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Acta Crystallogr Sect E Struct Rep Online. 2009 June 1; 65(Pt 6): o1255.
Published online 2009 May 14. doi:  10.1107/S1600536809016730
PMCID: PMC2969618

N,N′-Bis­[(E)-(6-methyl-2-pyridyl)­methyl­ene]hexane-1,6-diamine

Abstract

The title compound, C20H26N4, is composed of two (6-methyl-2-pyridyl)methyl­ene units linked by a 1,6-diamine hexane chain. The mol­ecule has Ci symmetry with the inversion center situated at the mid-point of the central C—C bond. The alkyl chain has an all-trans conformation, with all the non-H atoms sharing the same plane [maximum deviation 0.004 (3) Å]. The pyridylmethyl­ene groups are also planar [maximum deviation 0.009 (3) Å], making an angle of 53.78 (19)° with the hexane chain plane. In the crystal, the mol­ecules assemble in layers, stacking along the a axis. The stacks are hold together by attractive interactions between π electron systems.

Related literature

For salen ligands, their structures and possible applications, see: Cozzi (2004 [triangle]); Li et al. (2007 [triangle]); Renehan et al. (2005 [triangle]); Mohamed et al. (2006 [triangle]). For ruthenium–salen complexes, see: Wu & Gorden (2007 [triangle]). For the use of salen ligands to form metal-organic frameworks, see: Bu et al. (2001 [triangle]); van den Berga & Arean (2008 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1255-scheme1.jpg

Experimental

Crystal data

  • C20H26N4
  • M r = 322.45
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1255-efi1.jpg
  • a = 7.2713 (10) Å
  • b = 12.6671 (18) Å
  • c = 20.458 (3) Å
  • V = 1884.3 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.07 mm−1
  • T = 293 K
  • 0.17 × 0.12 × 0.09 mm

Data collection

  • Bruker SMART APEX CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 2000 [triangle]) T min = 0.891, T max = 0.991
  • 7591 measured reflections
  • 2308 independent reflections
  • 742 reflections with I > 2σ(I)
  • R int = 0.066

Refinement

  • R[F 2 > 2σ(F 2)] = 0.056
  • wR(F 2) = 0.184
  • S = 0.88
  • 2308 reflections
  • 111 parameters
  • H-atom parameters constrained
  • Δρmax = 0.12 e Å−3
  • Δρmin = −0.15 e Å−3

Data collection: SMART (Bruker, 2003 [triangle]); cell refinement: SAINT (Bruker, 2003 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEPII (Johnson, 1976 [triangle]); software used to prepare material for publication: SHELXL97.

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809016730/su2109sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809016730/su2109Isup2.hkl

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

Acknowledgments

This work was supported by Fundação para a Ciência e a Tecnologia (FCT).

supplementary crystallographic information

Comment

Schiff bases and their complexes (salen ligands) continue to raise interest, even after a hundred years of research, due to their novel structures, their application in reversible binding of oxygen, their catalytic activity in hydrogenation of olefins, intermolecular transfer of amino groups, and their complexing ability towards some toxic metals (Cozzi, 2004; Li et al., 2007; Renehan et al.; 2005, Mohamed et al., 2006). Two important examples are, copper(I)-salen complexes investigated as antitumor agents, and ruthenium-salen complexes studied as protein kinase inhibitors by mimicking the structure of organic indolocarbazoles (Wu & Gorden, 2007). Salen complexes have also been used to form metal-organic frameworks (MOFs), which are intensively sought for the storage of hydrogen and carbon dioxide (Berga & Arean, 2008).

The title compound was synthesized to be used as a ligand/spacer in the construction of MOFs. For such purposes long-chain bidentate ligands may be useful to alter the cavity size, as reported by Bu et al., who showed that in some Cu(II) coordination compounds, the cavity size depends on the chain length of bis-sulfinyl ligands used.

The title compound is illustrated in Fig. 1, and the geometrical parameters are available in the archived CIF. It crystallizes with half a molecule in the asymmetric unit. The center of inversion is located at the middle point of the alkyl chain (C10-C10a). The hexane chain adopts an all-trans conformation. The mean plane of the pyridylmethylene group makes an angle of 53.78 (19)° with the central chain plane. The short C7–N2 bond length of 1.257 (3) Å, shows the double bond character of this bond.

