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

Haddad, S.F.; Warad, I.; Jodeh, S.; Ben Hadda, T.

doi:10.1107/S1600536813007459

organic compounds

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ISSN: 2056-9890

Volume 69| Part 4| April 2013| Page o569

doi:10.1107/S1600536813007459

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

Salim F. Haddad,^a ^* Ismail Warad,^b Shehdeh Jodeh ^b and Taibi Ben Hadda ^c

^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 ); 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

Crystal data

C₁₄H₁₆N₄
M_r = 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 ) T_min = 0.98, T_max = 0.99
4640 measured reflections
2238 independent reflections
1656 reflections with I > 2σ(I)
R_int = 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
Δρ_max = 0.14 e Å⁻³
Δρ_min = −0.15 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; 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.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536813007459/nk2200sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536813007459/nk2200Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536813007459/nk2200Isup3.cml

checkCIF report

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%).

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

	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.
	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

C₁₄H₁₆N₄	F(000) = 512
M_r = 240.31	D_x = 1.265 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 1403 reflections
a = 14.2372 (14) Å	θ = 3.1–29.1°
b = 8.0302 (8) Å	µ = 0.08 mm⁻¹
c = 11.3277 (9) Å	T = 293 K
β = 103.075 (8)°	Parallelpiped, colourless
V = 1261.5 (2) Å³	0.3 × 0.2 × 0.15 mm
Z = 4

Data collection top

Agilent Xcalibur Eos diffractometer	2238 independent reflections
Radiation source: Enhance (Mo) X-ray Source	1656 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.023
Detector resolution: 16.0534 pixels mm^-1	θ_max = 25.0°, θ_min = 3.1°
ω scans	h = −16→15
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011)	k = −9→9
T_min = 0.98, T_max = 0.99	l = −13→13
4640 measured reflections

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)] = 0.041	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.108	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	w = 1/[σ²(F_o²) + (0.0446P)² + 0.061P] where P = (F_o² + 2F_c²)/3
2238 reflections	(Δ/σ)_max < 0.001
171 parameters	Δρ_max = 0.14 e Å⁻³
0 restraints	Δρ_min = −0.15 e Å⁻³

Crystal data top

C₁₄H₁₆N₄	V = 1261.5 (2) Å³
M_r = 240.31	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 14.2372 (14) Å	µ = 0.08 mm⁻¹
b = 8.0302 (8) Å	T = 293 K
c = 11.3277 (9) Å	0.3 × 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)
T_min = 0.98, T_max = 0.99	R_int = 0.023
4640 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.041	0 restraints
wR(F²) = 0.108	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	Δρ_max = 0.14 e Å⁻³
2238 reflections	Δρ_min = −0.15 e Å⁻³
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

