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Acta Cryst. (2007). E63, o3665    [ doi:10.1107/S1600536807036859 ]

1,3-Dibenzyl-2-phenylperhydropyrimidine

H.-T. Xia, Y.-F. Liu, D.-Q. Wang and W. Gao

Abstract top

In the title compound, C24H26N2, the dihedral angles between the phenyl ring at the 2-position and the other two phenyl rings are 78.53 (10) and 79.37 (10)°. The heterocyclic ring adopts a chair conformation. Molecules are linked into chains of rings and a three-dimensional network by C-H...[pi] hydrogen bonds.

Comment top

As part of our investigation of crystal structures of diamine derivatives, we report here the crystal structure of a new diamine derivative.

The molecular structure of the title compound is illustrated in Fig. 1. The bond lengths and angles are normal (Allen et al., 1987). A very closely related compound is 1,3-dibenzyl-2-phenylimidazolidine (Xia et al., 2007); it and the title compound have similar crystal structures. In the title compound, the dihedral angles between the central phenyl ring (C5—C10) and the other two phenyl rings are 78.53 (10)° (C12—C1) and 79.37 (10)° (C19—C24) (Fig. 1). Molecules are linked into chains of rings and a three-dimensional network by C—H···π hydrogen bonds (Fig. 2 and Fig. 3).

Related literature top

For bond- length data, see: Allen et al. (1987). For a related structure, see: Xia et al. (2007).

Experimental top

To a solution of benzaldehyde (20 mmol) in methanol (20 ml) propane-1,3-diamine (10 mmol) in methanol (10 ml) was added. The mixed solution was stirred for 10 min and then acetic acid catalyst was added. The reaction mixture was stirred continuously for 10 h at 338 K and then filtered. The solution was allowed to stand, slowly producing crystals of the title compound.

Refinement top

All H atoms were located in difference Fourier maps. They were then treated as riding, with C—H distances of 0.93 Å (aryl), 0.97 Å (methylene) and 0.98 Å (methine); Uiso(H) = 1.2Ueq(C).

Computing details top

Data collection: SMART (Siemens, 1996); cell refinement: SMART; data reduction: SAINT (Siemens, 1996); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997a); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997a); molecular graphics: SHELXTL (Sheldrick, 1997b); software used to prepare material for publication: SHELXTL.

