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ISSN: 2056-9890

2,2-Bis(pyridin-2-yl)-1,3-diazinane

aDepartment of Chemistry, The University of Jordan, Amman 11942, Jordan, bDepartment of Chemistry, An-Najah National University, Nablus, Palestinian Territories, and cLaboratoire LCM, Faculté Sciences, Université Mohammed Ier, Oujda 60000, Morocco
*Correspondence e-mail: hadsal2003@yahoo.com

(Received 10 February 2013; accepted 18 March 2013; online 23 March 2013)

In the title compound, C14H16N4, the six-membered hexa­hydro­pyrimidine ring adopts a chair conformation. In the crystal, one of the two pyrimidine N atoms engages in N—H⋯N hydrogen bonding with one of the pyridine N atoms, generating a helical chain running along the c axis. The helical pitch is the length of the c axis.

Related literature

For related structures, see: Song et al. (2010[Song, X.-P., Li, G.-C., Wu, C.-Z. & Yang, F.-L. (2010). Acta Cryst. E66, o1083.]); Jayaratna & Norman (2010[Jayaratna, N. B. & Norman, R. E. (2010). Acta Cryst. E66, o3149.]); Fun & Kia (2008[Fun, H.-K. & Kia, R. (2008). Acta Cryst. E64, o1840-o1841.]); Warad et al. (2012[Warad, I., Alruwaili, A., Al-Resayes, S. I., Choudhary, M. I. & Yousuf, S. (2012). Acta Cryst. E68, o1786.]). For competition between cyclization and bis­imine formation, see: Locke et al. (2009[Locke, J., Griffith, R., Bailey, T. & Crumbie, R. (2009). Tetrahedron, 65, 10685-10692.]). For the use of hexa­hydro­pyrimidines as polydentate ligands for the synthesis of transition metal coordination complexes, see: Schmidt et al. (2011[Schmidt, M., Wiedemann, D. & Grohmann, A. (2011). Inorg. Chim. Acta, 374, 514-520.]).

[Scheme 1]

Experimental

Crystal data
  • C14H16N4

  • Mr = 240.31

  • Monoclinic, P 21 /c

  • a = 14.2372 (14) Å

  • b = 8.0302 (8) Å

  • c = 11.3277 (9) Å

  • β = 103.075 (8)°

  • V = 1261.5 (2) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.08 mm−1

  • T = 293 K

  • 0.3 × 0.2 × 0.15 mm

Data collection
  • Agilent Xcalibur Eos diffractometer

  • Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011[Agilent (2011). CrysAlis PRO. Agilent Technologies UK Ltd, Yarnton, Enngland.]) Tmin = 0.98, Tmax = 0.99

  • 4640 measured reflections

  • 2238 independent reflections

  • 1656 reflections with I > 2σ(I)

  • Rint = 0.023

Refinement
  • R[F2 > 2σ(F2)] = 0.041

  • wR(F2) = 0.108

  • S = 1.05

  • 2238 reflections

  • 171 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.14 e Å−3

  • Δρmin = −0.15 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H3⋯N2i 0.878 (17) 2.425 (18) 3.2845 (19) 166.4 (15)
Symmetry code: (i) [x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}].

Data collection: CrysAlis PRO (Agilent, 2011[Agilent (2011). CrysAlis PRO. Agilent Technologies UK Ltd, Yarnton, Enngland.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) and ORTEP (Burnett & Johnson, 1996[Burnett, M. N. & Johnson, C. K. (1996). ORTEPIII. Report ORNL-6895. Oak Ridge National Laboratory, Tennessee, USA.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

Condensation of 1,3-diamines with 2-dipyridlketone is a well documented reaction for two potential products, hexahydropyrimidine and classical Schiff bases compounds (Warad et al., 2012; Song et al., 2010; Jayaratna & Norman, 2010; Fun & Kia, 2008). Both of these products are extensively utilized as polydentate ligands to synthesize coordination metal complexes. The title compound was obtained during our attempt to synthesize novel ligands in order to study their coordination chemistry.

