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

Tabatabaee, M.; Hakimi, F.; Roshani, M.; Mirjalili, M.; Kavasi, H.R.

doi:10.1107/S1600536808032583

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

M. Tabatabaee, F. Hakimi, M. Roshani, M. Mirjalili and H. R. Kavasi

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.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536808032583/bq2098sup1.cif Contains datablocks I, global
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536808032583/bq2098Isup2.hkl Contains datablock I

CCDC reference: 674967

checkCIF report

Key indicators

Single-crystal X-ray study
T = 296 K
Mean (C-C) = 0.004 Å
R factor = 0.058
wR factor = 0.140
Data-to-parameter ratio = 12.4

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT230_ALERT_2_B Hirshfeld Test Diff for    C3     --  C4      ..       8.49 su

Alert level C
            Value of measurement temperature given =   296.000
            Value of melting point given =     0.000
PLAT220_ALERT_2_C Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       2.65 Ratio
PLAT222_ALERT_3_C Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       3.58 Ratio
PLAT230_ALERT_2_C Hirshfeld Test Diff for    N1     --  C5      ..       5.27 su
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for         C1
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         C5
PLAT350_ALERT_3_C Short   C-H Bond (0.96A)   C4     -   H4     ...       0.82 Ang.

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

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

Comment top

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).

Related literature top

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 amines with aromatic aldehyde to prepare new ligands, see: Tabatabaee et al. (2006, 2007a,b, 2008). Cg1 is the centroid of the pyrimidine ring.

Experimental top

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%).

Computing details top

Data collection: X-AREA (Stoe & Cie, 2005); cell refinement: 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).

Figures top

	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.

1-(2-Pyridyl)-N,N'-dipyrimidin-2-ylmethanediamine top

Crystal data top

C₁₄H₁₃N₇	F(000) = 584
M_r = 279.31	D_x = 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

Data collection top

Stoe IPDS-II diffractometer	2997 independent reflections
Radiation source: fine-focus sealed tube	2443 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.032
rotation method scans	θ_max = 26.8°, θ_min = 2.4°
Absorption correction: numerical shape of crystal determined optically (Program? reference?)	h = −12→12
T_min = 0.970, T_max = 0.998	k = −11→11
12281 measured reflections	l = −20→17

Refinement top

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(F_o²) + (0.0555P)² + 0.3988P] where P = (F_o² + 2F_c²)/3
2997 reflections	(Δ/σ)_max = 0.002
242 parameters	Δρ_max = 0.15 e Å⁻³
0 restraints	Δρ_min = −0.16 e Å⁻³

Crystal data top

C₁₄H₁₃N₇	V = 1419.0 (5) Å³
M_r = 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)°

Data collection top

Stoe IPDS-II diffractometer	2997 independent reflections
Absorption correction: numerical shape of crystal determined optically (Program? reference?)	2443 reflections with I > 2σ(I)
T_min = 0.970, T_max = 0.998	R_int = 0.032
12281 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.058	0 restraints
wR(F²) = 0.140	All H-atom parameters refined
S = 1.12	Δρ_max = 0.15 e Å⁻³
2997 reflections	Δρ_min = −0.16 e Å⁻³
242 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq
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)

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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···Cg1^iv	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
M_r	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?)
T_min, T_max	0.970, 0.998
No. of measured, independent and observed [I > 2σ(I)] reflections	12281, 2997, 2443
R_int	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
Δρ_max, Δρ_min (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).