(E)-4-Meth­oxy-3,5-dimethyl-2-[(3-nitro­phen­yl)ethen­yl]pyridine

El Bakri, Y.; Ramli, Y.; Harmaoui, A.; Sebhaoui, J.; Essassi, E.M.; Mague, J.T.

doi:10.1107/S2414314616019660

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 1| Part 12| December 2016| x161966

https://doi.org/10.1107/S2414314616019660

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(E)-4-Methoxy-3,5-dimethyl-2-[(3-nitrophenyl)ethenyl]pyridine

Youness El Bakri,^a ^* Youssef Ramli,^b Abdallah Harmaoui,^a Jihad Sebhaoui,^a El Mokhtar Essassi ^a and Joel T. Mague ^c

^aLaboratoire de Chimie Organique Hétérocyclique, URAC 21, Pôle de Compétence Pharmacochimie, Av Ibn Battouta, BP 1014, Faculté des Sciences, Mohammed V University, Rabat, Morocco, ^bMedicinal Chemistry Laboratory, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, 10170 Rabat, Morocco, and ^cDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA
^*Correspondence e-mail: youness.chimie14@gmail.com

Edited by S. Bernès, Benemérita Universidad Autónoma de Puebla, México (Received 23 November 2016; accepted 8 December 2016; online 20 December 2016)

In the crystal of the title compound, C₁₆H₁₆N₂O₃, weak C—H⋯O hydrogen bonds involving the nitro group as acceptor form chains extending in the b-axis direction. The chains are arranged into layers by π–π stacking interactions along the c-axis direction between the substituted pyridine rings, separated by 3.624 (1) Å.

Keywords: crystal structure; hydrogen bond; π–π stacking.

CCDC reference: 1521533

Structure description

Pyridine derivatives form one of the most important classes of heterocyclic compounds and their prevalence in natural products and pharmaceuticals as well as their potent bioactivity have created significant interest in academia and the pharmaceutical industry (Daly et al., 1999 ). Indeed, pyridines have been studied for over a century as a result of their wide range of applications in many branches of chemistry, such as catalysis, drug design, molecular recognition, and materials science. Notably, many pyridine derivatives exhibit remarkable medicinal properties, including hypnotic and sedative, HIV antiviral (Harrison & Scott, 2005 ), or cholesterol and triglyceride regulator (Watts & Chan, 2008 ). Pyridines also form integral parts of more complex natural products, such as diploclidine and nakinadine (Kubota et al., 2007 ).

In the crystal of the title compound (Fig. 1), C6—H6⋯O2(x, 1 + y, z) weak hydrogen bonds form chains extending in the b-axis direction (Table 1 and Fig. 2). These chains are arranged into layers (Fig. 3) by π–π-stacking interactions between the substituted pyridine rings [Fig. 4, centroid–centroid distance = 3.624 (1) Å, dihedral angle between rings = 6.73 (6)°].

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C6—H6⋯O2ⁱ	0.97 (2)	2.45 (2)	3.414 (2)	174 (1)
Symmetry code: (i) x, y+1, z.

Figure 1
The title molecule with labeling scheme and 50% probability ellipsoids for non-H atoms.

Figure 2
Packing viewed along the c axis with C—H⋯O hydrogen bonds shown as dotted lines.

Figure 3
Packing viewed along the b axis emphasizing the layer structure.

Figure 4
Detail of the π–π stacking between substituted pyridine rings at (x, y, z) (top) and (x, $[{3\over 2}]$ − y, − $[{1\over 2}]$ + z) (bottom).