The pyrimidine ring in the molecule assumes a chair configuration allowing better disposition for H-bonding. The molecular units are connected via hydrogen bonding between one pyrimidine nitrogen atom, N3 and one pyridinic nitrogen atom, N2 in adjacent molecule as shown in Fig. 2. Hydrogen bond values are tabulated.

Related literature top

For related structures, see: Song et al. (2010); Jayaratna & Norman (2010); Fun & Kia (2008); Warad et al. (2012). For competition between cyclization and bisimine formation, see: Locke et al. (2009). For the use of hexahydropyrimidines as polydentate ligands for the synthesis of transition metal coordination complexes, see: Schmidt et al. (2011).

Experimental top

A solution of 2-dipyridlketone (0.25 g, 1.45 mmol) in anhydrous ethanol (20 ml) was mixed with 1,3-propanediamine (0.16 ml, 1.5 mmoL) and allowed to reflux for about four hours. The resulting mixture was concentrated under reduced pressure and the title compound was precipitated by the addition of 40 ml of ice cool distilled water. The precipitate was filtered off, washed three times with 40 ml of distilled water, recrystallized in ethanol and allowed to stand at room temperature. After three days, colourless crystals suitable for single-crystal X-ray data collection were obtained (0.24 g, yield 77%).

Refinement top

All nonhydrogen atoms were refined anisotropically. H atoms attached to C were positioned geometrically, with C—H = 0.93 and 0.96 Å for aromatic and methyl H, respectively, and constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq. The two H atoms attched to the pyrimidinic N atoms were located in a difference Fourier map and refined fully to values of 0.88 (2) Å for the H atom involved in intermolecular H-bonding, and 0.92 (2) Å for the H atom involved in the biforcatd intramolecular hydrogen bonding. Highest difference peak and hole are 0.14 and -0.15 e/Å3 .

