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

Abstract

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,

• a = 8.4070 (17) Å

• b = 10.371 (2) Å

• c = 11.363 (2) Å

• V = 990.7 (3) ų

• 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[F ² > 2σ(F ²)] = 0.044

• wR(F ²) = 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

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 ▶).

Supplementary Material

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

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) .

supplementary crystallographic information

Comment

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.

Experimental

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.

Refinement

Hydrogen atoms were refined isotropically and were constrained to the ideal geometry using an appropriate riding model with U_iso(H) fixed at 1.2 times U_eq of the pivot atom. The —NH hydrogen atoms was located from difference Fourier map and refined isotropically without constraints. 949 Friedel-pair reflections were merged for a weak anomalous scatterer structure.

Figures

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.

Crystal data

C10H15N3	F(000) = 384
Mr = 177.25	Dx = 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

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

Refinement

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(Fo2) + (0.0907P)2 + 0.0352P] where P = (Fo2 + 2Fc2)/3
1324 reflections	(Δ/σ)max < 0.001
128 parameters	Δρmax = 0.20 e Å−3
0 restraints	Δρmin = −0.34 e Å−3

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 (Ų)

	x	y	z	Uiso*/Ueq
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 (Ų)

	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, °)

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, °)

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 codes: (i) −x, y+1/2, −z+1/2.