organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2414-3146

N,N′-Bis(pyridin-2-yl)octa­nedi­amide

aFaculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland, and bFaculty of Chemical Technology and Engineering, University of Technology and Life Sciences, Seminaryjna 3, 85-326 Bydgoszcz, Poland
*Correspondence e-mail: bartosz.zarychta@uni.opole.pl

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 2 August 2016; accepted 13 August 2016; online 26 August 2016)

The complete mol­ecule of the title compound, C18H22N4O2, is generated by crystallographic inversion symmetry. In the crystal, N—H⋯N hydrogen bonds connect the mol­ecules into [010] chains, which feature R22(8) loops. The packing is consolidated by C—H⋯O inter­actions.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

In the last decade, bidentate, flexible ligands have gained considerable inter­est from the metal–organic framework (MOF) and crystal engineering communities owing to their use as building blocks for coordination polymers (Hennigar et al., 1997[Hennigar, T., MacQuarrie, D. C., Losier, P., Rogers, R. D. & Zaworotko, M. J. (1997). Angew. Chem. Int. Ed. Engl. 36, 972-973.]; Awaleh et al., 2005[Awaleh, M. O., Badia, A. & Brisse, F. (2005). Cryst. Growth Des. 5, 1897-1906.]; Chen et al., 2007[Chen, H.-C., Hu, H.-L., Chan, Z.-K., Yeh, C.-W., Jia, H.-W., Wu, C.-P., Chen, J.-D. & Wang, J.-C. (2007). Cryst. Growth Des. 7, 698-704.]; Cheng et al. 2009[Cheng, P.-C., Wu, C.-J., Chen, H.-C., Chen, J.-D. & Wang, J.-C. (2009). Acta Cryst. E65, o1825.]). For those ligands, the longer the backbone chain is, the less predictable the resulting network, resulting in a number of structural types. Herein we report the structure of N,N′-bis­(pyridin-2-yl)octa­nedi­amide, as a candidate to expand studies on self-assembly of MOFs (Ośmiałowski et al., 2010[Ośmiałowski, B., Kolehmainen, E., Dobosz, R., Gawinecki, R., Kauppinen, R., Valkonen, A., Koivukorpi, J. & Rissanen, K. (2010). J. Phys. Chem. A, 114, 10421-10426.], 2013[Ośmiałowski, B., Kolehmainen, E., Ejsmont, K., Ikonen, S., Valkonen, A., Rissanen, K. & Nonappa (2013). J. Mol. Struct. 1054-1055, 157-163.]).

There is one independent half-mol­ecule in the asymmetric unit (Fig. 1[link]), with an inversion centre at the mid-point of the C—C bond of the backbone chain. The mol­ecule is almost planar with C(N)—C(N)—C—C torsion angles in the range 174.3 (1) to 180.0 (1)°. The atoms in the backbone chain are arranged in an anti­periplanar conformation. The oxygen atom deviate most from the planarity of the mol­ecule. Nevertheless the distance between the plane defined by C1/N2/C6/C7/C8/C9 and the O1 atom is less than 0.10 Å. The pyridine ring is co-planar with the amide bond, and the C1—N2 bond length of 1.4000 (16) Å is notably shorter than its average literature value [1.465 (7) Å; Allen, et al. 2006[Allen, F. H., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (2006). International Tables for Crystallography, Vol. C, ch. 9.5, pp. 790-811.]]. This suggests partial conjugation between those two π-electron systems. An intra­molecular C2—H2⋯O1 hydrogen bond is observed.

[Figure 1]
Figure 1
The mol­ecular structure of the title compound, with displacement ellipsoids drawn at the 50% probability level. Only the asymmetric unit is labeled.

The crystal structure (Fig. 2[link]) features two symmetrically independent hydrogen bonds (Table 1[link]). The N2—H2A⋯N1(−x, −y + 1, −z + 2) hydrogen bond generates [010] chains incorporating inversion dimers. This is reinforced by the C4—H4⋯O1(−x + [{1\over 2}], y + [{1\over 2}], −z + [{3\over 2}]) inter­action, which generates (101) layers, connected to each other by weak ππ (pyridine ring) inter­actions and short H⋯H (backbone) contacts. The perpendicular separation of the mean planes through the rings is 3.287 Å while the H8B⋯H8B(−x, y, −z + [{3\over 2}]) distance is 2.290 Å (sum of van der Waals radii = 2.4 Å).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2A⋯N1i 0.86 2.45 3.3065 (15) 171
C2—H2⋯O1 0.93 2.28 2.8716 (15) 121
C4—H4⋯O1ii 0.93 2.42 3.1585 (15) 136
Symmetry codes: (i) -x, -y+1, -z+2; (ii) [-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{3\over 2}}].
[Figure 2]
Figure 2
The crystal packing of the title compound, viewed along the c axis showing the N2–H2A⋯N1 (−x, −y + 1, −z + 2) hydrogen bonds as dashed lines.

