2-Methyl-2-(2-pyrid­yl)hexa­hydro­pyrimidine

Al-Resayes, S.

doi:10.1107/S1600536809025963

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 65| Part 8| August 2009| Page o1874

doi:10.1107/S1600536809025963

Open

access

2-Methyl-2-(2-pyridyl)hexahydropyrimidine

Saud Al-Resayes ^a ^*

^aDepartment of Chemistry, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
^*Correspondence e-mail: sresayes@ksu.edu.sa

(Received 29 June 2009; accepted 4 July 2009; online 15 July 2009)

In the aminal-type title compound, C₁₀H₁₅N₃, the six-membered hexahydropyrimidine ring adopts a chair conformation and the N atoms are pyramidally coordinated. One of the two amido –NH units engages in intermolecular hydrogen bonding with the pyridyl N atom, generating a helical chain running along the b axis of the orthorhombic unit cell.

Related literature

The title compound is used in Fe(II) spin-crossover materials; see: Bréfuel et al. (2007 ).

Experimental

Crystal data

C₁₀H₁₅N₃
M_r = 177.25
Orthorhombic, P 2₁ 2₁ 2₁
a = 8.4070 (17) Å
b = 10.371 (2) Å
c = 11.363 (2) Å
V = 990.7 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.07 mm⁻¹
T = 294 K
0.35 × 0.15 × 0.15 mm

Data collection

Rigaku R-AXIS RAPID diffractometer
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2007 ) T_min = 0.97, T_max = 0.99
8017 measured reflections
1324 independent reflections
1206 reflections with I > 2σ(I)
R_int = 0.022

Refinement

R[F² > 2σ(F²)] = 0.044
wR(F²) = 0.115
S = 1.01
1324 reflections
128 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.20 e Å⁻³
Δρ_min = −0.34 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2A⋯N1ⁱ	0.89 (3)	2.31 (3)	3.188 (2)	168 (2)
Symmetry code: (i) $[-x, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: CrystalClear (Rigaku/MSC, 2007); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2006 ) and PLUTO (Motherwell et al., 1999 ); software used to prepare material for publication: publCIF (Westrip, 2009 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809025963/ng2608sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809025963/ng2608Isup2.hkl

checkCIF report

Comment top

The title compound was known as precursor for syntheses of umsymmetrical tetradentate Schiff base ligands that form bistable Fe(II) spin crossover materials (Bréfuel et al. 2007).

The molecular packing of the title compound is supported by N— H···N intermolecular hydrogen bondings at H···A distance of 2.31 (3) and D— H···A angle of 168 (2)° and calculated with Pluto (Motherwell et al., 1999), see Figure 2.

Related literature top

The title compound is used in Fe(II) spin-crossover materials; see: Bréfuel et al. (2007).

Experimental top

1,3-Propane diamine (1 g, 0.013 mmol) was mixed with 1-(2-pyridinyl)-1-ethanone (1.635 g, 0.013 mmol) in 30 ml e thanol. The mixture was stirred under reflux for 5 h. The solution was concentrated under reduced pressure and the product was precipitated by addition of 30 ml of cool distilled water. Product was filtered off and washed three times with 15 ml of distilled water then dried under vacuum. Crude product was recrystallized from ethanol and allowed to stand at room temperature. Crystals were collected after 2 weeks.

Computing details top

Data collection: CrystalClear (Rigaku/MSC, 2007); cell refinement: CrystalClear (Rigaku/MSC, 2007); data reduction: CrystalClear (Rigaku/MSC, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2006) and PLUTO (Motherwell et al., 1999); software used to prepare material for publication: publCIF (Westrip, 2009).

Figures top

	Fig. 1. Perspective drawings of the title compound showing the atom-numbering scheme. The atomic displacement ellipsoids are shown at the 50% probability level. Hydrogen atoms are drawn as spheres of arbitrary radius.
	Fig. 2. N— H···N intermolecular hydrogen bonding pattern of the title compound with hydrogen bonding shown as broken lines. Symmetry code: -x, y + 1/2, -z + 1/2.

2-Methyl-2-(2-pyridyl)hexahydropyrimidine top

Crystal data top

C₁₀H₁₅N₃	F(000) = 384
M_r = 177.25	D_x = 1.188 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 7168 reflections
a = 8.4070 (17) Å	θ = 3.0–27.5°
b = 10.371 (2) Å	µ = 0.07 mm⁻¹
c = 11.363 (2) Å	T = 294 K
V = 990.7 (3) Å³	Plate, yellow
Z = 4	0.35 × 0.15 × 0.15 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	1324 independent reflections
Radiation source: fine-focus sealed tube	1206 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.022
ω scans	θ_max = 27.5°, θ_min = 3.0°
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2007)	h = −10→10
T_min = 0.97, T_max = 0.99	k = −13→12
8017 measured reflections	l = −13→14