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level.
[Figure 2] Fig. 2. A portion of the crystal structure of the title compound, showing the formation of a hydrogen-bonded (dashed lines) sheet built from three C—H···π interactions. For clarity, H atoms not involved in hydrogen bonding have been omitted. [Symmetry code: (B) −1/2 + x, 3/2 − y, 1/2 + z, (D) −1 + x, y, z, (E) −3/2 + x, 3/2 − y, 1/2 + z].
[Figure 3] Fig. 3. The crystal structure of the title compound. Neighbouring sheets are connected by a pair of C—H···π hydrogen bonds (dashed lines). For clarity, H atoms not involved in the hydrogen bonding have been omitted. [Symmetry code: (A) (3/2 − x, −1/2 + y, 1/2 − z, (B) −1/2 + x, 3/2 − y, 1/2 + z, (C) 1 − x, 1 − y, 1 − z].
1,3-Dibenzyl-2-phenylperhydropyrimidine top
Crystal data top
C24H26N2F000 = 736
Mr = 342.47Dx = 1.138 Mg m−3
Monoclinic, P21/nMo Kα radiation
λ = 0.71073 Å
a = 6.0912 (11) ÅCell parameters from 926 reflections
b = 16.900 (2) Åθ = 2.4–18.6º
c = 19.621 (3) ŵ = 0.07 mm−1
β = 98.304 (2)ºT = 298 (2) K
V = 1998.7 (5) Å3Block, colorless
Z = 40.35 × 0.17 × 0.15 mm
Data collection top
Bruker SMART CCD area-detector
diffractometer		3522 independent reflections
Radiation source: fine-focus sealed tube1341 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.073
T = 298(2) Kθmax = 25.0º
φ and ω scansθmin = 1.6º
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		h = −7→6
Tmin = 0.977, Tmax = 0.990k = −20→17
9972 measured reflectionsl = −23→23
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.045H-atom parameters constrained
wR(F2) = 0.094  w = 1/[σ2(Fo2) + (0.0279P)2]
where P = (Fo2 + 2Fc2)/3
S = 0.75(Δ/σ)max < 0.001
3522 reflectionsΔρmax = 0.13 e Å−3
235 parametersΔρmin = −0.14 e Å−3
Primary atom site location: structure-invariant direct methodsExtinction correction: none
Crystal data top
C24H26N2V = 1998.7 (5) Å3
Mr = 342.47Z = 4
Monoclinic, P21/nMo Kα
a = 6.0912 (11) ŵ = 0.07 mm−1
b = 16.900 (2) ÅT = 298 (2) K
c = 19.621 (3) Å0.35 × 0.17 × 0.15 mm
β = 98.304 (2)º
Data collection top
Bruker SMART CCD area-detector
diffractometer		3522 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		1341 reflections with I > 2σ(I)
Tmin = 0.977, Tmax = 0.990Rint = 0.073
9972 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.045235 parameters
wR(F2) = 0.094H-atom parameters constrained
S = 0.75Δρmax = 0.13 e Å−3
3522 reflectionsΔρmin = −0.14 e Å−3
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 > 2sigma(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
N10.7318 (3)0.85935 (10)0.06611 (9)0.0516 (5)
N20.7249 (3)0.88698 (10)0.18657 (9)0.0521 (6)
C10.8029 (4)0.94061 (13)0.05542 (11)0.0692 (8)
H1A0.67370.97390.04270.083*
H1B0.89110.94180.01810.083*
C20.9374 (5)0.97215 (13)0.11995 (12)0.0740 (9)