	x	y	z	U_iso*/U_eq
N3	0.79810 (10)	0.13990 (18)	0.07018 (11)	0.0369 (4)
N2	0.79269 (10)	0.05042 (18)	−0.24206 (10)	0.0406 (4)
N4	0.82606 (10)	0.32537 (17)	−0.08565 (12)	0.0377 (4)
C14	0.76709 (11)	0.18825 (19)	−0.05728 (12)	0.0315 (4)
C10	0.76853 (11)	0.03058 (19)	−0.13524 (12)	0.0306 (4)
C5	0.66284 (12)	0.2490 (2)	−0.08265 (13)	0.0356 (4)
C11	0.90172 (13)	0.1041 (2)	0.10491 (14)	0.0456 (5)
H11A	0.9148	0.0036	0.0640	0.055*
H11B	0.9198	0.0835	0.1915	0.055*
C9	0.74371 (12)	−0.1230 (2)	−0.09704 (14)	0.0412 (4)
H9A	0.7238	−0.1323	−0.0246	0.049*
N1	0.63469 (11)	0.3400 (2)	−0.18294 (12)	0.0511 (4)
C6	0.79561 (13)	−0.0872 (2)	−0.30852 (15)	0.0506 (5)
H6A	0.8117	−0.0751	−0.3832	0.061*
C13	0.92964 (13)	0.2875 (2)	−0.05846 (14)	0.0474 (5)
H13A	0.9651	0.3833	−0.0774	0.057*
H13B	0.9417	0.1947	−0.1078	0.057*
C12	0.96337 (13)	0.2441 (3)	0.07420 (15)	0.0532 (5)
H12A	0.9582	0.3410	0.1235	0.064*
H12B	1.0304	0.2098	0.0911	0.064*
C1	0.54414 (16)	0.3966 (3)	−0.20904 (18)	0.0639 (6)
H1A	0.5240	0.4598	−0.2790	0.077*
C7	0.77636 (14)	−0.2439 (2)	−0.27331 (15)	0.0520 (5)
H7A	0.7821	−0.3359	−0.3210	0.062*
C4	0.60138 (14)	0.2111 (3)	−0.00797 (16)	0.0539 (5)
H4A	0.6222	0.1458	0.0608	0.065*
C8	0.74829 (13)	−0.2622 (2)	−0.16589 (15)	0.0503 (5)
H8A	0.7327	−0.3666	−0.1403	0.060*
C2	0.47951 (15)	0.3674 (3)	−0.13943 (19)	0.0647 (6)
H2A	0.4174	0.4109	−0.1607	0.078*
C3	0.50821 (15)	0.2726 (3)	−0.03762 (19)	0.0685 (6)
H3A	0.4655	0.2496	0.0114	0.082*
H4	0.8042 (12)	0.352 (2)	−0.1662 (16)	0.052 (5)*
H3	0.7859 (12)	0.224 (2)	0.1143 (14)	0.050 (5)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N3	0.0487 (9)	0.0332 (8)	0.0296 (7)	0.0036 (7)	0.0108 (6)	−0.0032 (6)
N2	0.0533 (10)	0.0376 (9)	0.0329 (7)	−0.0027 (7)	0.0141 (6)	−0.0042 (6)
N4	0.0455 (9)	0.0288 (8)	0.0398 (8)	−0.0039 (7)	0.0120 (6)	−0.0006 (6)
C14	0.0390 (10)	0.0265 (9)	0.0301 (8)	0.0004 (7)	0.0102 (6)	−0.0010 (6)
C10	0.0353 (9)	0.0274 (9)	0.0286 (7)	0.0023 (7)	0.0059 (6)	−0.0010 (6)
C5	0.0408 (10)	0.0297 (9)	0.0368 (9)	−0.0001 (7)	0.0099 (7)	−0.0050 (7)
C11	0.0493 (12)	0.0495 (11)	0.0348 (9)	0.0080 (9)	0.0030 (7)	−0.0025 (8)
C9	0.0557 (12)	0.0320 (10)	0.0350 (9)	−0.0030 (8)	0.0087 (7)	0.0008 (7)
N1	0.0506 (10)	0.0521 (10)	0.0490 (9)	0.0117 (8)	0.0078 (7)	0.0072 (7)
C6	0.0613 (13)	0.0550 (13)	0.0374 (9)	0.0009 (10)	0.0154 (8)	−0.0131 (9)
C13	0.0426 (11)	0.0482 (12)	0.0529 (10)	−0.0101 (9)	0.0139 (8)	−0.0064 (8)
C12	0.0451 (12)	0.0599 (14)	0.0512 (10)	−0.0036 (10)	0.0039 (8)	−0.0127 (9)
C1	0.0583 (14)	0.0653 (15)	0.0618 (12)	0.0154 (11)	−0.0001 (10)	0.0046 (10)
C7	0.0639 (13)	0.0400 (12)	0.0462 (10)	0.0107 (10)	0.0004 (9)	−0.0178 (9)
C4	0.0487 (12)	0.0639 (14)	0.0528 (11)	0.0017 (10)	0.0190 (9)	0.0024 (9)
C8	0.0639 (13)	0.0279 (10)	0.0518 (11)	−0.0024 (9)	−0.0024 (9)	−0.0018 (8)
C2	0.0448 (13)	0.0705 (16)	0.0731 (14)	0.0124 (11)	0.0012 (10)	−0.0182 (12)
C3	0.0452 (13)	0.0887 (18)	0.0779 (15)	0.0000 (12)	0.0269 (10)	−0.0126 (13)

Geometric parameters (Å, º) top

N3—C14	1.4635 (18)	N1—C1	1.336 (2)
N3—C11	1.467 (2)	C6—C7	1.367 (3)
N3—H3	0.878 (17)	C6—H6A	0.9300
N2—C10	1.3401 (18)	C13—C12	1.511 (2)
N2—C6	1.343 (2)	C13—H13A	0.9700
N4—C14	1.4638 (19)	C13—H13B	0.9700
N4—C13	1.468 (2)	C12—H12A	0.9700
N4—H4	0.921 (17)	C12—H12B	0.9700
C14—C5	1.527 (2)	C1—C2	1.361 (3)
C14—C10	1.546 (2)	C1—H1A	0.9300
C10—C9	1.379 (2)	C7—C8	1.372 (2)
C5—N1	1.334 (2)	C7—H7A	0.9300
C5—C4	1.381 (2)	C4—C3	1.384 (3)
C11—C12	1.514 (2)	C4—H4A	0.9300
C11—H11A	0.9700	C8—H8A	0.9300
C11—H11B	0.9700	C2—C3	1.365 (3)
C9—C8	1.373 (2)	C2—H2A	0.9300
C9—H9A	0.9300	C3—H3A	0.9300