Synthesis and crystallization

To a solution of 5-methoxy-2-[((4-methoxy-3,5-dimethylpyridin-2-yl)methyl)sulfinyl]-1H-benzo[d]imidazole (0.5 g, 1.45 mmol), was added sodium methanolate (0.06 g, 1.45 mmol), and 3-nitrobenzaldehyde (0.44 g, 2.9 mmol). The mixture was refluxed in 15 ml of N,N-dimethylformamide for 48 h. The solution was then concentrated to dryness under reduced pressure and the obtained residue was chromatographed on a silica gel column with a mixture of ethyl acetate/hexane (90/100) as eluent. (E)-4-Methoxy-3,5-dimethyl-2-[(3-nitrophenyl)ethenyl]pyridine was obtained and recrystallized from ethanol solution, to afford the compound as crystals, with a yield of 40%.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. The positions and isotropic factors for all H atoms were refined, since diffraction data were collected at low temperature.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₆H₁₆N₂O₃
M_r	284.31
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	150
a, b, c (Å)	23.3174 (7), 8.2979 (2), 7.2260 (2)
β (°)	90.899 (1)
V (Å³)	1397.95 (7)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	0.78
Crystal size (mm)	0.25 × 0.16 × 0.01

Data collection
Diffractometer	Bruker D8 VENTURE PHOTON 100 CMOS
Absorption correction	Multi-scan (SADABS; Bruker, 2016 )
T_min, T_max	0.87, 0.99
No. of measured, independent and observed [I > 2σ(I)] reflections	10335, 2764, 2395
R_int	0.032
(sin θ/λ)_max (Å⁻¹)	0.621

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.104, 1.05
No. of reflections	2764
No. of parameters	255
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.23, −0.20
Computer programs: APEX3 and SAINT (Bruker, 2016), SHELXT (Sheldrick, 2015a ), SHELXL2014 (Sheldrick, 2015b ), DIAMOND (Brandenburg & Putz, 2012 ) and SHELXTL (Sheldrick, 2008 ).

Structural data

CCDC reference: 1521533

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314616019660/bh4020sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314616019660/bh4020Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314616019660/bh4020Isup3.cdx

Supporting information file. DOI: https://doi.org/10.1107/S2414314616019660/bh4020Isup4.cml

checkCIF report

Computing details top

Data collection: APEX3 (Bruker, 2016); cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

(E)-4-Methoxy-3,5-dimethyl-2-[(3-nitrophenyl)ethenyl]pyridine top

Crystal data top

C₁₆H₁₆N₂O₃	F(000) = 600
M_r = 284.31	D_x = 1.351 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.54178 Å
a = 23.3174 (7) Å	Cell parameters from 7563 reflections
b = 8.2979 (2) Å	θ = 3.8–73.2°
c = 7.2260 (2) Å	µ = 0.78 mm⁻¹
β = 90.899 (1)°	T = 150 K
V = 1397.95 (7) Å³	Plate, colourless
Z = 4	0.25 × 0.16 × 0.01 mm

Data collection top

Bruker D8 VENTURE PHOTON 100 CMOS diffractometer	2764 independent reflections
Radiation source: INCOATEC IµS micro-focus source	2395 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.032
Detector resolution: 10.4167 pixels mm^-1	θ_max = 73.3°, θ_min = 3.8°
ω scans	h = −28→28
Absorption correction: multi-scan (SADABS; Bruker, 2016)	k = −10→9
T_min = 0.87, T_max = 0.99	l = −8→8
10335 measured reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F² > 2σ(F²)] = 0.039	All H-atom parameters refined
wR(F²) = 0.104	w = 1/[σ²(F_o²) + (0.0525P)² + 0.417P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max = 0.001
2764 reflections	Δρ_max = 0.23 e Å⁻³
255 parameters	Δρ_min = −0.20 e Å⁻³
0 restraints	Extinction correction: SHELXL2014 (Sheldrick, 2015b), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0024 (3)

