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Acta Crystallogr Sect E Struct Rep Online. 2008 December 1; 64(Pt 12): o2453.
Published online 2008 November 26. doi:  10.1107/S1600536808038877
PMCID: PMC2959919

(E)-2-(5,5-Dimethyl­hexa­hydro­pyrimidin-2-yl)-4-(phenyl­diazen­yl)phenol

Abstract

In the title Schiff base, C18H22N4O, the hexa­hydro­pyrimidinyl ring adopts a chair conformation. The dihedral angle between the aromatic rings of the 4-(2-phenyl­diazen­yl)phenol unit is 15.7 (1)°. There is an intra­molecular O—H(...)N hydrogen bond between the hydroxyl group and an N atom of the hexa­hydro­pyimidinyl unit. Inter­molecular N—H(...)O and N—H(...)N hydrogen bonds give rise to a layer structure.

Related literature

For applications and related structures, see: Farrell et al. (2007 [triangle]).

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Object name is e-64-o2453-scheme1.jpg

Experimental

Crystal data

  • C18H22N4O
  • M r = 310.40
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-64-o2453-efi1.jpg
  • a = 9.0287 (9) Å
  • b = 12.0767 (12) Å
  • c = 30.866 (3) Å
  • V = 3365.5 (6) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 120 (2) K
  • 0.23 × 0.20 × 0.16 mm

Data collection

  • Bruker SMART 1000 CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.970, T max = 0.987
  • 14483 measured reflections
  • 3134 independent reflections
  • 1574 reflections with I > 2σ(I)
  • R int = 0.078

Refinement

  • R[F 2 > 2σ(F 2)] = 0.050
  • wR(F 2) = 0.114
  • S = 0.81
  • 3134 reflections
  • 234 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.22 e Å−3
  • Δρmin = −0.22 e Å−3

Data collection: SMART (Bruker, 1998 [triangle]); cell refinement: SAINT-Plus (Bruker, 1998 [triangle]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: DIAMOND (Brandenburg, 2001 [triangle]); software used to prepare material for publication: PLATON (Spek, 2003 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808038877/ng2518sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808038877/ng2518Isup2.hkl

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

Acknowledgments

This work was supported by a grant from the University of Kerman and the University of Tehran.

supplementary crystallographic information

Comment

Heterocycles containing nitrogen atoms e.g. hexahydropyrimidines have applications in both inorganic and organic chemistry. Hexahydropyrimidines can be easily prepared from condensations of alkyl diamines and aldehydes. Our interest in synthesizing derivatives of these heterocycles was due to their anti-carcinoma, anti-lymphoma, and anti-biotic properties.

The molecular structure of (I) and the atom-numbering scheme are shown in Fig. 1. Two aromatic rings A (C5—C10) and B (C11—C16) show a little deviation from planarity with a dihedral angle of 15.7 (1)o. Hexahydropyrimidine has a chair conformation. Intramolecular hydrogen bonds are formed between the phenol hydroxyl groups and the nearest N atom in the hexahydropyimidine groups [O—H···N = 2.584 (2) Å]. The packing of the structure is stabilized by relatively strong N—H···O & N—H···N hydrogen bonds (see Tab. 1), and C—H···π contacts [C—H-cetroid = 2.70 Å] between neighboring molecules. No significant π-π interactions are found in the crystal structure.

Experimental

The title compound was prepared via condensation of (E)-5-(2-phenyldiazenyl)-2-hydroxybenzaldehyde and 2,2-dimethylpropane-1,3-diamine in 20 ml EtOH:CHCl3. The mixture solution was stirred and refluxed for 3 h. Colorless prismatic-shape crystals were obtained after evaporation of the excess solvent.

Refinement

Aromatic and methyl H atoms were placed in calculated positions (C—H = 0.93 Å, C—H = 0.96 Å, respectively) and constrained to ride on their parent atoms, with Uiso(H) = 1.2 and 1.5 Ueq(C), respectively. Methylene, hydroxyl and amine H atoms were located in difference density maps and their coordinates were refined freely with Uiso(H) = 1.5 Ueq(C, O & N).

Figures

Fig. 1.
Molecular structure of (I), with 50% probability displacement ellipsoids. H atoms are shown as circles of arbitrary radii.