In the crystal structure the molecules assemble in layers stacked along the a axis, as shown in Fig. 2.

Experimental

5.5 mmol of 1,6-diamine was added to 11 mmol of 6-methyl-pyridil-2-aldehyde in toluene (50 ml). The mixture was stirred at 160°C with reflux in a Dean-Stark system until all the water was removed (~2 h). The solution was washed with diluted HCl (30 ml) and NaHCO3 (15 ml) and dried with NaSO4 anhydrous (5 g). Solvent was evaporated in a stirring water bath at 40°C under nitrogen. The product was recrystallized from CH2Cl2 to give the title compound in 40% yield.

Refinement

The crystals of the title compound diffracted very poorly, displaying broad weak reflections, hence the ratio of observed/unique reflections is only 32%. H-atoms were positioned geometrically [C-H = 0.93 - 0.97 Å] and refined using a riding model [Uiso(H) = 1.2 or 1.5Ueq(parent C-atom)].

Figures

Fig. 1.
ORTEPII (Johnson, 1976) plot of the title compound. Displacement ellipsoids are drawn at the 50% probability level.
Fig. 2.
Crystal packing of the title compound viewed along the c axis.

Crystal data

C20H26N4F(000) = 696
Mr = 322.45Dx = 1.137 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 546 reflections
a = 7.2713 (10) Åθ = 3.2–20.3°
b = 12.6671 (18) ŵ = 0.07 mm1
c = 20.458 (3) ÅT = 293 K
V = 1884.3 (5) Å3Prism, yellow
Z = 40.17 × 0.12 × 0.09 mm

Data collection

Bruker APEX CCD area-detector diffractometer2308 independent reflections
Radiation source: fine-focus sealed tube742 reflections with I > 2σ(I)
graphiteRint = 0.066
[var phi] and ω scansθmax = 28.3°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Sheldrick, 2000)h = −9→8
Tmin = 0.891, Tmax = 0.991k = −16→12
7591 measured reflectionsl = −22→25

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.056Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.184H-atom parameters constrained
S = 0.88w = 1/[σ2(Fo2) + (0.0774P)2] where P = (Fo2 + 2Fc2)/3
2308 reflections(Δ/σ)max < 0.001
111 parametersΔρmax = 0.12 e Å3
0 restraintsΔρmin = −0.14 e Å3

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
N20.1193 (3)0.29540 (19)0.10261 (10)0.0731 (7)
C10.0485 (4)0.4665 (2)0.14588 (13)0.0633 (8)
N1−0.0101 (3)0.56245 (18)0.12827 (10)0.0667 (7)
C5−0.0300 (4)0.6357 (2)0.17502 (13)0.0683 (8)
C100.0506 (4)0.05151 (18)−0.00364 (12)0.0711 (8)
H10A0.00340.0880−0.04180.085*
H10B0.17960.0366−0.01150.085*
C90.0355 (4)0.1241 (2)0.05473 (12)0.0719 (8)
H9A−0.09320.14000.06240.086*
H9B0.08200.08770.09300.086*
C20.0901 (4)0.4398 (2)0.20945 (14)0.0792 (9)
H20.13120.37240.21990.095*
C70.0688 (4)0.3890 (2)0.09307 (13)0.0674 (8)
H70.04300.41020.05050.081*
C80.1391 (4)0.2259 (2)0.04644 (12)0.0760 (9)
H8A0.26840.21040.03990.091*
H8B0.09450.26190.00770.091*
C6−0.0943 (5)0.7425 (2)0.15397 (13)0.0892 (10)
H6A0.00120.79330.16160.134*
H6B−0.20180.76170.17850.134*
H6C−0.12380.74110.10820.134*
C40.0072 (4)0.6140 (2)0.23978 (14)0.0762 (9)
H4−0.00950.66580.27150.091*
C30.0690 (4)0.5156 (3)0.25715 (14)0.0852 (10)
H30.09630.50020.30050.102*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N20.0935 (18)0.0568 (16)0.0689 (14)−0.0005 (13)−0.0027 (13)−0.0059 (12)
C10.071 (2)0.061 (2)0.0577 (16)−0.0117 (15)0.0005 (15)−0.0023 (14)
N10.0852 (17)0.0543 (15)0.0605 (13)−0.0067 (13)0.0013 (12)−0.0032 (12)
C50.080 (2)0.064 (2)0.0614 (17)−0.0082 (16)−0.0006 (16)−0.0020 (15)
C100.091 (2)0.0550 (18)0.0675 (16)0.0042 (15)0.0070 (17)0.0000 (14)
C90.091 (2)0.0575 (18)0.0677 (17)0.0042 (17)0.0051 (16)−0.0029 (14)
C20.101 (3)0.067 (2)0.0701 (19)−0.0010 (18)−0.0052 (18)−0.0026 (17)
C70.081 (2)0.061 (2)0.0605 (16)−0.0091 (16)−0.0001 (15)−0.0005 (15)
C80.097 (2)0.065 (2)0.0654 (17)0.0011 (17)0.0064 (16)−0.0070 (15)
C60.130 (3)0.061 (2)0.0771 (18)0.0014 (19)0.000 (2)−0.0048 (16)
C40.095 (2)0.068 (2)0.0651 (19)−0.0068 (19)−0.0056 (16)−0.0116 (15)
C30.114 (3)0.081 (2)0.0602 (17)−0.004 (2)−0.0119 (18)0.0020 (18)