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

	x	y	z	U_iso*/U_eq
O1	0.95105 (5)	0.03936 (13)	0.34676 (19)	0.0474 (3)
O2	0.86494 (5)	−0.00204 (12)	0.44015 (18)	0.0428 (3)
O3	0.60432 (4)	1.08094 (11)	0.66857 (13)	0.0278 (2)
N1	0.66199 (4)	0.60746 (13)	0.65809 (15)	0.0247 (2)
N2	0.90441 (5)	0.08754 (14)	0.39837 (17)	0.0308 (3)
C1	0.83106 (5)	0.48038 (15)	0.48252 (18)	0.0247 (3)
C2	0.84183 (5)	0.31514 (15)	0.46961 (18)	0.0246 (3)
H2	0.8130 (7)	0.236 (2)	0.502 (2)	0.031 (4)*
C3	0.89481 (5)	0.26256 (15)	0.41017 (18)	0.0254 (3)
C4	0.93826 (6)	0.36645 (18)	0.3615 (2)	0.0316 (3)
H4	0.9740 (7)	0.326 (2)	0.324 (2)	0.036 (4)*
C5	0.92717 (6)	0.53084 (18)	0.3736 (2)	0.0366 (4)
H5	0.9565 (8)	0.605 (2)	0.343 (2)	0.044 (5)*
C6	0.87477 (6)	0.58745 (17)	0.4331 (2)	0.0327 (3)
H6	0.8689 (8)	0.703 (2)	0.434 (2)	0.043 (5)*
C7	0.77435 (5)	0.53257 (16)	0.54498 (19)	0.0260 (3)
H7	0.7471 (7)	0.4469 (19)	0.576 (2)	0.030 (4)*
C8	0.75595 (5)	0.68419 (16)	0.55851 (18)	0.0256 (3)
H8	0.7825 (7)	0.773 (2)	0.531 (2)	0.040 (5)*
C9	0.69782 (5)	0.72919 (15)	0.61500 (17)	0.0222 (3)
C10	0.68107 (5)	0.89220 (15)	0.61999 (17)	0.0226 (3)
C11	0.62485 (5)	0.92452 (15)	0.67111 (17)	0.0228 (3)
C12	0.58704 (5)	0.80139 (15)	0.71531 (17)	0.0240 (3)
C13	0.60879 (5)	0.64531 (15)	0.70639 (19)	0.0253 (3)
H13	0.5831 (6)	0.5569 (19)	0.736 (2)	0.024 (4)*
C14	0.72122 (6)	1.02562 (16)	0.5674 (2)	0.0282 (3)
H14A	0.7019 (11)	1.132 (3)	0.571 (3)	0.076 (7)*
H14B	0.7544 (8)	1.032 (2)	0.652 (3)	0.048 (5)*
H14C	0.7363 (9)	1.009 (2)	0.444 (3)	0.055 (6)*
C15	0.61979 (8)	1.17496 (18)	0.8279 (2)	0.0386 (4)
H15A	0.6201 (11)	1.282 (3)	0.789 (4)	0.084 (8)*
H15B	0.5878 (11)	1.164 (3)	0.920 (4)	0.084 (8)*
H15C	0.6548 (10)	1.142 (3)	0.881 (3)	0.060 (6)*
C16	0.52598 (6)	0.83394 (18)	0.7665 (2)	0.0319 (3)
H16A	0.5035 (8)	0.882 (2)	0.661 (3)	0.048 (5)*
H16B	0.5240 (8)	0.909 (2)	0.874 (3)	0.053 (5)*
H16C	0.5066 (8)	0.732 (2)	0.800 (2)	0.045 (5)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0351 (6)	0.0367 (6)	0.0708 (8)	0.0121 (5)	0.0170 (5)	−0.0044 (6)
O2	0.0385 (6)	0.0243 (5)	0.0660 (8)	−0.0005 (4)	0.0125 (5)	0.0002 (5)
O3	0.0305 (5)	0.0214 (4)	0.0314 (5)	0.0054 (4)	−0.0024 (4)	−0.0019 (4)
N1	0.0239 (5)	0.0224 (5)	0.0279 (6)	0.0002 (4)	0.0024 (4)	−0.0011 (4)
N2	0.0292 (6)	0.0270 (6)	0.0362 (6)	0.0054 (5)	0.0045 (5)	−0.0013 (5)
C1	0.0226 (6)	0.0245 (6)	0.0271 (6)	0.0007 (5)	0.0026 (5)	−0.0006 (5)
C2	0.0220 (6)	0.0242 (6)	0.0278 (6)	−0.0008 (5)	0.0039 (5)	0.0001 (5)
C3	0.0249 (6)	0.0230 (6)	0.0283 (6)	0.0019 (5)	0.0031 (5)	−0.0014 (5)
C4	0.0216 (6)	0.0335 (7)	0.0399 (8)	0.0014 (5)	0.0082 (5)	−0.0031 (6)
C5	0.0274 (7)	0.0300 (7)	0.0528 (9)	−0.0049 (6)	0.0114 (6)	−0.0008 (7)
C6	0.0284 (6)	0.0241 (6)	0.0457 (8)	−0.0006 (5)	0.0080 (6)	−0.0004 (6)
C7	0.0227 (6)	0.0261 (6)	0.0292 (7)	0.0002 (5)	0.0031 (5)	−0.0005 (5)
C8	0.0225 (6)	0.0258 (6)	0.0285 (7)	0.0004 (5)	0.0032 (5)	−0.0004 (5)
C9	0.0225 (6)	0.0221 (6)	0.0221 (6)	0.0001 (5)	0.0009 (5)	−0.0005 (5)
C10	0.0238 (6)	0.0224 (6)	0.0217 (6)	−0.0005 (5)	−0.0005 (5)	−0.0001 (5)
C11	0.0252 (6)	0.0213 (6)	0.0218 (6)	0.0029 (5)	−0.0013 (5)	−0.0010 (5)
C12	0.0226 (6)	0.0256 (6)	0.0237 (6)	0.0023 (5)	0.0018 (5)	−0.0008 (5)
C13	0.0233 (6)	0.0237 (6)	0.0291 (7)	−0.0019 (5)	0.0024 (5)	−0.0003 (5)
C14	0.0263 (6)	0.0232 (6)	0.0352 (7)	−0.0017 (5)	0.0020 (6)	0.0023 (6)
C15	0.0518 (9)	0.0255 (7)	0.0382 (8)	0.0090 (6)	−0.0106 (7)	−0.0078 (6)
C16	0.0242 (6)	0.0324 (7)	0.0393 (8)	0.0024 (5)	0.0059 (6)	−0.0007 (6)

