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ISSN: 2414-3146

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

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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 ππ stacking inter­actions along the c-axis direction between the substituted pyridine rings, separated by 3.624 (1) Å.

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

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[Daly, J. W., Garraffo, H. M. & Spande, T. F. (1999). Alkaloids: Chemical and Biological Perspectives, Vol. 13, edited by S. W. Pelletier, pp. 1-161. New York: Elsevier.]). 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[Harrison, T. S. & Scott, L. J. (2005). Drugs, 65, 2309-2336.]), or cholesterol and triglyceride regulator (Watts & Chan, 2008[Watts, G. F. & Chan, D. C. (2008). Arterioscler. Thromb. Vasc. Biol. 28, 1892-1895.]). Pyridines also form integral parts of more complex natural products, such as diploclidine and nakinadine (Kubota et al., 2007[Kubota, T., Nishi, T., Fukushi, E., Kawabata, J., Fromont, J. & Kobayashi, J. (2007). Tetrahedron Lett. 48, 4983-4985.]).

In the crystal of the title compound (Fig. 1[link]), C6—H6⋯O2(x, 1 + y, z) weak hydrogen bonds form chains extending in the b-axis direction (Table 1[link] and Fig. 2[link]). These chains are arranged into layers (Fig. 3[link]) by ππ-stacking inter­actions between the substituted pyridine rings [Fig. 4[link], 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 DA 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]
Figure 1
The title mol­ecule with labeling scheme and 50% probability ellipsoids for non-H atoms.
[Figure 2]
Figure 2
Packing viewed along the c axis with C—H⋯O hydrogen bonds shown as dotted lines.
[Figure 3]
Figure 3
Packing viewed along the b axis emphasizing the layer structure.
[Figure 4]
Figure 4
Detail of the ππ 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[link]. 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
Mr 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)
V3) 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[Bruker (2016). APEX3, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.87, 0.99
No. of measured, independent and observed [I > 2σ(I)] reflections 10335, 2764, 2395
Rint 0.032
(sin θ/λ)max−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
Δρmax, Δρmin (e Å−3) 0.23, −0.20
Computer programs: APEX3 and SAINT (Bruker, 2016[Bruker (2016). APEX3, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2014 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), DIAMOND (Brandenburg & Putz, 2012[Brandenburg, K. & Putz, H. (2012). DIAMOND. Crystal Impact GbR, Bonn, Germany.]) and SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]).