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)] = 0.044	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.115	H atoms treated by a mixture of independent and constrained refinement
S = 1.01	w = 1/[σ²(F_o²) + (0.0907P)² + 0.0352P] where P = (F_o² + 2F_c²)/3
1324 reflections	(Δ/σ)_max < 0.001
128 parameters	Δρ_max = 0.20 e Å⁻³
0 restraints	Δρ_min = −0.34 e Å⁻³

Crystal data top

C₁₀H₁₅N₃	V = 990.7 (3) Å³
M_r = 177.25	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 8.4070 (17) Å	µ = 0.07 mm⁻¹
b = 10.371 (2) Å	T = 294 K
c = 11.363 (2) Å	0.35 × 0.15 × 0.15 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	1324 independent reflections
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2007)	1206 reflections with I > 2σ(I)
T_min = 0.97, T_max = 0.99	R_int = 0.022
8017 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.044	0 restraints
wR(F²) = 0.115	H atoms treated by a mixture of independent and constrained refinement
S = 1.01	Δρ_max = 0.20 e Å⁻³
1324 reflections	Δρ_min = −0.34 e Å⁻³
128 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
N1	0.20810 (17)	0.34068 (14)	0.21846 (15)	0.0473 (4)
C1	0.3442 (2)	0.27459 (18)	0.2066 (2)	0.0562 (5)
H1	0.3416	0.1859	0.2183	0.067*
N2	0.05820 (18)	0.66511 (13)	0.16234 (14)	0.0475 (3)
H2A	−0.026 (3)	0.711 (2)	0.187 (2)	0.063 (6)*
C2	0.4872 (2)	0.3304 (2)	0.17791 (18)	0.0553 (5)
H2	0.5789	0.2809	0.1707	0.066*
N3	−0.08570 (15)	0.46514 (15)	0.18351 (14)	0.0436 (3)
H3A	−0.087 (3)	0.391 (2)	0.221 (2)	0.063 (6)*
C3	0.49114 (19)	0.4615 (2)	0.16021 (17)	0.0518 (4)
H3	0.5861	0.5025	0.1410	0.062*
C4	0.35197 (19)	0.53176 (17)	0.17129 (16)	0.0445 (4)
H4	0.3523	0.6205	0.1599	0.053*
C5	0.21182 (17)	0.46810 (14)	0.19969 (13)	0.0364 (3)
C6	0.05402 (18)	0.53948 (14)	0.22108 (14)	0.0385 (3)
C7	0.0394 (3)	0.5618 (2)	0.35388 (16)	0.0574 (5)
H7A	0.1299	0.6097	0.3812	0.086*
H7B	0.0352	0.4802	0.3936	0.086*
H7C	−0.0560	0.6095	0.3701	0.086*
C8	−0.0901 (2)	0.44394 (19)	0.05613 (18)	0.0536 (4)
H8A	−0.1817	0.3918	0.0356	0.064*
H8B	0.0051	0.3987	0.0311	0.064*
C9	−0.1001 (3)	0.5740 (2)	−0.00463 (18)	0.0630 (5)
H9A	−0.0978	0.5624	−0.0893	0.076*
H9B	−0.1990	0.6164	0.0161	0.076*
C10	0.0403 (2)	0.6562 (2)	0.03398 (18)	0.0574 (5)
H10A	0.1370	0.6202	0.0009	0.069*
H10B	0.0274	0.7424	0.0022	0.069*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0406 (7)	0.0382 (6)	0.0631 (9)	0.0007 (6)	0.0038 (7)	0.0057 (6)
C1	0.0532 (10)	0.0419 (8)	0.0737 (12)	0.0105 (8)	0.0012 (9)	0.0040 (9)
N2	0.0480 (7)	0.0342 (6)	0.0602 (8)	0.0046 (6)	0.0084 (7)	0.0023 (6)
C2	0.0406 (8)	0.0658 (11)	0.0594 (10)	0.0145 (8)	0.0010 (7)	−0.0043 (9)
N3	0.0321 (6)	0.0439 (7)	0.0549 (8)	−0.0012 (5)	0.0053 (5)	0.0062 (7)
C3	0.0340 (7)	0.0649 (10)	0.0564 (9)	−0.0048 (7)	0.0033 (7)	−0.0035 (9)
C4	0.0388 (7)	0.0425 (7)	0.0522 (9)	−0.0059 (6)	0.0040 (6)	−0.0022 (7)
C5	0.0340 (7)	0.0353 (7)	0.0400 (7)	−0.0006 (6)	0.0011 (6)	−0.0017 (6)
C6	0.0371 (7)	0.0359 (7)	0.0427 (7)	0.0006 (6)	0.0067 (6)	0.0007 (6)
C7	0.0614 (11)	0.0643 (11)	0.0466 (9)	0.0089 (9)	0.0088 (8)	−0.0057 (8)
C8	0.0415 (8)	0.0590 (10)	0.0603 (10)	−0.0022 (8)	−0.0019 (7)	−0.0084 (8)
C9	0.0568 (11)	0.0812 (13)	0.0509 (10)	0.0073 (10)	−0.0036 (8)	0.0088 (10)
C10	0.0591 (10)	0.0551 (9)	0.0579 (10)	0.0062 (9)	0.0097 (9)	0.0181 (9)