Computing details top

Data collection: CrysAlis PRO (Agilent, 2011); cell refinement: CrysAlis PRO (Agilent, 2011); data reduction: CrysAlis PRO (Agilent, 2011); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008) and ORTEP (Burnett & Johnson, 1996); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. An ORTEP (Burnett & Johnson, 1996) view of the title compound. Displacement ellipsoids are drawn at the 30% probability level. H atoms are represented as small spheres of arbitrary radii.
[Figure 2] Fig. 2. View approximately down b axis showing helical chains extending along c axis formed by intermolecular N—H···N hydrogen bonds joining one pyrimidinic nitrogen, N3, and one pyridinic nitrogen, N2 in adjacent molecule.
2,2-Bis(pyridin-2-yl)-1,3-diazinane top
Crystal data top
C14H16N4F(000) = 512
Mr = 240.31Dx = 1.265 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 1403 reflections
a = 14.2372 (14) Åθ = 3.1–29.1°
b = 8.0302 (8) ŵ = 0.08 mm1
c = 11.3277 (9) ÅT = 293 K
β = 103.075 (8)°Parallelpiped, colourless
V = 1261.5 (2) Å30.3 × 0.2 × 0.15 mm
Z = 4
Data collection top
Agilent Xcalibur Eos
diffractometer
2238 independent reflections
Radiation source: Enhance (Mo) X-ray Source1656 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.023
Detector resolution: 16.0534 pixels mm-1θmax = 25.0°, θmin = 3.1°
ω scansh = 1615
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2011)
k = 99
Tmin = 0.98, Tmax = 0.99l = 1313
4640 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.041Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.108H atoms treated by a mixture of independent and constrained refinement
S = 1.05 w = 1/[σ2(Fo2) + (0.0446P)2 + 0.061P]
where P = (Fo2 + 2Fc2)/3
2238 reflections(Δ/σ)max < 0.001
171 parametersΔρmax = 0.14 e Å3
0 restraintsΔρmin = 0.15 e Å3
Crystal data top
C14H16N4V = 1261.5 (2) Å3
Mr = 240.31Z = 4
Monoclinic, P21/cMo Kα radiation
a = 14.2372 (14) ŵ = 0.08 mm1
b = 8.0302 (8) ÅT = 293 K
c = 11.3277 (9) Å0.3 × 0.2 × 0.15 mm
β = 103.075 (8)°
Data collection top
Agilent Xcalibur Eos
diffractometer
2238 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2011)
1656 reflections with I > 2σ(I)
Tmin = 0.98, Tmax = 0.99Rint = 0.023
4640 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0410 restraints
wR(F2) = 0.108H atoms treated by a mixture of independent and constrained refinement
S = 1.05Δρmax = 0.14 e Å3
2238 reflectionsΔρmin = 0.15 e Å3
171 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
xyzUiso*/Ueq
N30.79810 (10)0.13990 (18)0.07018 (11)0.0369 (4)
N20.79269 (10)0.05042 (18)0.24206 (10)0.0406 (4)
N40.82606 (10)0.32537 (17)0.08565 (12)0.0377 (4)
C140.76709 (11)0.18825 (19)0.05728 (12)0.0315 (4)
C100.76853 (11)0.03058 (19)0.13524 (12)0.0306 (4)
C50.66284 (12)0.2490 (2)0.08265 (13)0.0356 (4)
C110.90172 (13)0.1041 (2)0.10491 (14)0.0456 (5)
H11A0.91480.00360.06400.055*
H11B0.91980.08350.19150.055*
C90.74371 (12)0.1230 (2)0.09704 (14)0.0412 (4)
H9A0.72380.13230.02460.049*
N10.63469 (11)0.3400 (2)0.18294 (12)0.0511 (4)
