Literature DB >> 22412736

2-(Morpholin-4-yl)-6-(1H-pyrrol-1-yl)-pyridine-3,5-dicarbonitrile.

Peter N Horton, Shaaban K Mohamed, Ahmed M Soliman, Eman M M Abdel-Raheem, Mehmet Akkurt.   

Abstract

In the title compound, C(15)H(13)N(5)O, the morpholine ring adopts a chair conformation. The dihedral angle between the pyrrole ring and the pyridine ring is 28.93 (14)°. In the crystal, the molecules are linked by C-H⋯O hydrogen bonds occur, and aromatic weak π-π stacking [centroid-centroid separation = 4.178 (2) Å] and C-H⋯π inter-actions consolidate the packing.

Entities:  

Year:  2012        PMID： 22412736      PMCID： PMC3297933          DOI： 10.1107/S160053681200815X

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN： 1600-5368


Related literature

For the biological activity of pyridine derivatives, see: Altomare et al. (2000 ▶); Basavaraja et al. (2010 ▶); Cho et al. (2001 ▶); Goda et al. (2004 ▶); Hosni & Abdualla (2008 ▶); Kovala-Demertzi et al. (2007 ▶); Mikail et al. (2001 ▶); Sylvie et al. (2002 ▶); Tiwari et al. (2002 ▶); Yeong et al. (2004 ▶). For the definition of puckering parameters, see: Cremer & Pople (1975 ▶).

Experimental

Crystal data

C15H13N5O M = 279.30 Triclinic, a = 8.633 (2) Å b = 8.763 (3) Å c = 9.559 (3) Å α = 91.715 (7)° β = 108.110 (8)° γ = 100.572 (7)° V = 672.7 (4) Å3 Z = 2 Mo Kα radiation μ = 0.09 mm−1 T = 120 K 0.52 × 0.44 × 0.18 mm

Data collection

Rigaku R-AXIS conversion diffractometer Absorption correction: multi-scan (CrystalClear-SM Expert; Rigaku, 2011 ▶) T min = 0.953, T max = 0.984 8461 measured reflections 3067 independent reflections 1884 reflections with I > 2σ(I) R int = 0.081