Crystal data

C18H22N4OF000 = 1328
Mr = 310.40Dx = 1.225 Mg m3
Orthorhombic, PbcaMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 14483 reflections
a = 9.0287 (9) Åθ = 3–60º
b = 12.0767 (12) ŵ = 0.08 mm1
c = 30.866 (3) ÅT = 120 (2) K
V = 3365.5 (6) Å3Prism, colorless
Z = 80.23 × 0.20 × 0.16 mm

Data collection

Bruker SMART 1000 CCD area-detector diffractometer3134 independent reflections
Radiation source: fine-focus sealed tube1574 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.078
T = 120(2) Kθmax = 25.5º
[var phi] and ω scansθmin = 2.6º
Absorption correction: multi-scan(SADABS; Sheldrick, 1996)h = −10→10
Tmin = 0.970, Tmax = 0.987k = −14→14
14483 measured reflectionsl = −32→37

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.050H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.114  w = 1/[σ2(Fo2) + (0.049P)2] where P = (Fo2 + 2Fc2)/3
S = 0.81(Δ/σ)max < 0.001
3134 reflectionsΔρmax = 0.22 e Å3
234 parametersΔρmin = −0.22 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

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 (Å2)

xyzUiso*/Ueq
O10.69820 (17)0.17061 (13)0.26940 (5)0.0314 (4)
H1A0.710 (3)0.121 (2)0.2433 (7)0.047*
N10.9722 (2)−0.15729 (17)0.40388 (6)0.0301 (5)
N20.9051 (2)−0.06703 (18)0.41075 (6)0.0312 (5)
N30.7588 (2)0.00338 (17)0.22029 (6)0.0259 (5)
H3A0.692 (3)−0.0499 (19)0.2283 (7)0.039*
N40.9679 (2)−0.11263 (17)0.24545 (6)0.0260 (5)
H4A0.911 (3)−0.1732 (19)0.2543 (7)0.039*
C10.8894 (3)−0.0082 (2)0.24903 (7)0.0237 (6)
H10.964 (2)0.0526 (18)0.2397 (6)0.036*
C20.8017 (3)−0.0160 (2)0.17456 (7)0.0261 (6)
H210.876 (3)0.0485 (19)0.1681 (7)0.039*
H220.707 (2)−0.0077 (18)0.1561 (7)0.039*
C31.0059 (3)−0.1371 (2)0.20003 (8)0.0277 (6)
H311.087 (2)−0.081 (2)0.1916 (7)0.042*
H321.048 (2)−0.212 (2)0.1986 (7)0.042*
C40.8774 (2)−0.1275 (2)0.16755 (7)0.0265 (6)
C50.8460 (2)0.0185 (2)0.29537 (7)0.0237 (6)
C60.7534 (2)0.11069 (19)0.30298 (7)0.0244 (6)
C70.7169 (3)0.1417 (2)0.34482 (7)0.0306 (6)
H70.65630.20280.34950.037*
C80.7703 (3)0.0821 (2)0.37939 (7)0.0302 (6)
H80.74710.10390.40750.036*
C90.8586 (2)−0.0104 (2)0.37271 (7)0.0267 (6)
C100.8971 (2)−0.0407 (2)0.33038 (7)0.0261 (6)
H100.9581−0.10170.32590.031*
C111.0190 (3)−0.2133 (2)0.44232 (7)0.0295 (6)
C121.0096 (3)−0.1697 (2)0.48356 (7)0.0423 (7)