H2A1.07140.94100.13140.089*
H2B0.97991.02650.11290.089*
C30.8003 (4)0.96792 (13)0.17753 (12)0.0671 (8)
H3A0.88780.98600.21990.080*
H3B0.67281.00260.16740.080*
C40.5999 (4)0.85434 (12)0.12315 (11)0.0517 (7)
H40.46160.88410.11120.062*
C50.5463 (5)0.76804 (13)0.13427 (11)0.0473 (6)
C60.7146 (4)0.71554 (14)0.15560 (11)0.0591 (7)
H60.85930.73410.16610.071*
C70.6732 (5)0.63590 (15)0.16175 (12)0.0708 (8)
H70.78930.60120.17590.085*
C80.4605 (6)0.60803 (16)0.14691 (13)0.0718 (9)
H80.43200.55430.15060.086*
C90.2902 (5)0.65937 (17)0.12665 (12)0.0683 (8)
H90.14590.64040.11640.082*
C100.3317 (5)0.73931 (15)0.12132 (10)0.0583 (7)
H100.21440.77410.10890.070*
C110.6008 (4)0.83060 (13)0.00211 (11)0.0606 (8)
H11A0.47520.8657−0.01000.073*
H11B0.54280.77860.01060.073*
C120.7262 (5)0.82518 (13)−0.05768 (12)0.0519 (7)
C130.9340 (5)0.79109 (14)−0.05116 (13)0.0653 (8)
H131.00020.7736−0.00810.078*
C141.0453 (5)0.78237 (14)−0.10665 (17)0.0744 (9)
H141.18460.7588−0.10110.089*
C150.9499 (6)0.80870 (16)−0.17072 (16)0.0817 (10)
H151.02530.8038−0.20850.098*
C160.7445 (6)0.84185 (16)−0.17795 (14)0.0802 (10)
H160.67840.8590−0.22110.096*
C170.6333 (5)0.85023 (13)−0.12196 (13)0.0648 (8)
H170.49310.8732−0.12780.078*
C180.5896 (4)0.88619 (13)0.24232 (11)0.0629 (8)
H18A0.50940.83650.24080.075*
H18B0.48100.92840.23450.075*
C190.7200 (5)0.89608 (13)0.31294 (12)0.0546 (7)
C200.9327 (5)0.86625 (13)0.32864 (14)0.0680 (8)
H201.00100.84280.29430.082*
C211.0450 (5)0.87117 (16)0.39527 (18)0.0851 (10)
H211.18870.85160.40540.102*
C220.9438 (7)0.9048 (2)0.44608 (17)0.0984 (13)
H221.01820.90710.49090.118*
C230.7348 (7)0.93502 (17)0.43139 (16)0.0968 (11)
H230.66710.95830.46600.116*
C240.6234 (5)0.93087 (14)0.36457 (14)0.0732 (9)
H240.48140.95190.35460.088*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0641 (16)0.0516 (12)0.0404 (12)−0.0082 (11)0.0117 (11)−0.0015 (9)
N20.0646 (16)0.0502 (13)0.0428 (12)−0.0040 (11)0.0117 (12)−0.0028 (9)
C10.093 (2)0.0613 (17)0.0557 (17)−0.0117 (16)0.0182 (16)0.0004 (13)
C20.104 (3)0.0551 (17)0.0645 (18)−0.0254 (16)0.0181 (18)−0.0069 (13)
C30.090 (2)0.0521 (17)0.0596 (18)−0.0055 (15)0.0115 (17)−0.0064 (13)
C40.056 (2)0.0507 (15)0.0484 (16)0.0031 (13)0.0064 (14)0.0011 (12)
C50.0499 (19)0.0489 (16)0.0443 (15)−0.0022 (15)0.0106 (13)−0.0009 (11)
C60.056 (2)0.0550 (18)0.0674 (18)−0.0019 (16)0.0131 (15)0.0020 (13)
C70.073 (3)0.0581 (19)0.083 (2)0.0035 (17)0.0167 (17)0.0032 (15)
C80.099 (3)0.0528 (18)0.0680 (19)−0.010 (2)0.0271 (18)−0.0052 (14)
C90.069 (2)0.075 (2)0.0628 (19)−0.0212 (18)0.0157 (16)−0.0071 (15)
C100.058 (2)0.0631 (19)0.0537 (16)0.0000 (16)0.0094 (14)0.0011 (13)
C110.066 (2)0.0688 (17)0.0466 (16)−0.0071 (14)0.0057 (15)−0.0015 (13)
C120.059 (2)0.0531 (15)0.0438 (17)−0.0041 (14)0.0073 (15)−0.0037 (12)
