Crystal structure of N,N′-bis­[(pyridin-4-yl)meth­yl]naphthalene di­imide

Nicolas-Gomez, M.; Martínez-Otero, D.; Dorazco-González, A.

doi:10.1107/S1600536814017917

organic compounds

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ISSN: 2056-9890

Volume 70| Part 9| September 2014| Pages o985-o986

doi:10.1107/S1600536814017917

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Crystal structure of N,N′-bis[(pyridin-4-yl)methyl]naphthalene diimide

Mariana Nicolas-Gomez,^a Diego Martínez-Otero ^a and Alejandro Dorazco-González ^a ^*

^aCentro Conjunto de Investigacion en Quimica Sustentable UAEM-UNAM, Instituto de Quimica, Universidad Nacional Autonoma de Mexico, Carretera Toluca-Atlacomulco Km 14.5 CP 50200 Toluca, Estado de Mexico, Mexico
^*Correspondence e-mail: adg@unam.mx

Edited by D.-J. Xu, Zhejiang University (Yuquan Campus), China (Received 19 July 2014; accepted 4 August 2014; online 9 August 2014)

In the centrosymmetric title compound, C₂₆H₁₆N₄O₄ {systematic name: 6,13-bis[(pyridin-4-yl)methyl]-6,13-diazatetracyclo[6.6.2.0^4,160^11,15]hexadeca-1,3,8,10,15-pantaene-5,7,12,14-tetrone}, the central ring system is essentially planar [maximum deviation = 0.0234 (8) Å] and approximately perpendicular to the terminal pyridine ring [dihedral angle = 84.38 (3)°]. The molecules displays a trans conformation with the (pyridin-4-yl)methyl groups on both sides of the central naphthalene diimide plane. In the crystal, molecules are linked by π–π stacking between parallel pyridine rings [centroid–centroid distances = 3.7014 (8) and 3.8553 (8) Å] and weak C—H⋯O hydrogen bonds, forming a three-dimensional supramolecular architecture.

Keywords: crystal structure; naphthalene diimide; transistors; organic supramolecular solids; hydrogen bonding; π–π stacking.

CCDC reference: 1017799

1. Related literature

For crystal structures of related compounds, see: Xu et al. (2011 ); Reczek et al. (2006 ); Li et al. (2009 ). For colorimetric applications and nanoscale properties, see: Pandeeswar et al. (2014 ); Trivedi et al. (2009 ); Matsunaga et al. (2014 ); Pantoş et al. (2007 ). For the design of transistors, see: Jung et al. (2009 ); Oh et al. (2010 ). For organic supramolecular solids, see: Cheney et al. (2007 ). For the design and synthesis of one-dimensional coordination polymers, see: Li et al. (2011 , 2012 ).

2. Experimental

2.1. Crystal data

C₂₆H₁₆N₄O₄
M_r = 448.43
Triclinic, $[P \overline 1]$
a = 5.5891 (4) Å
b = 7.5232 (5) Å
c = 11.9525 (8) Å
α = 77.093 (3)°
β = 88.445 (4)°
γ = 87.590 (4)°
V = 489.37 (6) Å³
Z = 1
Cu Kα radiation
μ = 0.87 mm⁻¹
T = 296 K
0.34 × 0.13 × 0.08 mm

2.2. Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2008 ) T_min = 0.555, T_max = 0.753
14032 measured reflections
1748 independent reflections
1643 reflections with I > 2σ(I)
R_int = 0.045

2.3. Refinement

R[F² > 2σ(F²)] = 0.037
wR(F²) = 0.106
S = 1.05
1748 reflections
154 parameters
H-atom parameters constrained
Δρ_max = 0.19 e Å⁻³
Δρ_min = −0.19 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C4—H4⋯O1ⁱ	0.93	2.59	3.5014 (15)	165
C13—H13⋯O2ⁱⁱ	0.93	2.51	3.3242 (15)	146
Symmetry codes: (i) x-1, y, z; (ii) -x-1, -y+2, -z+1.