Synthesis and crystallization

Suberoyl chloride (1 equivalent) was added as a solution in di­chloro­methane (20 ml) to a magnetically stirred mixture of 2-amino­pyridine (2 equivalents) and tri­ethyl­amine in di­chloro­methane (50 ml). The reaction was stirred for 24 h at room temperature and the solvent evaporated under vacuum. The residual organic phase was treated with saturated Na2CO3 solution and extracted with chloro­form. The obtained extracts were dried with MgSO4 and evaporated to dryness and recrystallized from ethanol solution. Crystals suitable for XRD analysis were obtained by dissolving a small portion of the title compound in chloro­form and allowing the solvent to evaporate slowly.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula C18H22N4O2
Mr 326.39
Crystal system, space group Monoclinic, C2/c
Temperature (K) 100
a, b, c (Å) 11.9289 (7), 13.2908 (6), 11.5000 (6)
β (°) 111.497 (7)
V3) 1696.43 (17)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.09
Crystal size (mm) 0.25 × 0.23 × 0.18
 
Data collection
Diffractometer Oxford Diffraction Xcalibur
No. of measured, independent and observed [I > 2σ(I)] reflections 5224, 1494, 1125
Rint 0.024
(sin θ/λ)max−1) 0.594
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.073, 0.95
No. of reflections 1494
No. of parameters 110
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.24, −0.15
Computer programs: CrysAlis CCD and CrysAlis RED (Oxford Diffraction, 2008[Oxford Diffraction (2008). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, England.]), SHELXS2013 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) and SHELXL2013 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]).

Structural data


Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2008); cell refinement: CrysAlis RED (Oxford Diffraction, 2008); data reduction: CrysAlis RED (Oxford Diffraction, 2008); program(s) used to solve structure: SHELXS2013 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015); molecular graphics: SHELXL2013 (Sheldrick, 2015); software used to prepare material for publication: SHELXL2013 (Sheldrick, 2015).