Geometric parameters (Å, °)

N2—C71.257 (3)C9—H9A0.9700
N2—C81.455 (3)C9—H9B0.9700
C1—N11.338 (3)C2—C31.377 (4)
C1—C21.377 (4)C2—H20.9300
C1—C71.467 (4)C7—H70.9300
N1—C51.340 (3)C8—H8A0.9700
C5—C41.380 (4)C8—H8B0.9700
C5—C61.495 (4)C6—H6A0.9600
C10—C10i1.506 (5)C6—H6B0.9600
C10—C91.511 (3)C6—H6C0.9600
C10—H10A0.9700C4—C31.373 (4)
C10—H10B0.9700C4—H40.9300
C9—C81.503 (3)C3—H30.9300
C7—N2—C8118.5 (2)C1—C2—H2120.9
N1—C1—C2123.2 (3)N2—C7—C1123.1 (3)
N1—C1—C7116.2 (2)N2—C7—H7118.5
C2—C1—C7120.6 (3)C1—C7—H7118.5
C1—N1—C5118.1 (2)N2—C8—C9112.4 (2)
N1—C5—C4121.7 (3)N2—C8—H8A109.1
N1—C5—C6117.1 (2)C9—C8—H8A109.1
C4—C5—C6121.2 (3)N2—C8—H8B109.1
C10i—C10—C9114.4 (3)C9—C8—H8B109.1
C10i—C10—H10A108.7H8A—C8—H8B107.9
C9—C10—H10A108.7C5—C6—H6A109.5
C10i—C10—H10B108.7C5—C6—H6B109.5
C9—C10—H10B108.7H6A—C6—H6B109.5
H10A—C10—H10B107.6C5—C6—H6C109.5
C8—C9—C10113.3 (2)H6A—C6—H6C109.5
C8—C9—H9A108.9H6B—C6—H6C109.5
C10—C9—H9A108.9C3—C4—C5119.6 (3)
C8—C9—H9B108.9C3—C4—H4120.2
C10—C9—H9B108.9C5—C4—H4120.2
H9A—C9—H9B107.7C4—C3—C2119.1 (3)
C3—C2—C1118.3 (3)C4—C3—H3120.5
C3—C2—H2120.9C2—C3—H3120.5
C2—C1—N1—C5−0.4 (4)N1—C1—C7—N2−178.7 (3)
C7—C1—N1—C5−179.8 (2)C2—C1—C7—N21.9 (4)
C1—N1—C5—C4−0.3 (4)C7—N2—C8—C9−127.9 (3)
C1—N1—C5—C6179.6 (3)C10—C9—C8—N2178.8 (2)
C10i—C10—C9—C8179.5 (3)N1—C5—C4—C31.0 (4)
N1—C1—C2—C30.4 (5)C6—C5—C4—C3−178.9 (3)
C7—C1—C2—C3179.9 (3)C5—C4—C3—C2−0.9 (5)
C8—N2—C7—C1−178.5 (2)C1—C2—C3—C40.3 (5)

Symmetry codes: (i) −x, −y, −z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: SU2109).

References

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