C130.073 (3)0.0735 (19)0.0478 (18)−0.0067 (17)0.0042 (17)−0.0040 (13)
C140.072 (2)0.0720 (19)0.080 (2)−0.0004 (16)0.014 (2)−0.0170 (17)
C150.106 (3)0.081 (2)0.065 (2)−0.024 (2)0.035 (2)−0.0200 (17)
C160.103 (3)0.090 (2)0.0460 (19)−0.008 (2)0.007 (2)0.0081 (15)
C170.077 (2)0.0652 (18)0.0518 (18)−0.0026 (15)0.0084 (17)0.0077 (14)
C180.072 (2)0.0606 (16)0.0574 (18)0.0007 (14)0.0125 (16)−0.0042 (13)
C190.071 (2)0.0518 (15)0.0434 (17)−0.0032 (15)0.0146 (16)−0.0002 (13)
C200.080 (3)0.0595 (17)0.065 (2)0.0001 (17)0.0114 (17)0.0063 (14)
C210.090 (3)0.076 (2)0.083 (2)−0.0110 (18)−0.009 (2)0.0248 (18)
C220.131 (4)0.101 (3)0.060 (2)−0.036 (3)0.003 (3)0.0060 (19)
C230.128 (4)0.102 (3)0.065 (3)−0.021 (2)0.033 (2)−0.0185 (19)
C240.089 (3)0.0736 (19)0.0603 (19)−0.0089 (16)0.0198 (18)−0.0079 (15)
Geometric parameters (Å, °) top
N1—C11.464 (2)C11—H11A0.9700
N1—C111.470 (2)C11—H11B0.9700
N1—C41.472 (3)C12—C171.373 (3)
N2—C181.462 (3)C12—C131.380 (3)
N2—C31.462 (2)C13—C141.371 (3)
N2—C41.469 (2)C13—H130.9300
C1—C21.503 (3)C14—C151.380 (3)
C1—H1A0.9700C14—H140.9300
C1—H1B0.9700C15—C161.359 (4)
C2—C31.501 (3)C15—H150.9300
C2—H2A0.9700C16—C171.379 (4)
C2—H2B0.9700C16—H160.9300
C3—H3A0.9700C17—H170.9300
C3—H3B0.9700C18—C191.504 (3)
C4—C51.517 (3)C18—H18A0.9700
C4—H40.9800C18—H18B0.9700
C5—C61.375 (3)C19—C241.375 (3)
C5—C101.383 (3)C19—C201.383 (3)
C6—C71.378 (3)C20—C211.388 (3)
C6—H60.9300C20—H200.9300
C7—C81.370 (3)C21—C221.369 (4)
C7—H70.9300C21—H210.9300
C8—C91.366 (3)C22—C231.364 (4)
C8—H80.9300C22—H220.9300
C9—C101.381 (3)C23—C241.388 (3)
C9—H90.9300C23—H230.9300
C10—H100.9300C24—H240.9300
C11—C121.492 (3)
C1—N1—C11108.85 (17)N1—C11—C12114.5 (2)
C1—N1—C4111.60 (18)N1—C11—H11A108.6
C11—N1—C4110.00 (19)C12—C11—H11A108.6
C18—N2—C3108.68 (18)N1—C11—H11B108.6
C18—N2—C4110.6 (2)C12—C11—H11B108.6
C3—N2—C4112.45 (17)H11A—C11—H11B107.6
N1—C1—C2110.40 (18)C17—C12—C13117.7 (3)
N1—C1—H1A109.6C17—C12—C11120.9 (3)
C2—C1—H1A109.6C13—C12—C11121.3 (2)
N1—C1—H1B109.6C14—C13—C12121.6 (3)
C2—C1—H1B109.6C14—C13—H13119.2
H1A—C1—H1B108.1C12—C13—H13119.2
C3—C2—C1108.8 (2)C13—C14—C15119.8 (3)
C3—C2—H2A109.9C13—C14—H14120.1
C1—C2—H2A109.9C15—C14—H14120.1
C3—C2—H2B109.9C16—C15—C14119.2 (3)
C1—C2—H2B109.9C16—C15—H15120.4
H2A—C2—H2B108.3C14—C15—H15120.4
N2—C3—C2110.77 (19)C15—C16—C17120.7 (3)
N2—C3—H3A109.5C15—C16—H16119.7
C2—C3—H3A109.5C17—C16—H16119.7
N2—C3—H3B109.5C12—C17—C16121.0 (3)
C2—C3—H3B109.5C12—C17—H17119.5
H3A—C3—H3B108.1C16—C17—H17119.5
N2—C4—N1110.4 (2)N2—C18—C19114.1 (2)
N2—C4—C5109.58 (17)N2—C18—H18A108.7
N1—C4—C5108.50 (18)C19—C18—H18A108.7
N2—C4—H4109.4N2—C18—H18B108.7
N1—C4—H4109.4C19—C18—H18B108.7
C5—C4—H4109.4H18A—C18—H18B107.6
C6—C5—C10118.2 (2)C24—C19—C20118.6 (3)
C6—C5—C4119.8 (2)C24—C19—C18120.1 (3)