Geometric parameters (Å, º) top

N1—C1	1.340 (2)	C4—H4	0.9300
N1—C5	1.339 (2)	C5—C6	1.539 (2)
C1—C2	1.374 (3)	C6—C7	1.532 (2)
C1—H1	0.9300	C7—H7A	0.9600
N2—C10	1.469 (3)	C7—H7B	0.9600
N2—C6	1.464 (2)	C7—H7C	0.9600
N2—H2A	0.89 (3)	C8—C9	1.517 (3)
C2—C3	1.375 (3)	C8—H8A	0.9700
C2—H2	0.9300	C8—H8B	0.9700
N3—C6	1.468 (2)	C9—C10	1.521 (3)
N3—C8	1.464 (3)	C9—H9A	0.9700
N3—H3A	0.88 (3)	C9—H9B	0.9700
C3—C4	1.384 (2)	C10—H10A	0.9700
C3—H3	0.9300	C10—H10B	0.9700
C4—C5	1.389 (2)

C1—N1—C5	117.95 (14)	N2—C6—C5	109.60 (12)
N1—C1—C2	123.75 (16)	C7—C6—C5	107.30 (14)
N1—C1—H1	118.1	C6—C7—H7A	109.5
C2—C1—H1	118.1	C6—C7—H7B	109.5
C10—N2—C6	113.21 (14)	H7A—C7—H7B	109.5
C10—N2—H2A	105.3 (17)	C6—C7—H7C	109.5
C6—N2—H2A	108.1 (16)	H7A—C7—H7C	109.5
C3—C2—C1	118.18 (16)	H7B—C7—H7C	109.5
C3—C2—H2	120.9	N3—C8—C9	108.52 (16)
C1—C2—H2	120.9	N3—C8—H8A	110.0
C6—N3—C8	112.72 (13)	C9—C8—H8A	110.0
C6—N3—H3A	109.1 (16)	N3—C8—H8B	110.0
C8—N3—H3A	110.1 (16)	C9—C8—H8B	110.0
C2—C3—C4	119.15 (16)	H8A—C8—H8B	108.4
C2—C3—H3	120.4	C10—C9—C8	108.91 (16)
C4—C3—H3	120.4	C10—C9—H9A	109.9
C5—C4—C3	119.22 (16)	C8—C9—H9A	109.9
C5—C4—H4	120.4	C10—C9—H9B	109.9
C3—C4—H4	120.4	C8—C9—H9B	109.9
N1—C5—C4	121.74 (15)	H9A—C9—H9B	108.3
N1—C5—C6	115.44 (13)	N2—C10—C9	113.65 (16)
C4—C5—C6	122.65 (13)	N2—C10—H10A	108.8
N3—C6—N2	110.72 (13)	C9—C10—H10A	108.8
N3—C6—C7	107.56 (13)	N2—C10—H10B	108.8
N2—C6—C7	108.46 (14)	C9—C10—H10B	108.8
N3—C6—C5	113.03 (12)	H10A—C10—H10B	107.7

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···N1ⁱ	0.89 (3)	2.31 (3)	3.188 (2)	168 (2)

Symmetry code: (i) −x, y+1/2, −z+1/2.

Experimental details

Crystal data
Chemical formula	C₁₀H₁₅N₃
M_r	177.25
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	294
a, b, c (Å)	8.4070 (17), 10.371 (2), 11.363 (2)
V (Å³)	990.7 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.07
Crystal size (mm)	0.35 × 0.15 × 0.15

Data collection
Diffractometer	Rigaku R-AXIS RAPID diffractometer
Absorption correction	Multi-scan (CrystalClear; Rigaku/MSC, 2007)
T_min, T_max	0.97, 0.99
No. of measured, independent and observed [I > 2σ(I)] reflections	8017, 1324, 1206
R_int	0.022
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.044, 0.115, 1.01
No. of reflections	1324
No. of parameters	128
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.20, −0.34

Computer programs: CrystalClear (Rigaku/MSC, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2006) and PLUTO (Motherwell et al., 1999), publCIF (Westrip, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···N1ⁱ	0.89 (3)	2.31 (3)	3.188 (2)	168 (2)

Symmetry code: (i) −x, y+1/2, −z+1/2.

References

Brandenburg, K. (2006). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Bréfuel, N., Shova, S. & Tuchagues, J.-P. (2007). Eur. J. Inorg. Chem. pp. 4326–4334. Google Scholar
Motherwell, W. D. S., Shields, G. P. & Allen, F. H. (1999). Acta Cryst. B55, 1044–1056. Web of Science CrossRef CAS IUCr Journals Google Scholar
Rigaku/MSC (2007). CrystalClear. Rigaku/MSC, The Woodlands, Texas, USA. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Westrip, S. P. (2009). publCIF. In preparation. Google Scholar

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.

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 65| Part 8| August 2009| Page o1874

doi:10.1107/S1600536809025963

Open

access