Refinement

R[F 2 > 2σ(F 2)] = 0.075 wR(F 2) = 0.225 S = 1.05 3067 reflections 190 parameters H-atom parameters constrained Δρmax = 0.35 e Å−3 Δρmin = −0.39 e Å−3 Data collection: CrystalClear-SM Expert (Rigaku, 2011 ▶); cell refinement: CrystalClear-SM Expert; data reduction: CrystalClear-SM Expert; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 ▶) and PLATON (Spek, 2009 ▶); software used to prepare material for publication: WinGX (Farrugia, 1999 ▶) and PLATON. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S160053681200815X/hg5182sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S160053681200815X/hg5182Isup2.hkl Supplementary material file. DOI: 10.1107/S160053681200815X/hg5182Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C15H13N5OZ = 2
Mr = 279.30F(000) = 292
Triclinic, P1Dx = 1.379 Mg m−3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 8.633 (2) ÅCell parameters from 3872 reflections
b = 8.763 (3) Åθ = 3.1–27.5°
c = 9.559 (3) ŵ = 0.09 mm−1
α = 91.715 (7)°T = 120 K
β = 108.110 (8)°Cut Block, colourless
γ = 100.572 (7)°0.52 × 0.44 × 0.18 mm
V = 672.7 (4) Å3
Rigaku R-AXIS conversion diffractometer3067 independent reflections
Radiation source: Sealed Tube1884 reflections with I > 2σ(I)
Graphite Monochromator monochromatorRint = 0.081
Detector resolution: 10.0000 pixels mm-1θmax = 27.5°, θmin = 3.1°
profile data from ω–scansh = −11→11
Absorption correction: multi-scan (CrystalClear-SM Expert; Rigaku, 2011)k = −11→11
Tmin = 0.953, Tmax = 0.984l = −12→12
8461 measured reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.075Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.225H-atom parameters constrained
S = 1.05w = 1/[σ2(Fo2) + (0.1134P)2] where P = (Fo2 + 2Fc2)/3
3067 reflections(Δ/σ)max < 0.001
190 parametersΔρmax = 0.35 e Å−3
0 restraintsΔρmin = −0.39 e Å−3
Experimental. Rigaku CrystalClear-SM Expert 2.0 r10
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles
Refinement. Refinement on F2 for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2 > σ(F2) is used only for calculating -R-factor-obs etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.
xyzUiso*/Ueq
O10.3867 (2)0.3040 (2)−0.00807 (19)0.0420 (6)
N10.4420 (3)0.2960 (2)0.4639 (2)0.0340 (7)
N20.5601 (3)0.1672 (2)0.6628 (2)0.0343 (7)
N30.3463 (3)0.4202 (3)0.2558 (2)0.0362 (7)
N40.1904 (3)−0.0380 (3)0.7594 (2)0.0435 (8)
N5−0.0679 (3)0.4902 (3)0.2845 (3)0.0481 (9)
C10.4195 (3)0.2145 (3)0.5715 (3)0.0315 (8)
C20.2626 (3)0.1732 (3)0.5944 (3)0.0332 (8)
C30.1383 (3)0.2445 (3)0.5105 (3)0.0362 (8)
C40.1611 (3)0.3373 (3)0.4010 (3)0.0341 (8)
C50.3158 (3)0.3500 (3)0.3710 (3)0.0327 (8)
C60.2270 (3)0.0584 (3)0.6897 (3)0.0368 (8)
C70.0352 (3)0.4214 (3)0.3333 (3)0.0383 (9)
C80.5972 (3)0.1465 (3)0.8128 (3)0.0363 (8)
C90.7503 (3)0.1120 (3)0.8612 (3)0.0395 (9)
C100.8110 (3)0.1098 (3)0.7379 (3)0.0405 (9)
C110.6950 (3)0.1461 (3)0.6203 (3)0.0385 (9)
C120.5130 (3)0.4356 (3)0.2379 (3)0.0366 (8)
C130.5100 (3)0.3023 (3)0.1320 (3)0.0383 (8)
C140.2248 (3)0.2914 (3)0.0054 (3)0.0389 (9)
C150.2197 (3)0.4214 (3)0.1118 (3)0.0384 (8)
H30.036900.229600.528300.0430*
H80.528600.154900.869700.0440*
H90.806100.093200.957200.0470*
H100.912500.087200.739000.0490*
H110.703700.155500.526300.0460*
H12A0.596000.433400.333000.0440*
H12B0.542000.534200.199600.0440*
H13A0.618500.311900.119300.0460*
H13B0.485300.204000.172500.0460*
H14A0.192700.191500.040400.0470*
H14B0.145100.29540−0.091000.0470*
H15A0.241200.521200.072800.0460*
H15B0.110300.406500.123300.0460*
U11U22U33U12U13U23
O10.0463 (11)0.0543 (12)0.0264 (9)0.0118 (9)0.0128 (9)−0.0030 (8)
N10.0395 (12)0.0407 (12)0.0237 (11)0.0128 (10)0.0107 (10)−0.0010 (9)
N20.0386 (12)0.0425 (12)0.0267 (11)0.0155 (10)0.0137 (10)0.0010 (9)
N30.0412 (12)0.0444 (13)0.0252 (11)0.0124 (10)0.0120 (10)0.0022 (9)
N40.0461 (13)0.0517 (15)0.0361 (13)0.0124 (12)0.0164 (11)0.0070 (11)
N50.0503 (14)0.0567 (16)0.0453 (15)0.0213 (13)0.0207 (12)0.0065 (12)