C10—C5—C4121.9 (2)C20—C19—C18121.2 (2)
C5—C6—C7121.3 (2)C19—C20—C21120.4 (3)
C5—C6—H6119.4C19—C20—H20119.8
C7—C6—H6119.4C21—C20—H20119.8
C8—C7—C6119.8 (3)C22—C21—C20119.9 (3)
C8—C7—H7120.1C22—C21—H21120.0
C6—C7—H7120.1C20—C21—H21120.0
C9—C8—C7119.9 (3)C23—C22—C21120.4 (3)
C9—C8—H8120.1C23—C22—H22119.8
C7—C8—H8120.1C21—C22—H22119.8
C8—C9—C10120.3 (3)C22—C23—C24119.7 (3)
C8—C9—H9119.9C22—C23—H23120.2
C10—C9—H9119.9C24—C23—H23120.2
C9—C10—C5120.5 (2)C19—C24—C23121.0 (3)
C9—C10—H10119.7C19—C24—H24119.5
C5—C10—H10119.7C23—C24—H24119.5
C11—N1—C1—C2179.9 (2)C4—C5—C10—C9174.78 (19)
C4—N1—C1—C258.3 (3)C1—N1—C11—C1263.4 (3)
N1—C1—C2—C3−57.8 (3)C4—N1—C11—C12−173.99 (19)
C18—N2—C3—C2−179.1 (2)N1—C11—C12—C17−137.0 (2)
C4—N2—C3—C2−56.4 (3)N1—C11—C12—C1346.5 (3)
C1—C2—C3—N256.7 (3)C17—C12—C13—C140.1 (4)
C18—N2—C4—N1176.79 (17)C11—C12—C13—C14176.7 (2)
C3—N2—C4—N155.1 (2)C12—C13—C14—C150.6 (4)
C18—N2—C4—C5−63.7 (2)C13—C14—C15—C16−1.1 (4)
C3—N2—C4—C5174.6 (2)C14—C15—C16—C170.9 (4)
C1—N1—C4—N2−56.0 (2)C13—C12—C17—C16−0.3 (3)
C11—N1—C4—N2−176.92 (16)C11—C12—C17—C16−176.9 (2)
C1—N1—C4—C5−176.11 (18)C15—C16—C17—C12−0.2 (4)
C11—N1—C4—C563.0 (2)C3—N2—C18—C19−72.8 (2)
N2—C4—C5—C6−56.2 (3)C4—N2—C18—C19163.38 (17)
N1—C4—C5—C664.5 (3)N2—C18—C19—C24150.9 (2)
N2—C4—C5—C10126.1 (2)N2—C18—C19—C20−33.2 (3)
N1—C4—C5—C10−113.3 (2)C24—C19—C20—C210.3 (4)
C10—C5—C6—C72.2 (3)C18—C19—C20—C21−175.6 (2)
C4—C5—C6—C7−175.6 (2)C19—C20—C21—C220.8 (4)
C5—C6—C7—C8−0.5 (4)C20—C21—C22—C23−1.3 (5)
C6—C7—C8—C9−0.6 (4)C21—C22—C23—C240.6 (5)
C7—C8—C9—C10−0.3 (4)C20—C19—C24—C23−1.0 (4)
C8—C9—C10—C52.1 (4)C18—C19—C24—C23174.9 (2)
C6—C5—C10—C9−3.0 (3)C22—C23—C24—C190.6 (4)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
C14—H14···Cg1i0.932.853.55 (3)132
C8—H8···Cg1ii0.933.073.79 (3)136
C21—H21···Cg2iii0.933.003.63 (4)126
Symmetry codes: (i) x+1/2, −y+3/2, z−1/2; (ii) −x+3/2, y−1/2, −z+1/2; (iii) x+1/2, −y+3/2, z+1/2.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
C14—H14···Cg1i0.932.853.55 (3)132
C8—H8···Cg1ii0.933.073.79 (3)136
C21—H21···Cg2iii0.933.003.63 (4)126
Symmetry codes: (i) x+1/2, −y+3/2, z−1/2; (ii) −x+3/2, y−1/2, −z+1/2; (iii) x+1/2, −y+3/2, z+1/2.
Acknowledgements top

The authors acknowledge financial support from the Huaihai Institute of Technology Science Foundation.

references
References top

Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.

Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.

Sheldrick, G. M. (1997a). SHELXL97 and SHELXS97. University of Göttingen, Germany.

Sheldrick, G. M. (1997b). SHELXTL. Version 5.10. Bruker AXS Inc., Madison, Wisconsin, USA.

Siemens (1996). SMART and SAINT. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.

Xia, H.-T., Liu, Y.-F., Wang, D.-Q. & Li, B. (2007). Acta Cryst. E63 [WN2158]. Submitted.