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information

CCDC reference: 1017799

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536814017917/xu5806sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536814017917/xu5806Isup2.hkl

checkCIF report

Comment top

The assembly of organic molecules in solid state has attracted much attention in supramolecular chemistry, especially in crystal engineering and materials science (Cheney et al., 2007). The study and understanding of intermolecular interactions in a crystal is a central topic for design and synthesis of functional organic materials with desirable optical, electronic and structural properties (Pandeeswar et al., 2014). Herein we report the crystal structure of the title compound, which was prepared from 1,4,5,8-naphthalene dianhydride and 4-aminomethyl-pyridine under reflux in dry DMF. Suitable single-crystals for X-ray diffraction, were obtained directly from reaction mixture after of 12 h. The compound with methanol solvate (1:1) has been reported (Li et al., 2009) and was obtained as by-product during preparation of transition polymeric complexes in a mixture (methanol:chloroform) under solvothermal conditions, structurally this solvated is similar to compound reported here, both trans conformation of N-(4-pyridilmethyl) groups as to the dihedral angles between central ring and pyridil groups (86.34°). The title compound has also been studied as a semi-rigid ditopic ligand to the synthesis of one-dimensional coordination polymers with Zn(II), Mn(II), Co(II), Cd(II) where the ligand plays the key role to determine the final conformation of the polymeric structures (Li et al., 2011, 2012). The coordination of (I) to the salts of ZnCl2, Zn(ClO₄)₂, Zn(CF₃SO₃)₂ generates one-dimensional polymeric structures where trans conformation of (I) is maintained and not significant structural changes observed. A series of one-dimensional metal-organic frameworks of Mn(SCN)₂, Co(SCN)₂ and Cd(SCN)₂ with (I) have been reported, in all cases (I) shows a Z mode conformation and links up two metal centers such that one-dimensional chains are formed with π-π stacking interactions (centroid-centroid distances = 3.92–4.14 Å).

Related literature top

For crystal structures of related compounds, see: Xu et al. (2011); Reczek et al. (2006); Li et al. (2009). For colorimetric applications and nanoscale properties, see: Pandeeswar et al. (2014); Trivedi et al. (2009); Matsunaga et al. (2014); Pantoş et al. (2007). For the design of transistors, see: Jung et al. (2009); Oh et al. (2010). For organic supramolecular solids, see: Cheney et al. (2007). For the design and synthesis of one-dimensional coordination polymers, see: Li et al. (2011, 2012).

Experimental top

All chemicals were acquired commercially and were used without further purification. A mixture of 1,4,5,8-naphthalene dianhydride (1.0 g, 0.005 mol) and 4-aminomethyl-pyridine (1.08 g, 0.01 mol) in dry DMF (35 ml) was heated under reflux in atmosphere of dinitrogen and stirring for 2 h. Afterwards the resulting yellow solution was cooling and pallid yellow crystals were obtained on the wall of the flask directly from the mixture which corresponds to the compound I pure according to 1H NMR in DMSO-d6. Yield: 95%. Elemental analysis calculated (%) for C₂₆H₁₆N₄O₄; C, 69.64; H, 3.60; N, 12.49; found: C, 69.60; H, 3.62; N, 12.45.

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The structure with displacement ellipsoids drawn at the 30% probability level and H atoms as small sphere of arbitrary radii.
	Fig. 2. View p-stacking interactions in the crystal.

6,13-Bis[(pyridin-4-yl)methyl]-6,13-diazatetracyclo[6.6.2.0^4,160^11,15]hexadeca-1,3,8,10,15-pantaene-5,7,12,14-tetrone top

Crystal data top

C₂₆H₁₆N₄O₄	Z = 1
M_r = 448.43	F(000) = 232
Triclinic, P1	D_x = 1.522 Mg m⁻³
a = 5.5891 (4) Å	Cu Kα radiation, λ = 1.54178 Å
b = 7.5232 (5) Å	Cell parameters from 9981 reflections
c = 11.9525 (8) Å	θ = 3.8–68.3°
α = 77.093 (3)°	µ = 0.87 mm⁻¹
β = 88.445 (4)°	T = 296 K
γ = 87.590 (4)°	Plate, colourless
V = 489.37 (6) Å³	0.34 × 0.13 × 0.08 mm

