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ISSN: 2056-9890

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

aChemistry Department, Shahid Bahonar University, Kerman, Iran, and bSchool of Chemistry, University College of Science, University of Tehran, Tehran, Iran
*Correspondence e-mail: aabbasi@khayam.ut.ac.ir

(Received 18 November 2008; accepted 19 November 2008; online 26 November 2008)

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[Farrell, J. R., Niconchuk, J., Higham, C. S. & Bergeron, B. W. (2007). Tetrahedron Lett. 48, 8034-8036.]).

[Scheme 1]

Experimental

Crystal data
  • C18H22N4O

  • Mr = 310.40

  • Orthorhombic, P b c a

  • 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[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.970, Tmax = 0.987

  • 14483 measured reflections

  • 3134 independent reflections

  • 1574 reflections with I > 2σ(I)

  • Rint = 0.078

Refinement
  • R[F2 > 2σ(F2)] = 0.050

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O1—H1A⋯N3 1.01 (2) 1.65 (2) 2.584 (2) 152 (2)
N3—H3A⋯N4i 0.92 (2) 2.30 (2) 3.159 (3) 155 (2)
N4—H4A⋯O1ii 0.93 (2) 2.18 (2) 3.106 (3) 172 (2)
Symmetry codes: (i) [x-{\script{1\over 2}}, y, -z+{\script{1\over 2}}]; (ii) [-x+{\script{3\over 2}}, y-{\script{1\over 2}}, z].

Data collection: SMART (Bruker, 1998[Bruker (1998). SAINT-Plus and SMART. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT-Plus (Bruker, 1998[Bruker (1998). SAINT-Plus and SMART. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: DIAMOND (Brandenburg, 2001[Brandenburg, K. (2001). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: PLATON (Spek, 2003[Spek, A. L. (2003). J. Appl. Cryst. 36, 7-13.]).

Supporting information


Comment top

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.

Related literature top

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

Experimental top

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 top

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).

Computing details top

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

Figures top
[Figure 1] Fig. 1. Molecular structure of (I), with 50% probability displacement ellipsoids. H atoms are shown as circles of arbitrary radii.
(E)-2-(5,5-Dimethylhexahydropyrimidin-2-yl)-4-(phenyldiazenyl)phenol top
Crystal data top
C18H22N4OF(000) = 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 = 3–60°
b = 12.0767 (12) ŵ = 0.08 mm1
c = 30.866 (3) ÅT = 120 K
V = 3365.5 (6) Å3Prism, colorless
Z = 80.23 × 0.20 × 0.16 mm
Data collection top
Bruker SMART 1000 CCD area-detector
diffractometer
3134 independent reflections
Radiation source: fine-focus sealed tube1574 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.078
ϕ and ω scansθmax = 25.5°, θmin = 2.6°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 1010
Tmin = 0.970, Tmax = 0.987k = 1414
14483 measured reflectionsl = 3237
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)] = 0.050Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.114H atoms treated by a mixture of independent and constrained refinement
S = 0.81 w = 1/[σ2(Fo2) + (0.049P)2]
where P = (Fo2 + 2Fc2)/3
3134 reflections(Δ/σ)max < 0.001
234 parametersΔρmax = 0.22 e Å3
0 restraintsΔρmin = 0.22 e Å3
Crystal data top
C18H22N4OV = 3365.5 (6) Å3
Mr = 310.40Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 9.0287 (9) ŵ = 0.08 mm1
b = 12.0767 (12) ÅT = 120 K
c = 30.866 (3) Å0.23 × 0.20 × 0.16 mm
Data collection top
Bruker SMART 1000 CCD area-detector
diffractometer
3134 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
1574 reflections with I > 2σ(I)
Tmin = 0.970, Tmax = 0.987Rint = 0.078
14483 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0500 restraints
wR(F2) = 0.114H atoms treated by a mixture of independent and constrained refinement
S = 0.81Δρmax = 0.22 e Å3
3134 reflectionsΔρmin = 0.22 e Å3
234 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
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)
H100.95810.10170.32590.031*
C111.0190 (3)0.2133 (2)0.44232 (7)0.0295 (6)
C121.0096 (3)0.1697 (2)0.48356 (7)0.0423 (7)
H120.97180.09890.48780.051*
C131.0566 (3)0.2317 (3)0.51851 (8)0.0508 (8)
H131.05030.20240.54630.061*
C141.1127 (3)0.3367 (3)0.51259 (8)0.0501 (8)
H141.14450.37780.53630.060*
C151.1217 (3)0.3807 (3)0.47163 (8)0.0481 (8)
H151.15870.45180.46760.058*
C161.0754 (3)0.3187 (2)0.43638 (8)0.0404 (7)
H161.08220.34810.40860.049*
C170.7683 (3)0.22207 (19)0.17308 (7)0.0326 (6)
H17A0.72660.21950.20170.049*
H17B0.81860.29130.16900.049*
H17C0.69050.21520.15200.049*
C180.9416 (3)0.1313 (2)0.12165 (7)0.0371 (7)
H18A0.86270.12580.10090.056*
H18B0.99360.19980.11750.056*
H18C1.00890.07050.11770.056*
Atomic displacement parameters (Å2) top
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, º) top
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—C80.4 (3)
C3—N4—C1—C5178.90 (19)C6—C7—C8—C91.2 (4)
C2—N3—C1—N455.2 (3)C7—C8—C9—C102.1 (3)
C2—N3—C1—C5176.64 (19)C7—C8—C9—N2178.7 (2)
C1—N3—C2—C455.4 (3)N1—N2—C9—C8173.0 (2)
C1—N4—C3—C450.2 (3)N1—N2—C9—C107.9 (3)
N3—C2—C4—C1769.7 (2)C6—C5—C10—C90.1 (3)
N3—C2—C4—C18170.09 (19)C1—C5—C10—C9177.5 (2)
N3—C2—C4—C352.4 (3)C8—C9—C10—C51.4 (3)
N4—C3—C4—C1771.9 (3)N2—C9—C10—C5179.4 (2)
N4—C3—C4—C250.1 (3)N2—N1—C11—C127.3 (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—C6172.34 (19)C11—C12—C13—C140.0 (4)
N3—C1—C5—C642.7 (3)C12—C13—C14—C150.3 (4)
C10—C5—C6—O1178.9 (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—C15179.0 (2)
C1—C5—C6—C7176.7 (2)C14—C15—C16—C110.6 (4)
Hydrogen-bond geometry (Å, º) top
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) x1/2, y, z+1/2; (ii) x+3/2, y1/2, z.

Experimental details

Crystal data
Chemical formulaC18H22N4O
Mr310.40
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)120
a, b, c (Å)9.0287 (9), 12.0767 (12), 30.866 (3)
V3)3365.5 (6)
Z8
Radiation typeMo Kα
µ (mm1)0.08
Crystal size (mm)0.23 × 0.20 × 0.16
Data collection
DiffractometerBruker SMART 1000 CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.970, 0.987
No. of measured, independent and
observed [I > 2σ(I)] reflections
14483, 3134, 1574
Rint0.078
(sin θ/λ)max1)0.606
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.050, 0.114, 0.81
No. of reflections3134
No. of parameters234
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.22, 0.22

Computer programs: SMART (Bruker, 1998), SAINT-Plus (Bruker, 1998), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2001), PLATON (Spek, 2003).

Hydrogen-bond geometry (Å, º) top
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) x1/2, y, z+1/2; (ii) x+3/2, y1/2, z.
 

Acknowledgements

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

References

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