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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.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536809025963/ng2608sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536809025963/ng2608Isup2.hkl
Contains datablock I

CCDC reference: 744388

Key indicators

  • Single-crystal X-ray study
  • T = 294 K
  • Mean [sigma](C-C) = 0.003 Å
  • R factor = 0.044
  • wR factor = 0.115
  • Data-to-parameter ratio = 10.3

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT420_ALERT_2_C D-H Without Acceptor N3 - H3A ... ?
Alert level G REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF. From the CIF: _diffrn_reflns_theta_max 27.47 From the CIF: _reflns_number_total 1324 Count of symmetry unique reflns 1325 Completeness (_total/calc) 99.92% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 0 Fraction of Friedel pairs measured 0.000 Are heavy atom types Z>Si present no
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 1 ALERT level C = Check and explain 1 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 1 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check

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.

Refinement top

Hydrogen atoms were refined isotropically and were constrained to the ideal geometry using an appropriate riding model with Uiso(H) fixed at 1.2 times Ueq 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.

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
[Figure 1] 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.
[Figure 2] 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
C10H15N3F(000) = 384
Mr = 177.25Dx = 1.188 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 7168 reflections
a = 8.4070 (17) Åθ = 3.0–27.5°
b = 10.371 (2) ŵ = 0.07 mm1
c = 11.363 (2) ÅT = 294 K
V = 990.7 (3) Å3Plate, yellow
Z = 40.35 × 0.15 × 0.15 mm
Data collection top
Rigaku R-AXIS RAPID
diffractometer
1324 independent reflections
Radiation source: fine-focus sealed tube1206 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.022
ω scansθmax = 27.5°, θmin = 3.0°
Absorption correction: multi-scan
(CrystalClear; Rigaku/MSC, 2007)
h = 1010
Tmin = 0.97, Tmax = 0.99k = 1312
8017 measured reflectionsl = 1314
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)] = 0.044Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.115H 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 parametersΔρmax = 0.20 e Å3
0 restraintsΔρmin = 0.34 e Å3
Crystal data top
C10H15N3V = 990.7 (3) Å3
Mr = 177.25Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 8.4070 (17) ŵ = 0.07 mm1
b = 10.371 (2) ÅT = 294 K
c = 11.363 (2) Å0.35 × 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)
Tmin = 0.97, Tmax = 0.99Rint = 0.022
8017 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0440 restraints
wR(F2) = 0.115H atoms treated by a mixture of independent and constrained refinement
S = 1.01Δρmax = 0.20 e Å3
1324 reflectionsΔρmin = 0.34 e Å3
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
xyzUiso*/Ueq
N10.20810 (17)0.34068 (14)0.21846 (15)0.0473 (4)
C10.3442 (2)0.27459 (18)0.2066 (2)0.0562 (5)
H10.34160.18590.21830.067*
N20.05820 (18)0.66511 (13)0.16234 (14)0.0475 (3)
H2A0.026 (3)0.711 (2)0.187 (2)0.063 (6)*
C20.4872 (2)0.3304 (2)0.17791 (18)0.0553 (5)
H20.57890.28090.17070.066*
N30.08570 (15)0.46514 (15)0.18351 (14)0.0436 (3)
H3A0.087 (3)0.391 (2)0.221 (2)0.063 (6)*
C30.49114 (19)0.4615 (2)0.16021 (17)0.0518 (4)
H30.58610.50250.14100.062*
C40.35197 (19)0.53176 (17)0.17129 (16)0.0445 (4)
H40.35230.62050.15990.053*
C50.21182 (17)0.46810 (14)0.19969 (13)0.0364 (3)