Data collection top

Bruker APEXII CCD diffractometer	1748 independent reflections
Radiation source: Incoatec ImuS	1643 reflections with I > 2σ(I)
Mirrors monochromator	R_int = 0.045
ω scans	θ_max = 68.3°, θ_min = 3.8°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −5→6
T_min = 0.555, T_max = 0.753	k = −9→9
14032 measured reflections	l = −14→14

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.037	H-atom parameters constrained
wR(F²) = 0.106	w = 1/[σ²(F_o²) + (0.0617P)² + 0.0799P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max < 0.001
1748 reflections	Δρ_max = 0.19 e Å⁻³
154 parameters	Δρ_min = −0.19 e Å⁻³

Crystal data top

C₂₆H₁₆N₄O₄	γ = 87.590 (4)°
M_r = 448.43	V = 489.37 (6) Å³
Triclinic, P1	Z = 1
a = 5.5891 (4) Å	Cu Kα radiation
b = 7.5232 (5) Å	µ = 0.87 mm⁻¹
c = 11.9525 (8) Å	T = 296 K
α = 77.093 (3)°	0.34 × 0.13 × 0.08 mm
β = 88.445 (4)°

Data collection top

Bruker APEXII CCD diffractometer	1748 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2008)	1643 reflections with I > 2σ(I)
T_min = 0.555, T_max = 0.753	R_int = 0.045
14032 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.037	0 restraints
wR(F²) = 0.106	H-atom parameters constrained
S = 1.05	Δρ_max = 0.19 e Å⁻³
1748 reflections	Δρ_min = −0.19 e Å⁻³
154 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.43898 (16)	0.61174 (13)	0.75255 (7)	0.0471 (3)
N1	−0.0333 (2)	0.68325 (18)	1.12186 (9)	0.0587 (3)
C1	0.1698 (3)	0.7665 (2)	1.09030 (12)	0.0600 (4)
H1	0.2727	0.7785	1.1478	0.072*
O2	−0.21818 (18)	0.96340 (12)	0.62202 (8)	0.0540 (3)
N2	0.10767 (18)	0.78494 (13)	0.68880 (8)	0.0375 (3)
C2	0.2394 (2)	0.83681 (19)	0.97785 (11)	0.0482 (3)
H2	0.3847	0.8938	0.9613	0.058*
C6	0.1602 (2)	0.90343 (17)	0.76740 (10)	0.0425 (3)
H6A	0.0742	1.0198	0.7428	0.051*
H6B	0.3301	0.9262	0.7628	0.051*
C3	0.0913 (2)	0.82151 (15)	0.89059 (9)	0.0372 (3)
