organic compounds
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
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.
CCDC reference: 1499041
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; Awaleh et al., 2005; Chen et al., 2007; Cheng et al. 2009). 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, 2013).
There is one independent half-molecule in the ), 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]. This suggests partial conjugation between those two π-electron systems. An intramolecular C2—H2⋯O1 hydrogen bond is observed.
(Fig. 1The ) features two symmetrically independent hydrogen bonds (Table 1). 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 + , y + , −z + ) interaction, which generates (101) layers, connected to each other by weak π–π (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 + ) distance is 2.290 Å (sum of van der Waals radii = 2.4 Å).
(Fig. 2Synthesis 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 .
details are summarized in Table 2Structural data
CCDC reference: 1499041
10.1107/S2414314616013092/hb4070sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S2414314616013092/hb4070Isup2.hkl
Supporting information file. DOI: 10.1107/S2414314616013092/hb4070Isup3.cml
Data collection: CrysAlis CCD (Oxford Diffraction, 2008); cell
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).C18H22N4O2 | F(000) = 696 |
Mr = 326.39 | Dx = 1.278 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
a = 11.9289 (7) Å | Cell parameters from 5224 reflections |
b = 13.2908 (6) Å | θ = 3.5–25.2° |
c = 11.5000 (6) Å | µ = 0.09 mm−1 |
β = 111.497 (7)° | T = 100 K |
V = 1696.43 (17) Å3 | Irregular, colourless |
Z = 4 | 0.25 × 0.23 × 0.18 mm |
Oxford Diffraction Xcalibur diffractometer | 1125 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.024 |
Graphite monochromator | θmax = 25.0°, θmin = 3.5° |
Detector resolution: 1024 x 1024 with blocks 2 x 2 pixels mm-1 | h = −14→13 |
ω–scan | k = −15→15 |
5224 measured reflections | l = −13→13 |
1494 independent reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.032 | H-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 reflections | Δρmax = 0.24 e Å−3 |
110 parameters | Δρmin = −0.15 e Å−3 |
0 restraints | Extinction correction: SHELXL2013 (Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0012 (3) |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.15817 (8) | 0.27316 (7) | 0.84143 (8) | 0.0259 (3) | |
N1 | 0.10057 (9) | 0.57410 (8) | 0.92312 (10) | 0.0228 (3) | |
N2 | 0.08189 (9) | 0.40263 (7) | 0.92055 (10) | 0.0189 (3) | |
H2A | 0.0393 | 0.4149 | 0.9652 | 0.023* | |
C1 | 0.12421 (10) | 0.48726 (9) | 0.87675 (11) | 0.0177 (3) | |
C2 | 0.18323 (11) | 0.48219 (10) | 0.79260 (12) | 0.0213 (3) | |
H2 | 0.1975 | 0.4206 | 0.7621 | 0.026* | |
C3 | 0.21992 (11) | 0.57095 (10) | 0.75567 (13) | 0.0238 (3) | |
H3 | 0.2594 | 0.5699 | 0.6994 | 0.029* | |
C4 | 0.19788 (11) | 0.66159 (10) | 0.80261 (12) | 0.0235 (3) | |
H4 | 0.2225 | 0.7223 | 0.7795 | 0.028* | |
C5 | 0.13834 (11) | 0.65855 (9) | 0.88437 (13) | 0.0253 (3) | |
H5 | 0.1229 | 0.7195 | 0.9154 | 0.030* | |
C6 | 0.09926 (11) | 0.30281 (9) | 0.90189 (11) | 0.0184 (3) | |
C7 | 0.03884 (11) | 0.23330 (9) | 0.96366 (11) | 0.0196 (3) | |
H7A | −0.0464 | 0.2492 | 0.9333 | 0.023* | |
H7B | 0.0713 | 0.2462 | 1.0529 | 0.023* | |
C8 | 0.05278 (11) | 0.12258 (9) | 0.94244 (12) | 0.0203 (3) | |
H8A | 0.1378 | 0.1071 | 0.9668 | 0.024* | |
H8B | 0.0141 | 0.1080 | 0.8540 | 0.024* | |
C9 | −0.00115 (12) | 0.05536 (9) | 1.01516 (12) | 0.0196 (3) | |
H9A | 0.0430 | 0.0652 | 1.1038 | 0.023* | |