C14—N3—C11	112.16 (12)	C7—C6—H6A	118.0
C14—N3—H3	107.7 (11)	N4—C13—C12	109.54 (14)
C11—N3—H3	108.3 (11)	N4—C13—H13A	109.8
C10—N2—C6	117.07 (15)	C12—C13—H13A	109.8
C14—N4—C13	113.39 (13)	N4—C13—H13B	109.8
C14—N4—H4	108.1 (11)	C12—C13—H13B	109.8
C13—N4—H4	110.8 (11)	H13A—C13—H13B	108.2
N3—C14—N4	110.86 (12)	C13—C12—C11	109.23 (14)
N3—C14—C5	109.51 (12)	C13—C12—H12A	109.8
N4—C14—C5	107.45 (13)	C11—C12—H12A	109.8
N3—C14—C10	107.83 (12)	C13—C12—H12B	109.8
N4—C14—C10	114.09 (12)	C11—C12—H12B	109.8
C5—C14—C10	106.97 (12)	H12A—C12—H12B	108.3
N2—C10—C9	121.72 (14)	N1—C1—C2	123.9 (2)
N2—C10—C14	117.23 (13)	N1—C1—H1A	118.0
C9—C10—C14	121.03 (13)	C2—C1—H1A	118.0
N1—C5—C4	122.15 (17)	C6—C7—C8	118.39 (16)
N1—C5—C14	115.30 (14)	C6—C7—H7A	120.8
C4—C5—C14	122.55 (15)	C8—C7—H7A	120.8
N3—C11—C12	113.15 (15)	C5—C4—C3	118.56 (19)
N3—C11—H11A	108.9	C5—C4—H4A	120.7
C12—C11—H11A	108.9	C3—C4—H4A	120.7
N3—C11—H11B	108.9	C7—C8—C9	118.52 (17)
C12—C11—H11B	108.9	C7—C8—H8A	120.7
H11A—C11—H11B	107.8	C9—C8—H8A	120.7
C8—C9—C10	120.09 (15)	C1—C2—C3	118.3 (2)
C8—C9—H9A	120.0	C1—C2—H2A	120.9
C10—C9—H9A	120.0	C3—C2—H2A	120.9
C5—N1—C1	117.65 (17)	C2—C3—C4	119.4 (2)
N2—C6—C7	124.09 (16)	C2—C3—H3A	120.3
N2—C6—H6A	118.0	C4—C3—H3A	120.3

C11—N3—C14—N4	−53.05 (17)	C10—C14—C5—C4	97.46 (17)
C11—N3—C14—C5	−171.44 (13)	C14—N3—C11—C12	53.15 (17)
C11—N3—C14—C10	72.50 (16)	N2—C10—C9—C8	3.5 (2)
C13—N4—C14—N3	56.96 (16)	C14—C10—C9—C8	−178.02 (15)
C13—N4—C14—C5	176.59 (11)	C4—C5—N1—C1	0.9 (3)
C13—N4—C14—C10	−65.00 (16)	C14—C5—N1—C1	−179.79 (15)
C6—N2—C10—C9	−2.7 (2)	C10—N2—C6—C7	−0.5 (3)
C6—N2—C10—C14	178.80 (14)	C14—N4—C13—C12	−58.22 (17)
N3—C14—C10—N2	−145.84 (13)	N4—C13—C12—C11	54.63 (19)
N4—C14—C10—N2	−22.22 (19)	N3—C11—C12—C13	−53.6 (2)
C5—C14—C10—N2	96.46 (16)	C5—N1—C1—C2	0.2 (3)
N3—C14—C10—C9	35.63 (19)	N2—C6—C7—C8	2.9 (3)
N4—C14—C10—C9	159.24 (14)	N1—C5—C4—C3	−1.2 (3)
C5—C14—C10—C9	−82.08 (17)	C14—C5—C4—C3	179.54 (16)
N3—C14—C5—N1	161.53 (13)	C6—C7—C8—C9	−2.0 (3)
N4—C14—C5—N1	41.03 (17)	C10—C9—C8—C7	−1.0 (2)
C10—C14—C5—N1	−81.87 (16)	N1—C1—C2—C3	−1.0 (3)
N3—C14—C5—C4	−19.1 (2)	C1—C2—C3—C4	0.6 (3)
N4—C14—C5—C4	−139.63 (16)	C5—C4—C3—C2	0.4 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3···N2ⁱ	0.878 (17)	2.425 (18)	3.2845 (19)	166.4 (15)
N4—H4···N1	0.921 (17)	2.379 (17)	2.701 (2)	100.3 (12)
N4—H4···N2	0.921 (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 formula	C₁₄H₁₆N₄
M_r	240.31
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	14.2372 (14), 8.0302 (8), 11.3277 (9)
β (°)	103.075 (8)
V (Å³)	1261.5 (2)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.08
Crystal size (mm)	0.3 × 0.2 × 0.15

Data collection
Diffractometer	Agilent Xcalibur Eos diffractometer
Absorption correction	Multi-scan (CrysAlis PRO; Agilent, 2011)
T_min, T_max	0.98, 0.99
No. of measured, independent and observed [I > 2σ(I)] reflections	4640, 2238, 1656
R_int	0.023
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.041, 0.108, 1.05
No. of reflections	2238
No. of parameters	171
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	D—H···A
N3—H3···N2ⁱ	0.878 (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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