C60.79561 (13)0.0872 (2)0.30852 (15)0.0506 (5)
H6A0.81170.07510.38320.061*
C130.92964 (13)0.2875 (2)0.05846 (14)0.0474 (5)
H13A0.96510.38330.07740.057*
H13B0.94170.19470.10780.057*
C120.96337 (13)0.2441 (3)0.07420 (15)0.0532 (5)
H12A0.95820.34100.12350.064*
H12B1.03040.20980.09110.064*
C10.54414 (16)0.3966 (3)0.20904 (18)0.0639 (6)
H1A0.52400.45980.27900.077*
C70.77636 (14)0.2439 (2)0.27331 (15)0.0520 (5)
H7A0.78210.33590.32100.062*
C40.60138 (14)0.2111 (3)0.00797 (16)0.0539 (5)
H4A0.62220.14580.06080.065*
C80.74829 (13)0.2622 (2)0.16589 (15)0.0503 (5)
H8A0.73270.36660.14030.060*
C20.47951 (15)0.3674 (3)0.13943 (19)0.0647 (6)
H2A0.41740.41090.16070.078*
C30.50821 (15)0.2726 (3)0.03762 (19)0.0685 (6)
H3A0.46550.24960.01140.082*
H40.8042 (12)0.352 (2)0.1662 (16)0.052 (5)*
H30.7859 (12)0.224 (2)0.1143 (14)0.050 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N30.0487 (9)0.0332 (8)0.0296 (7)0.0036 (7)0.0108 (6)0.0032 (6)
N20.0533 (10)0.0376 (9)0.0329 (7)0.0027 (7)0.0141 (6)0.0042 (6)
N40.0455 (9)0.0288 (8)0.0398 (8)0.0039 (7)0.0120 (6)0.0006 (6)
C140.0390 (10)0.0265 (9)0.0301 (8)0.0004 (7)0.0102 (6)0.0010 (6)
C100.0353 (9)0.0274 (9)0.0286 (7)0.0023 (7)0.0059 (6)0.0010 (6)
C50.0408 (10)0.0297 (9)0.0368 (9)0.0001 (7)0.0099 (7)0.0050 (7)
C110.0493 (12)0.0495 (11)0.0348 (9)0.0080 (9)0.0030 (7)0.0025 (8)
C90.0557 (12)0.0320 (10)0.0350 (9)0.0030 (8)0.0087 (7)0.0008 (7)
N10.0506 (10)0.0521 (10)0.0490 (9)0.0117 (8)0.0078 (7)0.0072 (7)
C60.0613 (13)0.0550 (13)0.0374 (9)0.0009 (10)0.0154 (8)0.0131 (9)
C130.0426 (11)0.0482 (12)0.0529 (10)0.0101 (9)0.0139 (8)0.0064 (8)
C120.0451 (12)0.0599 (14)0.0512 (10)0.0036 (10)0.0039 (8)0.0127 (9)
C10.0583 (14)0.0653 (15)0.0618 (12)0.0154 (11)0.0001 (10)0.0046 (10)
C70.0639 (13)0.0400 (12)0.0462 (10)0.0107 (10)0.0004 (9)0.0178 (9)
C40.0487 (12)0.0639 (14)0.0528 (11)0.0017 (10)0.0190 (9)0.0024 (9)
C80.0639 (13)0.0279 (10)0.0518 (11)0.0024 (9)0.0024 (9)0.0018 (8)
C20.0448 (13)0.0705 (16)0.0731 (14)0.0124 (11)0.0012 (10)0.0182 (12)
C30.0452 (13)0.0887 (18)0.0779 (15)0.0000 (12)0.0269 (10)0.0126 (13)
Geometric parameters (Å, º) top
N3—C141.4635 (18)N1—C11.336 (2)
N3—C111.467 (2)C6—C71.367 (3)
N3—H30.878 (17)C6—H6A0.9300
N2—C101.3401 (18)C13—C121.511 (2)
N2—C61.343 (2)C13—H13A0.9700
N4—C141.4638 (19)C13—H13B0.9700
N4—C131.468 (2)C12—H12A0.9700
N4—H40.921 (17)C12—H12B0.9700
C14—C51.527 (2)C1—C21.361 (3)
C14—C101.546 (2)C1—H1A0.9300
C10—C91.379 (2)C7—C81.372 (2)
C5—N11.334 (2)C7—H7A0.9300
C5—C41.381 (2)C4—C31.384 (3)
C11—C121.514 (2)C4—H4A0.9300
C11—H11A0.9700C8—H8A0.9300
C11—H11B0.9700C2—C31.365 (3)
C9—C81.373 (2)C2—H2A0.9300
C9—H9A0.9300C3—H3A0.9300
C14—N3—C11112.16 (12)C7—C6—H6A118.0
C14—N3—H3107.7 (11)N4—C13—C12109.54 (14)
C11—N3—H3108.3 (11)N4—C13—H13A109.8
C10—N2—C6117.07 (15)C12—C13—H13A109.8
C14—N4—C13113.39 (13)N4—C13—H13B109.8
C14—N4—H4108.1 (11)C12—C13—H13B109.8
C13—N4—H4110.8 (11)H13A—C13—H13B108.2
N3—C14—N4110.86 (12)C13—C12—C11109.23 (14)
N3—C14—C5109.51 (12)C13—C12—H12A109.8
N4—C14—C5107.45 (13)C11—C12—H12A109.8
N3—C14—C10107.83 (12)C13—C12—H12B109.8