Geometric parameters (Å, º) top

O1—N2	1.2224 (15)	C7—H7	0.982 (16)
O2—N2	1.2246 (16)	C8—C9	1.4699 (17)
O3—C11	1.3835 (14)	C8—H8	0.982 (18)
O3—C15	1.4320 (17)	C9—C10	1.4084 (17)
N1—C13	1.3316 (16)	C10—C11	1.3936 (17)
N1—C9	1.3503 (16)	C10—C14	1.5026 (17)
N2—C3	1.4722 (17)	C11—C12	1.3900 (18)
C1—C2	1.3973 (17)	C12—C13	1.3928 (17)
C1—C6	1.4025 (18)	C12—C16	1.5011 (17)
C1—C7	1.4693 (17)	C13—H13	0.972 (15)
C2—C3	1.3848 (17)	C14—H14A	0.99 (2)
C2—H2	0.968 (17)	C14—H14B	0.98 (2)
C3—C4	1.3802 (19)	C14—H14C	0.97 (2)
C4—C5	1.391 (2)	C15—H15A	0.93 (3)
C4—H4	0.942 (17)	C15—H15B	1.01 (3)
C5—C6	1.3838 (19)	C15—H15C	0.94 (2)
C5—H5	0.949 (19)	C16—H16A	1.00 (2)
C6—H6	0.965 (19)	C16—H16B	1.00 (2)
C7—C8	1.3333 (18)	C16—H16C	0.99 (2)