C5	−0.1744 (3)	0.66899 (19)	1.03678 (12)	0.0511 (3)
H5	−0.3183	0.6110	1.0560	0.061*
C4	−0.1216 (2)	0.73457 (17)	0.92155 (10)	0.0435 (3)
H4	−0.2276	0.7204	0.8658	0.052*
C7	0.2667 (2)	0.63581 (16)	0.69075 (9)	0.0360 (3)
C8	0.2169 (2)	0.51409 (15)	0.61294 (9)	0.0337 (3)
C9	0.02134 (19)	0.55699 (14)	0.53820 (8)	0.0315 (3)
C10	−0.1324 (2)	0.71073 (15)	0.53795 (9)	0.0340 (3)
C11	−0.0899 (2)	0.83074 (15)	0.61813 (9)	0.0376 (3)
C12	0.3627 (2)	0.36316 (16)	0.61186 (9)	0.0383 (3)
H12	0.4906	0.3354	0.6618	0.046*
C13	−0.3204 (2)	0.74975 (16)	0.46403 (10)	0.0384 (3)
H13	−0.4206	0.8516	0.4641	0.046*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0449 (5)	0.0592 (6)	0.0403 (5)	−0.0028 (4)	−0.0085 (4)	−0.0169 (4)
N1	0.0686 (8)	0.0691 (8)	0.0368 (6)	0.0111 (6)	0.0030 (5)	−0.0118 (5)
C1	0.0676 (10)	0.0771 (10)	0.0401 (7)	0.0099 (7)	−0.0136 (6)	−0.0243 (7)
O2	0.0626 (6)	0.0463 (5)	0.0580 (6)	0.0133 (4)	−0.0097 (4)	−0.0237 (4)
N2	0.0465 (6)	0.0387 (5)	0.0292 (5)	−0.0039 (4)	0.0003 (4)	−0.0113 (4)
C2	0.0479 (8)	0.0572 (8)	0.0454 (7)	0.0002 (5)	−0.0060 (5)	−0.0234 (6)
C6	0.0530 (7)	0.0405 (6)	0.0372 (6)	−0.0087 (5)	0.0007 (5)	−0.0143 (5)
C3	0.0436 (6)	0.0356 (6)	0.0358 (6)	0.0031 (4)	−0.0018 (4)	−0.0156 (4)
C5	0.0508 (8)	0.0541 (7)	0.0456 (7)	0.0033 (6)	0.0064 (6)	−0.0074 (6)
C4	0.0454 (7)	0.0467 (7)	0.0391 (6)	−0.0006 (5)	−0.0036 (5)	−0.0108 (5)
C7	0.0376 (6)	0.0437 (6)	0.0264 (5)	−0.0056 (4)	0.0017 (4)	−0.0069 (4)
C8	0.0368 (6)	0.0388 (6)	0.0249 (5)	−0.0027 (4)	0.0023 (4)	−0.0060 (4)
C9	0.0349 (6)	0.0351 (6)	0.0235 (5)	−0.0026 (4)	0.0032 (4)	−0.0044 (4)
C10	0.0384 (6)	0.0356 (6)	0.0272 (5)	−0.0012 (4)	0.0026 (4)	−0.0055 (4)
C11	0.0436 (7)	0.0364 (6)	0.0325 (6)	−0.0003 (5)	0.0021 (4)	−0.0077 (4)
C12	0.0376 (6)	0.0453 (6)	0.0304 (6)	0.0027 (5)	−0.0051 (4)	−0.0055 (5)
C13	0.0420 (6)	0.0376 (6)	0.0346 (6)	0.0061 (5)	−0.0002 (4)	−0.0071 (4)