C60.05402 (18)0.53948 (14)0.22108 (14)0.0385 (3)
C70.0394 (3)0.5618 (2)0.35388 (16)0.0574 (5)
H7A0.12990.60970.38120.086*
H7B0.03520.48020.39360.086*
H7C0.05600.60950.37010.086*
C80.0901 (2)0.44394 (19)0.05613 (18)0.0536 (4)
H8A0.18170.39180.03560.064*
H8B0.00510.39870.03110.064*
C90.1001 (3)0.5740 (2)0.00463 (18)0.0630 (5)
H9A0.09780.56240.08930.076*
H9B0.19900.61640.01610.076*
C100.0403 (2)0.6562 (2)0.03398 (18)0.0574 (5)
H10A0.13700.62020.00090.069*
H10B0.02740.74240.00220.069*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0406 (7)0.0382 (6)0.0631 (9)0.0007 (6)0.0038 (7)0.0057 (6)
C10.0532 (10)0.0419 (8)0.0737 (12)0.0105 (8)0.0012 (9)0.0040 (9)
N20.0480 (7)0.0342 (6)0.0602 (8)0.0046 (6)0.0084 (7)0.0023 (6)
C20.0406 (8)0.0658 (11)0.0594 (10)0.0145 (8)0.0010 (7)0.0043 (9)
N30.0321 (6)0.0439 (7)0.0549 (8)0.0012 (5)0.0053 (5)0.0062 (7)
C30.0340 (7)0.0649 (10)0.0564 (9)0.0048 (7)0.0033 (7)0.0035 (9)
C40.0388 (7)0.0425 (7)0.0522 (9)0.0059 (6)0.0040 (6)0.0022 (7)
C50.0340 (7)0.0353 (7)0.0400 (7)0.0006 (6)0.0011 (6)0.0017 (6)
C60.0371 (7)0.0359 (7)0.0427 (7)0.0006 (6)0.0067 (6)0.0007 (6)
C70.0614 (11)0.0643 (11)0.0466 (9)0.0089 (9)0.0088 (8)0.0057 (8)
C80.0415 (8)0.0590 (10)0.0603 (10)0.0022 (8)0.0019 (7)0.0084 (8)
C90.0568 (11)0.0812 (13)0.0509 (10)0.0073 (10)0.0036 (8)0.0088 (10)
C100.0591 (10)0.0551 (9)0.0579 (10)0.0062 (9)0.0097 (9)0.0181 (9)
Geometric parameters (Å, º) top
N1—C11.340 (2)C4—H40.9300
N1—C51.339 (2)C5—C61.539 (2)
C1—C21.374 (3)C6—C71.532 (2)
C1—H10.9300C7—H7A0.9600
N2—C101.469 (3)C7—H7B0.9600
N2—C61.464 (2)C7—H7C0.9600
N2—H2A0.89 (3)C8—C91.517 (3)
C2—C31.375 (3)C8—H8A0.9700
C2—H20.9300C8—H8B0.9700
N3—C61.468 (2)C9—C101.521 (3)
N3—C81.464 (3)C9—H9A0.9700
N3—H3A0.88 (3)C9—H9B0.9700
C3—C41.384 (2)C10—H10A0.9700
C3—H30.9300C10—H10B0.9700
C4—C51.389 (2)
C1—N1—C5117.95 (14)N2—C6—C5109.60 (12)
N1—C1—C2123.75 (16)C7—C6—C5107.30 (14)
N1—C1—H1118.1C6—C7—H7A109.5
C2—C1—H1118.1C6—C7—H7B109.5
C10—N2—C6113.21 (14)H7A—C7—H7B109.5
C10—N2—H2A105.3 (17)C6—C7—H7C109.5
C6—N2—H2A108.1 (16)H7A—C7—H7C109.5
C3—C2—C1118.18 (16)H7B—C7—H7C109.5
C3—C2—H2120.9N3—C8—C9108.52 (16)
C1—C2—H2120.9N3—C8—H8A110.0
C6—N3—C8112.72 (13)C9—C8—H8A110.0
C6—N3—H3A109.1 (16)N3—C8—H8B110.0
C8—N3—H3A110.1 (16)C9—C8—H8B110.0
C2—C3—C4119.15 (16)H8A—C8—H8B108.4
C2—C3—H3120.4C10—C9—C8108.91 (16)
C4—C3—H3120.4C10—C9—H9A109.9
C5—C4—C3119.22 (16)C8—C9—H9A109.9
C5—C4—H4120.4C10—C9—H9B109.9
C3—C4—H4120.4C8—C9—H9B109.9
N1—C5—C4121.74 (15)H9A—C9—H9B108.3
N1—C5—C6115.44 (13)N2—C10—C9113.65 (16)
C4—C5—C6122.65 (13)N2—C10—H10A108.8
N3—C6—N2110.72 (13)C9—C10—H10A108.8
N3—C6—C7107.56 (13)N2—C10—H10B108.8
N2—C6—C7108.46 (14)C9—C10—H10B108.8
N3—C6—C5113.03 (12)H10A—C10—H10B107.7
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2A···N1i0.89 (3)2.31 (3)3.188 (2)168 (2)
Symmetry code: (i) x, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC10H15N3
Mr177.25
Crystal system, space groupOrthorhombic, P212121
Temperature (K)294
a, b, c (Å)8.4070 (17), 10.371 (2), 11.363 (2)
V3)990.7 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.07
Crystal size (mm)0.35 × 0.15 × 0.15
Data collection
DiffractometerRigaku R-AXIS RAPID
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku/MSC, 2007)
Tmin, Tmax0.97, 0.99
No. of measured, independent and
observed [I > 2σ(I)] reflections
8017, 1324, 1206
Rint0.022
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.044, 0.115, 1.01
No. of reflections1324
No. of parameters128
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
N2—H2A···N1i0.89 (3)2.31 (3)3.188 (2)168 (2)
Symmetry code: (i) x, y+1/2, z+1/2.
 

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