Structural data


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
C16H16N2O3F(000) = 600
Mr = 284.31Dx = 1.351 Mg m3
Monoclinic, P21/cCu Kα radiation, λ = 1.54178 Å
a = 23.3174 (7) ÅCell parameters from 7563 reflections
b = 8.2979 (2) Åθ = 3.8–73.2°
c = 7.2260 (2) ŵ = 0.78 mm1
β = 90.899 (1)°T = 150 K
V = 1397.95 (7) Å3Plate, colourless
Z = 40.25 × 0.16 × 0.01 mm
Data collection top
Bruker D8 VENTURE PHOTON 100 CMOS
diffractometer
2764 independent reflections
Radiation source: INCOATEC IµS micro-focus source2395 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.032
Detector resolution: 10.4167 pixels mm-1θmax = 73.3°, θmin = 3.8°
ω scansh = 2828
Absorption correction: multi-scan
(SADABS; Bruker, 2016)
k = 109
Tmin = 0.87, Tmax = 0.99l = 88
10335 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.039All H-atom parameters refined
wR(F2) = 0.104 w = 1/[σ2(Fo2) + (0.0525P)2 + 0.417P]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max = 0.001
2764 reflectionsΔρmax = 0.23 e Å3
255 parametersΔρmin = 0.20 e Å3
0 restraintsExtinction correction: SHELXL2014 (Sheldrick, 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0024 (3)
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.95105 (5)0.03936 (13)0.34676 (19)0.0474 (3)
O20.86494 (5)0.00204 (12)0.44015 (18)0.0428 (3)
O30.60432 (4)1.08094 (11)0.66857 (13)0.0278 (2)
N10.66199 (4)0.60746 (13)0.65809 (15)0.0247 (2)
N20.90441 (5)0.08754 (14)0.39837 (17)0.0308 (3)
C10.83106 (5)0.48038 (15)0.48252 (18)0.0247 (3)
C20.84183 (5)0.31514 (15)0.46961 (18)0.0246 (3)
H20.8130 (7)0.236 (2)0.502 (2)0.031 (4)*
C30.89481 (5)0.26256 (15)0.41017 (18)0.0254 (3)
C40.93826 (6)0.36645 (18)0.3615 (2)0.0316 (3)
H40.9740 (7)0.326 (2)0.324 (2)0.036 (4)*
C50.92717 (6)0.53084 (18)0.3736 (2)0.0366 (4)
H50.9565 (8)0.605 (2)0.343 (2)0.044 (5)*
C60.87477 (6)0.58745 (17)0.4331 (2)0.0327 (3)
H60.8689 (8)0.703 (2)0.434 (2)0.043 (5)*
C70.77435 (5)0.53257 (16)0.54498 (19)0.0260 (3)
H70.7471 (7)0.4469 (19)0.576 (2)0.030 (4)*
C80.75595 (5)0.68419 (16)0.55851 (18)0.0256 (3)
H80.7825 (7)0.773 (2)0.531 (2)0.040 (5)*
C90.69782 (5)0.72919 (15)0.61500 (17)0.0222 (3)
C100.68107 (5)0.89220 (15)0.61999 (17)0.0226 (3)
C110.62485 (5)0.92452 (15)0.67111 (17)0.0228 (3)
C120.58704 (5)0.80139 (15)0.71531 (17)0.0240 (3)
C130.60879 (5)0.64531 (15)0.70639 (19)0.0253 (3)
H130.5831 (6)0.5569 (19)0.736 (2)0.024 (4)*
C140.72122 (6)1.02562 (16)0.5674 (2)0.0282 (3)
H14A0.7019 (11)1.132 (3)0.571 (3)0.076 (7)*
H14B0.7544 (8)1.032 (2)0.652 (3)0.048 (5)*
H14C0.7363 (9)1.009 (2)0.444 (3)0.055 (6)*
C150.61979 (8)1.17496 (18)0.8279 (2)0.0386 (4)
H15A0.6201 (11)1.282 (3)0.789 (4)0.084 (8)*
H15B0.5878 (11)1.164 (3)0.920 (4)0.084 (8)*
H15C0.6548 (10)1.142 (3)0.881 (3)0.060 (6)*
C160.52598 (6)0.83394 (18)0.7665 (2)0.0319 (3)
H16A0.5035 (8)0.882 (2)0.661 (3)0.048 (5)*
H16B0.5240 (8)0.909 (2)0.874 (3)0.053 (5)*
H16C0.5066 (8)0.732 (2)0.800 (2)0.045 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0351 (6)0.0367 (6)0.0708 (8)0.0121 (5)0.0170 (5)0.0044 (6)
O20.0385 (6)0.0243 (5)0.0660 (8)0.0005 (4)0.0125 (5)0.0002 (5)
O30.0305 (5)0.0214 (4)0.0314 (5)0.0054 (4)0.0024 (4)0.0019 (4)
N10.0239 (5)0.0224 (5)0.0279 (6)0.0002 (4)0.0024 (4)0.0011 (4)
N20.0292 (6)0.0270 (6)0.0362 (6)0.0054 (5)0.0045 (5)0.0013 (5)
C10.0226 (6)0.0245 (6)0.0271 (6)0.0007 (5)0.0026 (5)0.0006 (5)
C20.0220 (6)0.0242 (6)0.0278 (6)0.0008 (5)0.0039 (5)0.0001 (5)
C30.0249 (6)0.0230 (6)0.0283 (6)0.0019 (5)0.0031 (5)0.0014 (5)
C40.0216 (6)0.0335 (7)0.0399 (8)0.0014 (5)0.0082 (5)0.0031 (6)
C50.0274 (7)0.0300 (7)0.0528 (9)0.0049 (6)0.0114 (6)0.0008 (7)
C60.0284 (6)0.0241 (6)0.0457 (8)0.0006 (5)0.0080 (6)0.0004 (6)