Geometric parameters (Å, º) top

N1—C1	1.325 (2)	C5—H5	0.9300
N1—C5	1.3293 (19)	C6—H6A	0.9700
N2—C11	1.3931 (16)	C6—H6B	0.9700
N2—C7	1.3982 (16)	C7—C8	1.4823 (16)
N2—C6	1.4746 (14)	C8—C12	1.3718 (16)
O1—C7	1.2123 (14)	C8—C9	1.4110 (16)
O2—C11	1.2127 (15)	C9—C10	1.4113 (16)
C1—C2	1.382 (2)	C9—C9ⁱ	1.416 (2)
C1—H1	0.9300	C10—C13	1.3708 (17)
C2—C3	1.3766 (17)	C10—C11	1.4855 (16)
C2—H2	0.9300	C12—C13ⁱ	1.4046 (17)
C3—C4	1.3836 (18)	C12—H12	0.9300
C3—C6	1.5100 (16)	C13—C12ⁱ	1.4046 (17)
C4—C5	1.3834 (18)	C13—H13	0.9300
C4—H4	0.9300

C1—N1—C5	115.61 (12)	C3—C6—H6B	109.0
C11—N2—C7	125.48 (10)	H6A—C6—H6B	107.8
C11—N2—C6	118.44 (10)	O1—C7—N2	120.35 (10)
C7—N2—C6	116.06 (10)	O1—C7—C8	122.58 (11)
N1—C1—C2	124.53 (13)	N2—C7—C8	117.06 (10)
N1—C1—H1	117.7	C12—C8—C9	120.29 (11)
C2—C1—H1	117.7	C12—C8—C7	120.26 (11)
C3—C2—C1	119.25 (13)	C9—C8—C7	119.44 (10)
C3—C2—H2	120.4	C8—C9—C10	121.50 (11)
C1—C2—H2	120.4	C8—C9—C9ⁱ	119.18 (13)
C2—C3—C4	117.23 (11)	C10—C9—C9ⁱ	119.32 (13)
C2—C3—C6	120.00 (11)	C13—C10—C9	120.29 (11)
C4—C3—C6	122.74 (11)	C13—C10—C11	119.95 (10)
C5—C4—C3	118.95 (12)	C9—C10—C11	119.77 (11)
C5—C4—H4	120.5	O2—C11—N2	120.98 (11)
C3—C4—H4	120.5	O2—C11—C10	122.31 (11)
N1—C5—C4	124.44 (13)	N2—C11—C10	116.70 (10)
N1—C5—H5	117.8	C8—C12—C13ⁱ	120.51 (11)
C4—C5—H5	117.8	C8—C12—H12	119.7
N2—C6—C3	112.85 (9)	C13ⁱ—C12—H12	119.7
N2—C6—H6A	109.0	C10—C13—C12ⁱ	120.41 (10)
C3—C6—H6A	109.0	C10—C13—H13	119.8
N2—C6—H6B	109.0	C12ⁱ—C13—H13	119.8

C5—N1—C1—C2	0.1 (2)	C12—C8—C9—C10	179.61 (9)
N1—C1—C2—C3	0.0 (2)	C7—C8—C9—C10	−1.78 (16)
C11—N2—C6—C3	104.43 (12)	C12—C8—C9—C9ⁱ	−0.36 (19)
C7—N2—C6—C3	−76.70 (13)	C7—C8—C9—C9ⁱ	178.25 (10)
C1—C2—C3—C4	−0.20 (18)	C8—C9—C10—C13	179.67 (9)
C1—C2—C3—C6	177.80 (12)	C9ⁱ—C9—C10—C13	−0.36 (19)
N2—C6—C3—C2	139.13 (11)	C8—C9—C10—C11	−0.25 (17)
N2—C6—C3—C4	−42.99 (16)	C9ⁱ—C9—C10—C11	179.72 (10)
C1—N1—C5—C4	−0.1 (2)	C7—N2—C11—O2	−179.77 (10)
N1—C5—C4—C3	0.0 (2)	C6—N2—C11—O2	−1.01 (17)
C2—C3—C4—C5	0.19 (17)	C7—N2—C11—C10	−0.43 (17)
C6—C3—C4—C5	−177.75 (11)	C6—N2—C11—C10	178.33 (9)
C11—N2—C7—O1	177.16 (10)	C13—C10—C11—O2	0.79 (18)
C6—N2—C7—O1	−1.63 (16)	C9—C10—C11—O2	−179.29 (10)
C11—N2—C7—C8	−1.55 (16)	C13—C10—C11—N2	−178.55 (9)
C6—N2—C7—C8	179.67 (8)	C9—C10—C11—N2	1.38 (16)
O1—C7—C8—C12	2.58 (17)	C9—C8—C12—C13ⁱ	0.44 (17)
N2—C7—C8—C12	−178.75 (9)	C7—C8—C12—C13ⁱ	−178.16 (9)
O1—C7—C8—C9	−176.03 (10)	C9—C10—C13—C12ⁱ	0.29 (18)
N2—C7—C8—C9	2.64 (15)	C11—C10—C13—C12ⁱ	−179.78 (10)

Symmetry code: (i) −x, −y+1, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C4—H4···O1ⁱⁱ	0.93	2.59	3.5014 (15)	165
C13—H13···O2ⁱⁱⁱ	0.93	2.51	3.3242 (15)	146

Symmetry codes: (ii) x−1, y, z; (iii) −x−1, −y+2, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C4—H4···O1ⁱ	0.93	2.59	3.5014 (15)	165
C13—H13···O2ⁱⁱ	0.93	2.51	3.3242 (15)	146

Symmetry codes: (i) x−1, y, z; (ii) −x−1, −y+2, −z+1.

Acknowledgements

ADG thanks CONACyT for the repatriation fellowship 203539 and M. Sc. María de las Nieves Zavala Segovia for technical assistance.

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