N4—C14—C10114.09 (12)C11—C12—H12B109.8
C5—C14—C10106.97 (12)H12A—C12—H12B108.3
N2—C10—C9121.72 (14)N1—C1—C2123.9 (2)
N2—C10—C14117.23 (13)N1—C1—H1A118.0
C9—C10—C14121.03 (13)C2—C1—H1A118.0
N1—C5—C4122.15 (17)C6—C7—C8118.39 (16)
N1—C5—C14115.30 (14)C6—C7—H7A120.8
C4—C5—C14122.55 (15)C8—C7—H7A120.8
N3—C11—C12113.15 (15)C5—C4—C3118.56 (19)
N3—C11—H11A108.9C5—C4—H4A120.7
C12—C11—H11A108.9C3—C4—H4A120.7
N3—C11—H11B108.9C7—C8—C9118.52 (17)
C12—C11—H11B108.9C7—C8—H8A120.7
H11A—C11—H11B107.8C9—C8—H8A120.7
C8—C9—C10120.09 (15)C1—C2—C3118.3 (2)
C8—C9—H9A120.0C1—C2—H2A120.9
C10—C9—H9A120.0C3—C2—H2A120.9
C5—N1—C1117.65 (17)C2—C3—C4119.4 (2)
N2—C6—C7124.09 (16)C2—C3—H3A120.3
N2—C6—H6A118.0C4—C3—H3A120.3
C11—N3—C14—N453.05 (17)C10—C14—C5—C497.46 (17)
C11—N3—C14—C5171.44 (13)C14—N3—C11—C1253.15 (17)
C11—N3—C14—C1072.50 (16)N2—C10—C9—C83.5 (2)
C13—N4—C14—N356.96 (16)C14—C10—C9—C8178.02 (15)
C13—N4—C14—C5176.59 (11)C4—C5—N1—C10.9 (3)
C13—N4—C14—C1065.00 (16)C14—C5—N1—C1179.79 (15)
C6—N2—C10—C92.7 (2)C10—N2—C6—C70.5 (3)
C6—N2—C10—C14178.80 (14)C14—N4—C13—C1258.22 (17)
N3—C14—C10—N2145.84 (13)N4—C13—C12—C1154.63 (19)
N4—C14—C10—N222.22 (19)N3—C11—C12—C1353.6 (2)
C5—C14—C10—N296.46 (16)C5—N1—C1—C20.2 (3)
N3—C14—C10—C935.63 (19)N2—C6—C7—C82.9 (3)
N4—C14—C10—C9159.24 (14)N1—C5—C4—C31.2 (3)
C5—C14—C10—C982.08 (17)C14—C5—C4—C3179.54 (16)
N3—C14—C5—N1161.53 (13)C6—C7—C8—C92.0 (3)
N4—C14—C5—N141.03 (17)C10—C9—C8—C71.0 (2)
C10—C14—C5—N181.87 (16)N1—C1—C2—C31.0 (3)
N3—C14—C5—C419.1 (2)C1—C2—C3—C40.6 (3)
N4—C14—C5—C4139.63 (16)C5—C4—C3—C20.4 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3···N2i0.878 (17)2.425 (18)3.2845 (19)166.4 (15)
N4—H4···N10.921 (17)2.379 (17)2.701 (2)100.3 (12)
N4—H4···N20.921 (17)2.564 (17)2.8034 (19)95.3 (12)
Symmetry code: (i) x, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC14H16N4
Mr240.31
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)14.2372 (14), 8.0302 (8), 11.3277 (9)
β (°) 103.075 (8)
V3)1261.5 (2)
Z4
Radiation typeMo Kα
µ (mm1)0.08
Crystal size (mm)0.3 × 0.2 × 0.15
Data collection
DiffractometerAgilent Xcalibur Eos
diffractometer
Absorption correctionMulti-scan
(CrysAlis PRO; Agilent, 2011)
Tmin, Tmax0.98, 0.99
No. of measured, independent and
observed [I > 2σ(I)] reflections
4640, 2238, 1656
Rint0.023
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.041, 0.108, 1.05
No. of reflections2238
No. of parameters171
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.14, 0.15

Computer programs: CrysAlis PRO (Agilent, 2011), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008) and ORTEP (Burnett & Johnson, 1996), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3···N2i0.878 (17)2.425 (18)3.2845 (19)166.4 (15)
Symmetry code: (i) x, y+1/2, z+1/2.
 

Acknowledgements

The X-ray structural work was done at Hamdi Mango Center for Scientific research at The University of Jordan, Amman 11942, Jordan.

References

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ISSN: 2056-9890
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