C70.0227 (6)0.0261 (6)0.0292 (7)0.0002 (5)0.0031 (5)0.0005 (5)
C80.0225 (6)0.0258 (6)0.0285 (7)0.0004 (5)0.0032 (5)0.0004 (5)
C90.0225 (6)0.0221 (6)0.0221 (6)0.0001 (5)0.0009 (5)0.0005 (5)
C100.0238 (6)0.0224 (6)0.0217 (6)0.0005 (5)0.0005 (5)0.0001 (5)
C110.0252 (6)0.0213 (6)0.0218 (6)0.0029 (5)0.0013 (5)0.0010 (5)
C120.0226 (6)0.0256 (6)0.0237 (6)0.0023 (5)0.0018 (5)0.0008 (5)
C130.0233 (6)0.0237 (6)0.0291 (7)0.0019 (5)0.0024 (5)0.0003 (5)
C140.0263 (6)0.0232 (6)0.0352 (7)0.0017 (5)0.0020 (6)0.0023 (6)
C150.0518 (9)0.0255 (7)0.0382 (8)0.0090 (6)0.0106 (7)0.0078 (6)
C160.0242 (6)0.0324 (7)0.0393 (8)0.0024 (5)0.0059 (6)0.0007 (6)
Geometric parameters (Å, º) top
O1—N21.2224 (15)C7—H70.982 (16)
O2—N21.2246 (16)C8—C91.4699 (17)
O3—C111.3835 (14)C8—H80.982 (18)
O3—C151.4320 (17)C9—C101.4084 (17)
N1—C131.3316 (16)C10—C111.3936 (17)
N1—C91.3503 (16)C10—C141.5026 (17)
N2—C31.4722 (17)C11—C121.3900 (18)
C1—C21.3973 (17)C12—C131.3928 (17)
C1—C61.4025 (18)C12—C161.5011 (17)
C1—C71.4693 (17)C13—H130.972 (15)
C2—C31.3848 (17)C14—H14A0.99 (2)
C2—H20.968 (17)C14—H14B0.98 (2)
C3—C41.3802 (19)C14—H14C0.97 (2)
C4—C51.391 (2)C15—H15A0.93 (3)
C4—H40.942 (17)C15—H15B1.01 (3)
C5—C61.3838 (19)C15—H15C0.94 (2)
C5—H50.949 (19)C16—H16A1.00 (2)
C6—H60.965 (19)C16—H16B1.00 (2)
C7—C81.3333 (18)C16—H16C0.99 (2)
C11—O3—C15114.69 (10)C10—C9—C8120.55 (11)
C13—N1—C9117.79 (11)C11—C10—C9117.00 (11)
O1—N2—O2123.54 (12)C11—C10—C14121.17 (11)
O1—N2—C3118.50 (11)C9—C10—C14121.81 (11)
O2—N2—C3117.96 (11)O3—C11—C12118.16 (11)
C2—C1—C6118.20 (12)O3—C11—C10120.26 (11)
C2—C1—C7118.25 (11)C12—C11—C10121.48 (11)
C6—C1—C7123.55 (12)C11—C12—C13116.11 (11)
C3—C2—C1119.47 (12)C11—C12—C16122.13 (11)
C3—C2—H2119.2 (9)C13—C12—C16121.75 (12)
C1—C2—H2121.4 (9)N1—C13—C12124.95 (12)
C4—C3—C2122.98 (12)N1—C13—H13117.3 (9)
C4—C3—N2119.24 (11)C12—C13—H13117.7 (9)
C2—C3—N2117.78 (11)C10—C14—H14A111.2 (14)
C3—C4—C5117.28 (12)C10—C14—H14B111.7 (11)
C3—C4—H4120.6 (10)H14A—C14—H14B107.0 (18)
C5—C4—H4122.1 (10)C10—C14—H14C111.5 (12)
C6—C5—C4121.22 (13)H14A—C14—H14C108.9 (18)
C6—C5—H5119.8 (11)H14B—C14—H14C106.4 (16)
C4—C5—H5118.9 (11)O3—C15—H15A106.2 (16)
C5—C6—C1120.85 (13)O3—C15—H15B107.5 (15)
C5—C6—H6117.7 (10)H15A—C15—H15B107 (2)
C1—C6—H6121.4 (10)O3—C15—H15C112.3 (13)
C8—C7—C1126.36 (12)H15A—C15—H15C113 (2)
C8—C7—H7117.1 (9)H15B—C15—H15C110.7 (19)
C1—C7—H7116.5 (9)C12—C16—H16A111.7 (11)
C7—C8—C9124.01 (12)C12—C16—H16B111.1 (11)
C7—C8—H8119.0 (10)H16A—C16—H16B108.4 (16)
C9—C8—H8117.0 (10)C12—C16—H16C110.3 (11)
N1—C9—C10122.67 (11)H16A—C16—H16C107.0 (15)
N1—C9—C8116.77 (11)H16B—C16—H16C108.2 (15)
C6—C1—C2—C30.4 (2)C7—C8—C9—N11.2 (2)
C7—C1—C2—C3179.66 (12)C7—C8—C9—C10177.88 (13)
C1—C2—C3—C40.3 (2)N1—C9—C10—C110.35 (18)
C1—C2—C3—N2179.96 (12)C8—C9—C10—C11178.63 (11)
O1—N2—C3—C40.5 (2)N1—C9—C10—C14178.60 (12)
O2—N2—C3—C4179.11 (13)C8—C9—C10—C140.38 (19)
O1—N2—C3—C2179.74 (13)C15—O3—C11—C12102.35 (15)
O2—N2—C3—C20.61 (19)C15—O3—C11—C1081.30 (16)
C2—C3—C4—C50.1 (2)C9—C10—C11—O3176.17 (11)
N2—C3—C4—C5179.58 (13)C14—C10—C11—O32.08 (18)
C3—C4—C5—C60.4 (2)C9—C10—C11—C120.05 (18)
C4—C5—C6—C10.2 (3)C14—C10—C11—C12178.30 (12)
C2—C1—C6—C50.2 (2)O3—C11—C12—C13176.66 (11)
C7—C1—C6—C5179.39 (14)C10—C11—C12—C130.36 (18)
C2—C1—C7—C8177.22 (14)O3—C11—C12—C162.31 (18)
C6—C1—C7—C82.0 (2)C10—C11—C12—C16178.61 (12)
C1—C7—C8—C9177.47 (12)C9—N1—C13—C120.3 (2)
C13—N1—C9—C100.21 (19)C11—C12—C13—N10.5 (2)
C13—N1—C9—C8178.80 (11)C16—C12—C13—N1178.44 (13)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C6—H6···O2i0.97 (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.

References

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