C10.0359 (13)0.0348 (14)0.0255 (12)0.0098 (11)0.0110 (11)−0.0015 (10)
C20.0389 (14)0.0374 (14)0.0261 (13)0.0102 (12)0.0133 (11)−0.0007 (10)
C30.0390 (14)0.0423 (15)0.0292 (13)0.0117 (12)0.0123 (12)−0.0044 (11)
C40.0366 (14)0.0396 (14)0.0269 (13)0.0115 (12)0.0095 (12)−0.0009 (11)
C50.0391 (14)0.0356 (14)0.0241 (12)0.0082 (12)0.0111 (11)−0.0015 (10)
C60.0383 (14)0.0463 (16)0.0282 (13)0.0149 (13)0.0112 (12)−0.0025 (11)
C70.0435 (15)0.0468 (16)0.0297 (14)0.0150 (14)0.0158 (13)0.0028 (12)
C80.0464 (15)0.0375 (14)0.0277 (13)0.0108 (12)0.0145 (12)0.0028 (10)
C90.0452 (15)0.0417 (16)0.0298 (14)0.0131 (13)0.0071 (12)0.0012 (11)
C100.0390 (14)0.0489 (17)0.0372 (15)0.0154 (13)0.0134 (13)0.0055 (12)
C110.0400 (14)0.0492 (17)0.0314 (14)0.0169 (13)0.0143 (12)0.0010 (11)
C120.0412 (14)0.0439 (15)0.0245 (12)0.0082 (12)0.0107 (12)0.0016 (11)
C130.0403 (14)0.0460 (16)0.0298 (13)0.0114 (13)0.0119 (12)0.0004 (11)
C140.0425 (15)0.0460 (16)0.0290 (14)0.0110 (13)0.0117 (12)0.0009 (11)
C150.0456 (15)0.0459 (15)0.0252 (13)0.0155 (13)0.0101 (12)0.0030 (11)
O1—C131.431 (3)C8—C91.352 (4)
O1—C141.428 (3)C9—C101.432 (4)
N1—C11.313 (3)C10—C111.344 (4)
N1—C51.346 (4)C12—C131.514 (4)
N2—C11.398 (4)C14—C151.520 (4)
N2—C81.394 (3)C3—H30.9300
N2—C111.387 (4)C8—H80.9300
N3—C51.350 (3)C9—H90.9300
N3—C121.484 (4)C10—H100.9300
N3—C151.469 (3)C11—H110.9300
N4—C61.151 (4)C12—H12A0.9700
N5—C71.153 (4)C12—H12B0.9700
C1—C21.422 (4)C13—H13A0.9700
C2—C31.388 (4)C13—H13B0.9700
C2—C61.432 (4)C14—H14A0.9700
C3—C41.384 (4)C14—H14B0.9700
C4—C51.437 (4)C15—H15A0.9700
C4—C71.424 (4)C15—H15B0.9700
C13—O1—C14111.61 (19)C2—C3—H3119.00
C1—N1—C5120.8 (3)C4—C3—H3119.00
C1—N2—C8127.1 (2)N2—C8—H8126.00
C1—N2—C11124.7 (2)C9—C8—H8126.00
C8—N2—C11108.1 (2)C8—C9—H9126.00
C5—N3—C12119.8 (2)C10—C9—H9126.00
C5—N3—C15124.4 (2)C9—C10—H10126.00
C12—N3—C15110.1 (2)C11—C10—H10126.00
N1—C1—N2115.8 (2)N2—C11—H11126.00
N1—C1—C2123.1 (3)C10—C11—H11126.00
N2—C1—C2121.2 (2)N3—C12—H12A110.00
C1—C2—C3115.8 (2)N3—C12—H12B110.00
C1—C2—C6123.7 (2)C13—C12—H12A110.00
C3—C2—C6120.4 (3)C13—C12—H12B110.00
C2—C3—C4121.8 (3)H12A—C12—H12B108.00
C3—C4—C5117.3 (2)O1—C13—H13A110.00
C3—C4—C7117.9 (3)O1—C13—H13B110.00
C5—C4—C7124.6 (2)C12—C13—H13A110.00
N1—C5—N3116.6 (3)C12—C13—H13B110.00
N1—C5—C4119.9 (2)H13A—C13—H13B108.00
N3—C5—C4123.5 (3)O1—C14—H14A109.00
N4—C6—C2176.0 (3)O1—C14—H14B109.00
N5—C7—C4176.9 (3)C15—C14—H14A109.00
N2—C8—C9108.1 (2)C15—C14—H14B109.00
C8—C9—C10107.6 (2)H14A—C14—H14B108.00
C9—C10—C11107.8 (2)N3—C15—H15A110.00
N2—C11—C10108.5 (2)N3—C15—H15B110.00
N3—C12—C13109.2 (2)C14—C15—H15A110.00
O1—C13—C12110.1 (2)C14—C15—H15B110.00
O1—C14—C15111.6 (2)H15A—C15—H15B108.00
N3—C15—C14109.3 (2)
C14—O1—C13—C12−58.8 (3)C5—N3—C15—C14−96.4 (3)
C13—O1—C14—C1557.6 (3)C12—N3—C5—N1−0.5 (4)
C1—N1—C5—C48.6 (4)N2—C1—C2—C6−12.6 (4)
C5—N1—C1—N2−178.8 (2)N2—C1—C2—C3171.4 (2)
C5—N1—C1—C22.3 (4)N1—C1—C2—C3−9.8 (4)
C1—N1—C5—N3−174.1 (2)N1—C1—C2—C6166.3 (2)
C8—N2—C1—C2−32.7 (4)C6—C2—C3—C4−169.8 (3)
C1—N2—C11—C10176.3 (2)C1—C2—C3—C46.3 (4)
C8—N2—C1—N1148.3 (2)C2—C3—C4—C7−172.3 (3)
C1—N2—C8—C9−175.3 (2)C2—C3—C4—C53.6 (4)
C11—N2—C8—C9−0.6 (3)C3—C4—C5—N1−11.4 (4)
C8—N2—C11—C101.4 (3)C7—C4—C5—N3−13.0 (4)
C11—N2—C1—C2153.4 (2)C7—C4—C5—N1164.2 (2)
C11—N2—C1—N1−25.6 (3)C3—C4—C5—N3171.5 (3)
C12—N3—C15—C1456.8 (3)N2—C8—C9—C10−0.4 (3)
C15—N3—C5—C4−32.6 (4)C8—C9—C10—C111.3 (3)
C5—N3—C12—C1395.8 (3)C9—C10—C11—N2−1.7 (3)
C15—N3—C12—C13−58.8 (3)N3—C12—C13—O159.0 (3)
C15—N3—C5—N1150.2 (2)O1—C14—C15—N3−56.1 (3)
C12—N3—C5—C4176.7 (2)
D—H···AD—HH···AD···AD—H···A
C8—H8···O1i0.932.443.294 (3)152
C12—H12A···N10.972.312.692 (3)103
C12—H12B···O1ii0.972.513.397 (3)153
C12—H12A···Cg3iii0.972.923.429 (3)114
Table 1

Hydrogen-bond geometry (Å, °)

Cg3 is the centroid of the N1/C1–C5 pyridine ring.

D—H⋯AD—HH⋯AD⋯AD—H⋯A
C8—H8⋯O1i0.932.443.294 (3)152
C12—H12B⋯O1ii0.972.513.397 (3)153
C12—H12A⋯Cg3iii0.972.923.429 (3)114

Symmetry codes: (i) ; (ii) ; (iii) .

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