H9B | −0.0839 | 0.0756 | 0.9973 | 0.023* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0303 (5) | 0.0225 (5) | 0.0322 (6) | 0.0020 (4) | 0.0199 (5) | −0.0011 (4) |
N1 | 0.0243 (6) | 0.0180 (6) | 0.0279 (7) | −0.0012 (5) | 0.0117 (5) | 0.0013 (5) |
N2 | 0.0216 (6) | 0.0172 (6) | 0.0227 (6) | 0.0009 (5) | 0.0138 (5) | 0.0007 (5) |
C1 | 0.0144 (6) | 0.0184 (7) | 0.0180 (7) | −0.0003 (5) | 0.0032 (5) | 0.0028 (5) |
C2 | 0.0187 (7) | 0.0242 (7) | 0.0215 (7) | 0.0010 (6) | 0.0080 (6) | 0.0004 (6) |
C3 | 0.0176 (7) | 0.0335 (8) | 0.0211 (7) | −0.0009 (6) | 0.0081 (6) | 0.0057 (6) |
C4 | 0.0193 (7) | 0.0247 (8) | 0.0271 (8) | −0.0011 (6) | 0.0091 (6) | 0.0064 (6) |
C5 | 0.0265 (8) | 0.0185 (8) | 0.0330 (8) | −0.0014 (6) | 0.0133 (6) | 0.0005 (6) |
C6 | 0.0168 (6) | 0.0192 (7) | 0.0173 (7) | 0.0011 (5) | 0.0040 (6) | −0.0003 (5) |
C7 | 0.0199 (7) | 0.0200 (7) | 0.0198 (7) | 0.0010 (5) | 0.0084 (6) | −0.0001 (5) |
C8 | 0.0231 (7) | 0.0190 (7) | 0.0200 (7) | 0.0009 (5) | 0.0093 (6) | 0.0002 (5) |
C9 | 0.0199 (7) | 0.0203 (7) | 0.0174 (7) | 0.0021 (5) | 0.0055 (6) | −0.0002 (5) |
O1—C6 | 1.2209 (14) | C4—H4 | 0.9300 |
N1—C1 | 1.3440 (16) | C5—H5 | 0.9300 |
N1—C5 | 1.3448 (16) | C6—C7 | 1.5010 (17) |
N2—C6 | 1.3717 (16) | C7—C8 | 1.5108 (17) |
N2—C1 | 1.4000 (16) | C7—H7A | 0.9700 |
N2—H2A | 0.8600 | C7—H7B | 0.9700 |
C1—C2 | 1.3914 (18) | C8—C9 | 1.5185 (18) |
C2—C3 | 1.3783 (17) | C8—H8A | 0.9700 |
C2—H2 | 0.9300 | C8—H8B | 0.9700 |
C3—C4 | 1.3840 (18) | C9—C9i | 1.515 (2) |
C3—H3 | 0.9300 | C9—H9A | 0.9700 |
C4—C5 | 1.3711 (19) | C9—H9B | 0.9700 |
C1—N1—C5 | 116.16 (11) | O1—C6—C7 | 123.17 (11) |
C6—N2—C1 | 128.73 (11) | N2—C6—C7 | 113.27 (10) |
C6—N2—H2A | 115.6 | C6—C7—C8 | 115.01 (10) |
C1—N2—H2A | 115.6 | C6—C7—H7A | 108.5 |
N1—C1—C2 | 123.42 (11) | C8—C7—H7A | 108.5 |
N1—C1—N2 | 113.04 (11) | C6—C7—H7B | 108.5 |
C2—C1—N2 | 123.53 (12) | C8—C7—H7B | 108.5 |
C3—C2—C1 | 118.14 (12) | H7A—C7—H7B | 107.5 |
C3—C2—H2 | 120.9 | C7—C8—C9 | 112.96 (10) |
C1—C2—H2 | 120.9 | C7—C8—H8A | 109.0 |
C2—C3—C4 | 119.85 (13) | C9—C8—H8A | 109.0 |
C2—C3—H3 | 120.1 | C7—C8—H8B | 109.0 |
C4—C3—H3 | 120.1 | C9—C8—H8B | 109.0 |
C5—C4—C3 | 117.52 (12) | H8A—C8—H8B | 107.8 |
C5—C4—H4 | 121.2 | C9i—C9—C8 | 113.43 (13) |
C3—C4—H4 | 121.2 | C9i—C9—H9A | 108.9 |
N1—C5—C4 | 124.92 (12) | C8—C9—H9A | 108.9 |
N1—C5—H5 | 117.5 | C9i—C9—H9B | 108.9 |
C4—C5—H5 | 117.5 | C8—C9—H9B | 108.9 |
O1—C6—N2 | 123.56 (12) | H9A—C9—H9B | 107.7 |
Symmetry code: (i) −x, −y, −z+2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···N1ii | 0.86 | 2.45 | 3.3065 (15) | 171 |
C2—H2···O1 | 0.93 | 2.28 | 2.8716 (15) | 121 |
C4—H4···O1iii | 0.93 | 2.42 | 3.1585 (15) | 136 |
Symmetry codes: (ii) −x, −y+1, −z+2; (iii) −x+1/2, y+1/2, −z+3/2. |
References
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. Google Scholar
Awaleh, M. O., Badia, A. & Brisse, F. (2005). Cryst. Growth Des. 5, 1897–1906. Web of Science CSD CrossRef CAS Google Scholar
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. Web of Science CSD CrossRef CAS Google Scholar
Cheng, 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
Hennigar, T., MacQuarrie, D. C., Losier, P., Rogers, R. D. & Zaworotko, M. J. (1997). Angew. Chem. Int. Ed. Engl. 36, 972–973. Google Scholar
Ośmiałowski, 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
Ośmiałowski, B., Kolehmainen, E., Ejsmont, K., Ikonen, S., Valkonen, A., Rissanen, K. & Nonappa (2013). J. Mol. Struct. 1054–1055, 157–163. Google Scholar
Oxford Diffraction (2008). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, England. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
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