C11—O3—C15	114.69 (10)	C10—C9—C8	120.55 (11)
C13—N1—C9	117.79 (11)	C11—C10—C9	117.00 (11)
O1—N2—O2	123.54 (12)	C11—C10—C14	121.17 (11)
O1—N2—C3	118.50 (11)	C9—C10—C14	121.81 (11)
O2—N2—C3	117.96 (11)	O3—C11—C12	118.16 (11)
C2—C1—C6	118.20 (12)	O3—C11—C10	120.26 (11)
C2—C1—C7	118.25 (11)	C12—C11—C10	121.48 (11)
C6—C1—C7	123.55 (12)	C11—C12—C13	116.11 (11)
C3—C2—C1	119.47 (12)	C11—C12—C16	122.13 (11)
C3—C2—H2	119.2 (9)	C13—C12—C16	121.75 (12)
C1—C2—H2	121.4 (9)	N1—C13—C12	124.95 (12)
C4—C3—C2	122.98 (12)	N1—C13—H13	117.3 (9)
C4—C3—N2	119.24 (11)	C12—C13—H13	117.7 (9)
C2—C3—N2	117.78 (11)	C10—C14—H14A	111.2 (14)
C3—C4—C5	117.28 (12)	C10—C14—H14B	111.7 (11)
C3—C4—H4	120.6 (10)	H14A—C14—H14B	107.0 (18)
C5—C4—H4	122.1 (10)	C10—C14—H14C	111.5 (12)
C6—C5—C4	121.22 (13)	H14A—C14—H14C	108.9 (18)
C6—C5—H5	119.8 (11)	H14B—C14—H14C	106.4 (16)
C4—C5—H5	118.9 (11)	O3—C15—H15A	106.2 (16)
C5—C6—C1	120.85 (13)	O3—C15—H15B	107.5 (15)
C5—C6—H6	117.7 (10)	H15A—C15—H15B	107 (2)
C1—C6—H6	121.4 (10)	O3—C15—H15C	112.3 (13)
C8—C7—C1	126.36 (12)	H15A—C15—H15C	113 (2)
C8—C7—H7	117.1 (9)	H15B—C15—H15C	110.7 (19)
C1—C7—H7	116.5 (9)	C12—C16—H16A	111.7 (11)
C7—C8—C9	124.01 (12)	C12—C16—H16B	111.1 (11)
C7—C8—H8	119.0 (10)	H16A—C16—H16B	108.4 (16)
C9—C8—H8	117.0 (10)	C12—C16—H16C	110.3 (11)
N1—C9—C10	122.67 (11)	H16A—C16—H16C	107.0 (15)
N1—C9—C8	116.77 (11)	H16B—C16—H16C	108.2 (15)

C6—C1—C2—C3	0.4 (2)	C7—C8—C9—N1	1.2 (2)
C7—C1—C2—C3	179.66 (12)	C7—C8—C9—C10	−177.88 (13)
C1—C2—C3—C4	−0.3 (2)	N1—C9—C10—C11	−0.35 (18)
C1—C2—C3—N2	−179.96 (12)	C8—C9—C10—C11	178.63 (11)
O1—N2—C3—C4	0.5 (2)	N1—C9—C10—C14	−178.60 (12)
O2—N2—C3—C4	−179.11 (13)	C8—C9—C10—C14	0.38 (19)
O1—N2—C3—C2	−179.74 (13)	C15—O3—C11—C12	102.35 (15)
O2—N2—C3—C2	0.61 (19)	C15—O3—C11—C10	−81.30 (16)
C2—C3—C4—C5	−0.1 (2)	C9—C10—C11—O3	−176.17 (11)
N2—C3—C4—C5	179.58 (13)	C14—C10—C11—O3	2.08 (18)
C3—C4—C5—C6	0.4 (2)	C9—C10—C11—C12	0.05 (18)
C4—C5—C6—C1	−0.2 (3)	C14—C10—C11—C12	178.30 (12)
C2—C1—C6—C5	−0.2 (2)	O3—C11—C12—C13	176.66 (11)
C7—C1—C6—C5	−179.39 (14)	C10—C11—C12—C13	0.36 (18)
C2—C1—C7—C8	−177.22 (14)	O3—C11—C12—C16	−2.31 (18)
C6—C1—C7—C8	2.0 (2)	C10—C11—C12—C16	−178.61 (12)
C1—C7—C8—C9	177.47 (12)	C9—N1—C13—C12	0.3 (2)
C13—N1—C9—C10	0.21 (19)	C11—C12—C13—N1	−0.5 (2)
C13—N1—C9—C8	−178.80 (11)	C16—C12—C13—N1	178.44 (13)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C6—H6···O2ⁱ	0.97 (2)	2.45 (2)	3.414 (2)	174 (1)

Symmetry code: (i) x, y+1, z.

Acknowledgements

The support of NSF–MRI Grant No. 1228232 for the purchase of the diffractometer and Tulane University for support of the Tulane Crystallography Laboratory are gratefully acknowledged.

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