N,N′-Bis(pyridin-2-yl)octa­nedi­amide

Dziuk, B.; Ośmiałowski, B.; Ejsmont, K.; Zarychta, B.

doi:10.1107/S2414314616013092

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 1| Part 8| August 2016| x161309

doi:10.1107/S2414314616013092

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N,N′-Bis(pyridin-2-yl)octanediamide

Błażej Dziuk,^a Borys Ośmiałowski,^b Krzysztof Ejsmont ^a and Bartosz Zarychta ^a ^*

^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.

Keywords: crystal structure; adamantane; antiviral effects; MOF self-assembly; hydrogen bonding.

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 asymmetric unit (Fig. 1), 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.

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) 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 + $[{1\over 2}]$ , y + $[{1\over 2}]$ , −z + $[{3\over 2}]$ ) 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 + $[{3\over 2}]$ ) 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	D⋯A	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
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.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₈H₂₂N₄O₂
M_r	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)
V (Å³)	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
R_int	0.024
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (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 ) and SHELXL2013 (Sheldrick, 2015 ).

Structural data

CCDC reference: 1499041

Crystal structure: contains datablocks I, global. DOI: 10.1107/S2414314616013092/hb4070sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2414314616013092/hb4070Isup2.hkl

Supporting information file. DOI: 10.1107/S2414314616013092/hb4070Isup3.cml

checkCIF report

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

C₁₈H₂₂N₄O₂	F(000) = 696
M_r = 326.39	D_x = 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

Data collection top

Oxford Diffraction Xcalibur diffractometer	1125 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.024
Graphite monochromator	θ_max = 25.0°, θ_min = 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 top

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(F_o²) + (0.0429P)²] where P = (F_o² + 2F_c²)/3
S = 0.95	(Δ/σ)_max < 0.001
1494 reflections	Δρ_max = 0.24 e Å⁻³
110 parameters	Δρ_min = −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)

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

	x	y	z	U_iso*/U_eq
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*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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.

Hydrogen-bond geometry (Å, º) top

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.

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