N,N'-Bis(pyridin-2-yl)octanediamide top
Crystal data top
C18H22N4O2F(000) = 696
Mr = 326.39Dx = 1.278 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
a = 11.9289 (7) ÅCell parameters from 5224 reflections
b = 13.2908 (6) Åθ = 3.5–25.2°
c = 11.5000 (6) ŵ = 0.09 mm1
β = 111.497 (7)°T = 100 K
V = 1696.43 (17) Å3Irregular, colourless
Z = 40.25 × 0.23 × 0.18 mm
Data collection top
Oxford Diffraction Xcalibur
diffractometer
1125 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.024
Graphite monochromatorθmax = 25.0°, θmin = 3.5°
Detector resolution: 1024 x 1024 with blocks 2 x 2 pixels mm-1h = 1413
ω–scank = 1515
5224 measured reflectionsl = 1313
1494 independent reflections
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)] = 0.032H-atom parameters constrained
wR(F2) = 0.073 w = 1/[σ2(Fo2) + (0.0429P)2]
where P = (Fo2 + 2Fc2)/3
S = 0.95(Δ/σ)max < 0.001
1494 reflectionsΔρmax = 0.24 e Å3
110 parametersΔρmin = 0.15 e Å3
0 restraintsExtinction correction: SHELXL2013 (Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0012 (3)
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.15817 (8)0.27316 (7)0.84143 (8)0.0259 (3)
N10.10057 (9)0.57410 (8)0.92312 (10)0.0228 (3)
N20.08189 (9)0.40263 (7)0.92055 (10)0.0189 (3)
H2A0.03930.41490.96520.023*
C10.12421 (10)0.48726 (9)0.87675 (11)0.0177 (3)
C20.18323 (11)0.48219 (10)0.79260 (12)0.0213 (3)
H20.19750.42060.76210.026*
C30.21992 (11)0.57095 (10)0.75567 (13)0.0238 (3)
H30.25940.56990.69940.029*
C40.19788 (11)0.66159 (10)0.80261 (12)0.0235 (3)
H40.22250.72230.77950.028*
C50.13834 (11)0.65855 (9)0.88437 (13)0.0253 (3)
H50.12290.71950.91540.030*
C60.09926 (11)0.30281 (9)0.90189 (11)0.0184 (3)
C70.03884 (11)0.23330 (9)0.96366 (11)0.0196 (3)
H7A0.04640.24920.93330.023*
H7B0.07130.24621.05290.023*
C80.05278 (11)0.12258 (9)0.94244 (12)0.0203 (3)
H8A0.13780.10710.96680.024*
H8B0.01410.10800.85400.024*
C90.00115 (12)0.05536 (9)1.01516 (12)0.0196 (3)
H9A0.04300.06521.10380.023*
H9B0.08390.07560.99730.023*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0303 (5)0.0225 (5)0.0322 (6)0.0020 (4)0.0199 (5)0.0011 (4)
N10.0243 (6)0.0180 (6)0.0279 (7)0.0012 (5)0.0117 (5)0.0013 (5)
N20.0216 (6)0.0172 (6)0.0227 (6)0.0009 (5)0.0138 (5)0.0007 (5)
C10.0144 (6)0.0184 (7)0.0180 (7)0.0003 (5)0.0032 (5)0.0028 (5)
C20.0187 (7)0.0242 (7)0.0215 (7)0.0010 (6)0.0080 (6)0.0004 (6)
C30.0176 (7)0.0335 (8)0.0211 (7)0.0009 (6)0.0081 (6)0.0057 (6)
C40.0193 (7)0.0247 (8)0.0271 (8)0.0011 (6)0.0091 (6)0.0064 (6)
C50.0265 (8)0.0185 (8)0.0330 (8)0.0014 (6)0.0133 (6)0.0005 (6)
C60.0168 (6)0.0192 (7)0.0173 (7)0.0011 (5)0.0040 (6)0.0003 (5)
C70.0199 (7)0.0200 (7)0.0198 (7)0.0010 (5)0.0084 (6)0.0001 (5)
C80.0231 (7)0.0190 (7)0.0200 (7)0.0009 (5)0.0093 (6)0.0002 (5)
C90.0199 (7)0.0203 (7)0.0174 (7)0.0021 (5)0.0055 (6)0.0002 (5)
Geometric parameters (Å, º) top
O1—C61.2209 (14)C4—H40.9300
N1—C11.3440 (16)C5—H50.9300
N1—C51.3448 (16)C6—C71.5010 (17)
N2—C61.3717 (16)C7—C81.5108 (17)
N2—C11.4000 (16)C7—H7A0.9700
N2—H2A0.8600C7—H7B0.9700
C1—C21.3914 (18)C8—C91.5185 (18)
C2—C31.3783 (17)C8—H8A0.9700
C2—H20.9300C8—H8B0.9700
C3—C41.3840 (18)C9—C9i1.515 (2)
C3—H30.9300C9—H9A0.9700
C4—C51.3711 (19)C9—H9B0.9700
C1—N1—C5116.16 (11)O1—C6—C7123.17 (11)
C6—N2—C1128.73 (11)N2—C6—C7113.27 (10)
C6—N2—H2A115.6C6—C7—C8115.01 (10)
C1—N2—H2A115.6C6—C7—H7A108.5
N1—C1—C2123.42 (11)C8—C7—H7A108.5
N1—C1—N2113.04 (11)C6—C7—H7B108.5
C2—C1—N2123.53 (12)C8—C7—H7B108.5
C3—C2—C1118.14 (12)H7A—C7—H7B107.5
C3—C2—H2120.9C7—C8—C9112.96 (10)
C1—C2—H2120.9C7—C8—H8A109.0
C2—C3—C4119.85 (13)C9—C8—H8A109.0
C2—C3—H3120.1C7—C8—H8B109.0
C4—C3—H3120.1C9—C8—H8B109.0
C5—C4—C3117.52 (12)H8A—C8—H8B107.8
C5—C4—H4121.2C9i—C9—C8113.43 (13)
C3—C4—H4121.2C9i—C9—H9A108.9
N1—C5—C4124.92 (12)C8—C9—H9A108.9
N1—C5—H5117.5C9i—C9—H9B108.9
C4—C5—H5117.5C8—C9—H9B108.9
O1—C6—N2123.56 (12)H9A—C9—H9B107.7
Symmetry code: (i) x, y, z+2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2A···N1ii0.862.453.3065 (15)171
C2—H2···O10.932.282.8716 (15)121
C4—H4···O1iii0.932.423.1585 (15)136
Symmetry codes: (ii) x, y+1, z+2; (iii) x+1/2, y+1/2, z+3/2.
 

References

First citationAllen, F. H., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (2006). International Tables for Crystallography, Vol. C, ch. 9.5, pp. 790–811.  Google Scholar
First citationAwaleh, M. O., Badia, A. & Brisse, F. (2005). Cryst. Growth Des. 5, 1897–1906.  Web of Science CSD CrossRef CAS Google Scholar
First citationChen, H.-C., Hu, H.-L., Chan, Z.-K., Yeh, C.-W., Jia, H.-W., Wu, C.-P., Chen, J.-D. & Wang, J.-C. (2007). Cryst. Growth Des. 7, 698–704.  Web of Science CSD CrossRef CAS Google Scholar
First citationCheng, P.-C., Wu, C.-J., Chen, H.-C., Chen, J.-D. & Wang, J.-C. (2009). Acta Cryst. E65, o1825.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationHennigar, T., MacQuarrie, D. C., Losier, P., Rogers, R. D. & Zaworotko, M. J. (1997). Angew. Chem. Int. Ed. Engl. 36, 972–973.  Google Scholar
First citationOśmiałowski, B., Kolehmainen, E., Dobosz, R., Gawinecki, R., Kauppinen, R., Valkonen, A., Koivukorpi, J. & Rissanen, K. (2010). J. Phys. Chem. A, 114, 10421–10426.  PubMed Google Scholar
First citationOśmiałowski, B., Kolehmainen, E., Ejsmont, K., Ikonen, S., Valkonen, A., Rissanen, K. & Nonappa (2013). J. Mol. Struct. 1054–1055, 157–163.  Google Scholar
First citationOxford Diffraction (2008). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, England.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSheldrick, G. M. (2015). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar

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