)C8—C91.355 (3)
C1—N11.350 (4)C8—H81.07 (3)
C1—H11.03 (4)C9—C101.357 (4)
C2—C31.343 (6)C9—H90.99 (3)
C2—H20.93 (4)C10—N41.334 (3)
C3—C41.408 (4)C10—H100.98 (3)
C3—H30.87 (4)C11—N61.341 (2)
C4—C51.346 (3)C11—N71.348 (2)
C4—H40.82 (2)C11—N51.354 (2)
C5—N11.338 (3)C12—N61.333 (2)
C5—C61.513 (3)C12—C131.366 (3)
C6—N21.446 (2)C12—H121.00 (2)
C6—N51.452 (2)C13—C141.371 (3)
C6—H60.97 (2)C13—H130.96 (3)
C7—N31.331 (2)C14—N71.335 (2)
C7—N41.349 (2)C14—H141.00 (2)
C7—N21.350 (2)N2—H2B0.89 (2)
C8—N31.334 (3)N5—H5B0.79 (2)
C2—C1—N1123.8 (4)C8—C9—H9120.8 (17)
C2—C1—H1121 (2)C10—C9—H9122.4 (17)
N1—C1—H1115 (2)N4—C10—C9123.6 (2)
C1—C2—C3119.2 (3)N4—C10—H10114.7 (15)
C1—C2—H2120 (3)C9—C10—H10121.8 (15)
C3—C2—H2120 (2)N6—C11—N7126.46 (15)
C2—C3—C4119.1 (3)N6—C11—N5117.52 (16)
C2—C3—H3135 (3)N7—C11—N5116.02 (16)
C4—C3—H3106 (3)N6—C12—C13123.62 (19)
C5—C4—C3118.3 (3)N6—C12—H12113.6 (13)
C5—C4—H4118.9 (18)C13—C12—H12122.7 (13)
C3—C4—H4122.7 (18)C12—C13—C14116.41 (18)
N1—C5—C4122.5 (2)C12—C13—H13124.8 (16)
N1—C5—C6114.40 (18)C14—C13—H13118.7 (16)
C4—C5—C6123.1 (2)N7—C14—C13123.1 (2)
N2—C6—N5109.37 (15)N7—C14—H14115.2 (14)
N2—C6—C5109.70 (14)C13—C14—H14121.6 (14)
N5—C6—C5113.47 (15)C5—N1—C1117.0 (3)
N2—C6—H6105.9 (11)C7—N2—C6122.37 (15)
N5—C6—H6109.2 (11)C7—N2—H2B119.2 (13)
C5—C6—H6108.9 (11)C6—N2—H2B118.4 (13)
N3—C7—N4125.93 (16)C7—N3—C8115.86 (17)
N3—C7—N2118.29 (15)C10—N4—C7114.85 (17)
N4—C7—N2115.78 (16)C11—N5—C6122.74 (16)
N3—C8—C9123.0 (2)C11—N5—H5B117.0 (15)
N3—C8—H8114.3 (15)C6—N5—H5B120.0 (15)
C9—C8—H8122.5 (15)C12—N6—C11115.09 (17)
C8—C9—C10116.7 (2)C14—N7—C11115.17 (17)
N1—C1—C2—C30.4 (6)N5—C6—N2—C785.7 (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—N11.1 (4)N2—C7—N3—C8176.9 (2)
C3—C4—C5—C6−179.6 (2)C9—C8—N3—C70.2 (4)
N1—C5—C6—N271.8 (2)C9—C10—N4—C7−0.6 (4)
C4—C5—C6—N2−107.6 (2)N3—C7—N4—C102.9 (3)
N1—C5—C6—N5−165.58 (18)N2—C7—N4—C10−176.74 (19)
C4—C5—C6—N515.0 (3)N6—C11—N5—C6−1.2 (3)
N3—C8—C9—C101.8 (5)N7—C11—N5—C6178.94 (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—C1182.2 (2)
C12—C13—C14—N7−1.5 (4)C13—C12—N6—C112.9 (3)
C4—C5—N1—C1−1.1 (4)N7—C11—N6—C12−3.3 (3)
C6—C5—N1—C1179.5 (3)N5—C11—N6—C12176.80 (17)
C2—C1—N1—C50.4 (5)C13—C14—N7—C111.2 (3)
N3—C7—N2—C63.6 (3)N6—C11—N7—C141.4 (3)
N4—C7—N2—C6−176.73 (17)N5—C11—N7—C14−178.76 (18)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2B···N4i0.885 (19)2.181 (19)3.064 (2)175.3 (19)
N5—H5B···N7ii0.787 (19)2.259 (19)3.042 (3)174 (2)
C4—H4···N50.82 (3)2.53 (3)2.851 (3)105 (2)
C6—H6···N30.968 (19)2.373 (19)2.756 (3)102.9 (13)
C12—H12···N3iii1.00 (3)2.57 (2)3.304 (3)130.4 (15)
C9—H9···Cg1iv0.99 (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.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BQ2098).

References

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