H120.9718−0.09890.48780.051*
C131.0566 (3)−0.2317 (3)0.51851 (8)0.0508 (8)
H131.0503−0.20240.54630.061*
C141.1127 (3)−0.3367 (3)0.51259 (8)0.0501 (8)
H141.1445−0.37780.53630.060*
C151.1217 (3)−0.3807 (3)0.47163 (8)0.0481 (8)
H151.1587−0.45180.46760.058*
C161.0754 (3)−0.3187 (2)0.43638 (8)0.0404 (7)
H161.0822−0.34810.40860.049*
C170.7683 (3)−0.22207 (19)0.17308 (7)0.0326 (6)
H17A0.7266−0.21950.20170.049*
H17B0.8186−0.29130.16900.049*
H17C0.6905−0.21520.15200.049*
C180.9416 (3)−0.1313 (2)0.12165 (7)0.0371 (7)
H18A0.8627−0.12580.10090.056*
H18B0.9936−0.19980.11750.056*
H18C1.0089−0.07050.11770.056*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0319 (10)0.0309 (11)0.0312 (10)0.0044 (8)0.0002 (8)0.0017 (8)
N10.0269 (12)0.0339 (13)0.0294 (12)−0.0031 (11)−0.0025 (9)0.0034 (10)
N20.0262 (12)0.0355 (13)0.0320 (12)−0.0021 (11)−0.0005 (10)0.0029 (10)
N30.0220 (11)0.0308 (13)0.0249 (11)−0.0014 (10)−0.0025 (9)0.0016 (10)
N40.0241 (12)0.0288 (12)0.0250 (11)−0.0012 (10)0.0007 (9)0.0020 (10)
C10.0190 (13)0.0262 (14)0.0259 (13)0.0022 (12)−0.0040 (11)0.0008 (11)
C20.0242 (14)0.0292 (15)0.0250 (14)0.0024 (12)0.0000 (11)0.0011 (11)
C30.0239 (14)0.0315 (16)0.0277 (14)0.0011 (12)−0.0007 (11)−0.0021 (12)
C40.0236 (13)0.0310 (15)0.0250 (13)−0.0040 (12)−0.0002 (11)0.0021 (11)
C50.0173 (12)0.0276 (14)0.0260 (13)−0.0033 (11)−0.0014 (10)−0.0003 (11)
C60.0205 (13)0.0237 (14)0.0290 (13)−0.0048 (11)0.0002 (12)0.0031 (11)
C70.0286 (15)0.0290 (15)0.0342 (15)0.0004 (12)0.0018 (12)−0.0032 (12)
C80.0282 (15)0.0328 (15)0.0297 (14)−0.0045 (13)0.0040 (12)−0.0040 (11)
C90.0241 (14)0.0308 (15)0.0251 (13)−0.0072 (12)−0.0008 (11)0.0014 (11)
C100.0203 (13)0.0284 (15)0.0295 (14)−0.0005 (11)−0.0008 (11)−0.0008 (11)
C110.0282 (14)0.0354 (16)0.0250 (14)−0.0024 (13)−0.0027 (11)0.0050 (12)
C120.0562 (19)0.0416 (18)0.0292 (15)−0.0041 (15)−0.0075 (14)0.0021 (14)
C130.066 (2)0.058 (2)0.0279 (15)−0.0043 (18)−0.0083 (14)0.0001 (15)
C140.055 (2)0.063 (2)0.0325 (17)−0.0007 (17)−0.0086 (15)0.0163 (15)
C150.0481 (19)0.050 (2)0.0462 (18)0.0091 (16)−0.0025 (15)0.0125 (15)
C160.0401 (17)0.0511 (19)0.0300 (15)0.0032 (15)−0.0031 (13)0.0007 (13)
C170.0339 (15)0.0339 (16)0.0299 (13)0.0007 (13)−0.0056 (12)−0.0002 (11)
C180.0368 (16)0.0435 (17)0.0310 (14)0.0005 (14)0.0038 (12)−0.0007 (13)

Geometric parameters (Å, °)

O1—C61.358 (2)C7—C81.375 (3)
O1—H1A1.01 (2)C7—H70.9300
N1—N21.265 (3)C8—C91.387 (3)
N1—C111.429 (3)C8—H80.9300
N2—C91.422 (3)C9—C101.401 (3)
N3—C21.482 (3)C10—H100.9300
N3—C11.483 (3)C11—C121.380 (3)
N3—H3A0.92 (2)C11—C161.384 (3)
N4—C11.451 (3)C12—C131.380 (3)
N4—C31.473 (3)C12—H120.9300
N4—H4A0.93 (2)C13—C141.377 (4)
C1—C51.518 (3)C13—H130.9300
C1—H11.04 (2)C14—C151.374 (3)
C2—C41.525 (3)C14—H140.9300
C2—H211.05 (2)C15—C161.385 (3)
C2—H221.03 (2)C15—H150.9300
C3—C41.537 (3)C16—H160.9300
C3—H311.03 (2)C17—H17A0.9600
C3—H320.98 (2)C17—H17B0.9600
C4—C171.518 (3)C17—H17C0.9600
C4—C181.531 (3)C18—H18A0.9600
C5—C101.375 (3)C18—H18B0.9600
C5—C61.412 (3)C18—H18C0.9600
C6—C71.385 (3)
C6—O1—H1A104.5 (13)C6—C7—H7120.1
N2—N1—C11114.21 (19)C7—C8—C9120.5 (2)
N1—N2—C9114.67 (19)C7—C8—H8119.7
C2—N3—C1110.27 (18)C9—C8—H8119.7
C2—N3—H3A108.7 (14)C8—C9—C10119.4 (2)
C1—N3—H3A107.3 (14)C8—C9—N2115.7 (2)
C1—N4—C3111.13 (19)C10—C9—N2124.8 (2)
C1—N4—H4A113.1 (14)C5—C10—C9120.9 (2)
C3—N4—H4A104.4 (14)C5—C10—H10119.5
N4—C1—N3115.15 (19)C9—C10—H10119.5
N4—C1—C5112.51 (19)C12—C11—C16119.7 (2)
N3—C1—C5109.76 (18)C12—C11—N1124.5 (2)
N4—C1—H1106.2 (12)C16—C11—N1115.7 (2)
N3—C1—H1106.5 (12)C11—C12—C13119.6 (3)
C5—C1—H1106.1 (11)C11—C12—H12120.2
N3—C2—C4113.06 (19)C13—C12—H12120.2
N3—C2—H21103.4 (12)C14—C13—C12120.6 (2)
C4—C2—H21110.0 (13)C14—C13—H13119.7
N3—C2—H22107.0 (12)C12—C13—H13119.7
C4—C2—H22112.2 (13)C15—C14—C13120.0 (3)
H21—C2—H22110.8 (17)C15—C14—H14120.0
N4—C3—C4115.46 (19)C13—C14—H14120.0
N4—C3—H31105.8 (12)C14—C15—C16119.8 (3)
C4—C3—H31108.8 (12)C14—C15—H15120.1
N4—C3—H32108.5 (13)C16—C15—H15120.1
C4—C3—H32109.2 (13)C11—C16—C15120.3 (2)
H31—C3—H32108.9 (18)C11—C16—H16119.9
C17—C4—C2110.9 (2)C15—C16—H16119.9
C17—C4—C18109.10 (19)C4—C17—H17A109.5
C2—C4—C18109.10 (19)C4—C17—H17B109.5
C17—C4—C3111.07 (19)H17A—C17—H17B109.5
C2—C4—C3108.18 (19)C4—C17—H17C109.5
C18—C4—C3108.39 (19)H17A—C17—H17C109.5
C10—C5—C6118.6 (2)H17B—C17—H17C109.5
C10—C5—C1122.9 (2)C4—C18—H18A109.5
C6—C5—C1118.5 (2)C4—C18—H18B109.5
O1—C6—C7118.7 (2)H18A—C18—H18B109.5
O1—C6—C5120.7 (2)C4—C18—H18C109.5
C7—C6—C5120.6 (2)H18A—C18—H18C109.5
C8—C7—C6119.9 (2)H18B—C18—H18C109.5
C8—C7—H7120.1
C11—N1—N2—C9179.73 (19)O1—C6—C7—C8179.6 (2)
C3—N4—C1—N352.1 (3)C5—C6—C7—C8−0.4 (3)
C3—N4—C1—C5178.90 (19)C6—C7—C8—C9−1.2 (4)
C2—N3—C1—N4−55.2 (3)C7—C8—C9—C102.1 (3)
C2—N3—C1—C5176.64 (19)C7—C8—C9—N2−178.7 (2)
C1—N3—C2—C455.4 (3)N1—N2—C9—C8173.0 (2)
C1—N4—C3—C4−50.2 (3)N1—N2—C9—C10−7.9 (3)
N3—C2—C4—C1769.7 (2)C6—C5—C10—C9−0.1 (3)
N3—C2—C4—C18−170.09 (19)C1—C5—C10—C9177.5 (2)
N3—C2—C4—C3−52.4 (3)C8—C9—C10—C5−1.4 (3)
N4—C3—C4—C17−71.9 (3)N2—C9—C10—C5179.4 (2)
N4—C3—C4—C250.1 (3)N2—N1—C11—C12−7.3 (3)
N4—C3—C4—C18168.3 (2)N2—N1—C11—C16171.9 (2)
N4—C1—C5—C1010.1 (3)C16—C11—C12—C130.0 (4)
N3—C1—C5—C10139.7 (2)N1—C11—C12—C13179.2 (2)
N4—C1—C5—C6−172.34 (19)C11—C12—C13—C140.0 (4)
N3—C1—C5—C6−42.7 (3)C12—C13—C14—C15−0.3 (4)
C10—C5—C6—O1−178.9 (2)C13—C14—C15—C160.6 (4)
C1—C5—C6—O13.4 (3)C12—C11—C16—C150.3 (4)
C10—C5—C6—C71.0 (3)N1—C11—C16—C15−179.0 (2)
C1—C5—C6—C7−176.7 (2)C14—C15—C16—C11−0.6 (4)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1—H1A···N31.01 (2)1.65 (2)2.584 (2)152 (2)
N3—H3A···N4i0.92 (2)2.30 (2)3.159 (3)155 (2)
N4—H4A···O1ii0.93 (2)2.18 (2)3.106 (3)172 (2)

Symmetry codes: (i) x−1/2, y, −z+1/2; (ii) −x+3/2, y−1/2, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: NG2518).

References

  • Brandenburg, K. (2001). DIAMOND Crystal Impact GbR, Bonn, Germany.
  • Bruker (1998). SAINT-Plus and SMART Bruker AXS Inc., Madison, Wisconsin, USA.
  • Farrell, J. R., Niconchuk, J., Higham, C. S. & Bergeron, B. W. (2007). Tetrahedron Lett.48, 8034–8036.
  • Sheldrick, G. M. (1996). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2003). J. Appl. Cryst.36, 7–13.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography