1,3,5-Tri-2-pyridylpentane-1,5-dione

Jian, F.-F.; Wang, J.-H.; Yang, X.-Y.; Wei, Y.-X.

doi:10.1107/S1600536807058953

1,3,5-Tri-2-pyridylpentane-1,5-dione

F.-F. Jian, J.-H. Wang, X.-Y. Yang and Y.-X. Wei

The title compound, C₂₀H₁₇N₃O₂, was prepared by the reaction of 1-(2-pyridyl)ethanone and pyridine-2-carbaldehyde in an ethanol solution at room temperature. The dihedral angles between the pyridine rings are 14.69 (12), 89.2 (1) and 87.1 (1)°. There are weak intermolecular C—H

O and intramolecular C—H

N hydrogen bonds in the crystal structure.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807058953/xu2353sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536807058953/xu2353Isup2.hkl Contains datablock I

CCDC reference: 665647

checkCIF report

Key indicators

Single-crystal X-ray study
T = 295 K
Mean (C-C) = 0.003 Å
R factor = 0.044
wR factor = 0.113
Data-to-parameter ratio = 13.6

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No syntax errors found



Alert level C
PLAT152_ALERT_1_C Supplied and Calc Volume s.u. Inconsistent .....          ?
PLAT154_ALERT_1_C The su's on the Cell Angles are Equal  (x 10000)       3000 Deg.
PLAT180_ALERT_3_C Check Cell Rounding: # of Values Ending with 0 =          3

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   3 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Comment top

In the previous research on Dracena cochinchinensit, we found that chalcone and it derivative have significant antifungal activities (Hu et al., 2001). They are important constituents commonly existing in biologically active natural products and synthetic compounds of medicinal interest (Kong et al., 2004). In recent years, various protocols for the construction of the compounds via solid-phase strategies have been reported (Gelen et al., 2003; Krchna & Holladay, 2002; Phoon & Sim, 2002; Franzen, 2000). The title compound has been synthesized and its crystal structure is presented here.

In the molecular structure (Fig. 1), the dihedral angles between pyridine (N1, C1, C2, C3, C4 and C5) and pyridine (N2, C16, C17, C18, C19 and C20) rings with the plane through the pyridine ring (N3, C9, C10, C11, C12 and C13) are 87.13 (10) and 89.15 (10)°, respectively. The C6═O1 bond length of 1.2078 (19) Å and C15═O2 bond length of 1.2066 (18) Å indicate the typical double bonds. Intramolecular C—H···N as well as intermolecular C—H···O hydrogen bonds are observed in the crystal structure.

Related literature top

For general background, see: Franzen (2000); Gelen et al. (2003); Hu et al. (2001); Kong et al. (2004); Krchna & Holladay (2002); Phoon & Sim (2002).

Experimental top

A mixture of 1-pyridin-2-yl-ethanone (0.02 mol) and pyridine-2-carbaldehyde (0.01 mol) and sodium hydroxide (0.034 mol) in ethanol (30 ml) was stirred at 293 K for 3 h. The hydrochloric acid solution (0.05 M) was dropped into the above solution to pH = 6 to get the title compound (1.0 g, yield 30%). Single crystals were obtained by recrystallization from an ethanol solution at room temperature.

Computing details top

Data collection: CAD-4 Software (Enraf–Nonius, 1989); cell refinement: CAD-4 Software (Enraf–Nonius, 1989); data reduction: NRCVAX (Gabe et al., 1989); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL/PC (Sheldrick, 1990); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top

Fig. 1. The molecular structure of the title compound with the atom-labeling scheme. Displacement ellipsoids are drawn at the 30% probability level.

1,3,5-Tri-2-pyridylpentane-1,5-dione top

Crystal data top

C₂₀H₁₇N₃O₂	Z = 2
M_r = 331.37	F(000) = 348
Triclinic, P1	D_x = 1.314 Mg m⁻³
Hall symbol: -P 1	Melting point: 124 K
a = 8.3830 (17) Å	Mo Kα radiation, λ = 0.71073 Å
b = 10.750 (2) Å	Cell parameters from 25 reflections
c = 10.950 (2) Å	θ = 4–14°
α = 101.92 (3)°	µ = 0.09 mm⁻¹
β = 104.71 (3)°	T = 295 K
γ = 111.51 (3)°	Block, colourless
V = 837.3 (3) Å³	0.20 × 0.15 × 0.11 mm

Data collection top

Enraf–Nonius CAD-4 diffractometer	R_int = 0.018
Radiation source: fine-focus sealed tube	θ_max = 25.5°, θ_min = 2.0°
Graphite monochromator	h = −10→9
ω/2θ scans	k = −7→13
4623 measured reflections	l = −13→13
3084 independent reflections	3 standard reflections every 100 reflections
2353 reflections with I > 2σ(I)	intensity decay: 0.1%

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.044	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.113	H-atom parameters constrained
S = 1.04	w = 1/[σ²(F_o²) + (0.0477P)² + 0.1482P] where P = (F_o² + 2F_c²)/3
3084 reflections	(Δ/σ)_max < 0.001
226 parameters	Δρ_max = 0.13 e Å⁻³
0 restraints	Δρ_min = −0.21 e Å⁻³

Crystal data top

C₂₀H₁₇N₃O₂	γ = 111.51 (3)°
M_r = 331.37	V = 837.3 (3) Å³
Triclinic, P1	Z = 2
a = 8.3830 (17) Å	Mo Kα radiation
b = 10.750 (2) Å	µ = 0.09 mm⁻¹
c = 10.950 (2) Å	T = 295 K
α = 101.92 (3)°	0.20 × 0.15 × 0.11 mm
β = 104.71 (3)°

Data collection top

Enraf–Nonius CAD-4 diffractometer	R_int = 0.018
4623 measured reflections	3 standard reflections every 100 reflections
3084 independent reflections	intensity decay: 0.1%
2353 reflections with I > 2σ(I)

Refinement top

R[F² > 2σ(F²)] = 0.044	0 restraints
wR(F²) = 0.113	H-atom parameters constrained
S = 1.04	Δρ_max = 0.13 e Å⁻³
3084 reflections	Δρ_min = −0.21 e Å⁻³
226 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.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) 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.

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

	x	y	z	U_iso*/U_eq
O1	0.57178 (18)	−0.27893 (12)	0.07393 (13)	0.0640 (4)
O2	0.78779 (19)	0.19726 (12)	0.04347 (12)	0.0612 (4)
N1	0.41992 (19)	−0.30815 (15)	0.34078 (14)	0.0560 (4)
N2	0.8417 (2)	0.45083 (15)	0.32752 (14)	0.0557 (4)
N3	0.97442 (18)	0.09329 (14)	0.36515 (13)	0.0478 (3)
C1	0.3457 (3)	−0.4064 (2)	0.3933 (2)	0.0721 (6)
H1B	0.3208	−0.3782	0.4697	0.087*
C2	0.3047 (3)	−0.5456 (2)	0.3409 (3)	0.0811 (7)
H2B	0.2529	−0.6102	0.3810	0.097*
C3	0.3399 (3)	−0.5888 (2)	0.2301 (3)	0.0846 (7)
H3B	0.3126	−0.6835	0.1927	0.101*
C4	0.4162 (3)	−0.49125 (19)	0.1741 (2)	0.0672 (5)
H4A	0.4424	−0.5181	0.0980	0.081*
C5	0.4536 (2)	−0.35289 (16)	0.23193 (16)	0.0453 (4)
C6	0.5366 (2)	−0.24400 (16)	0.17207 (16)	0.0440 (4)
C7	0.5694 (2)	−0.09482 (16)	0.23362 (16)	0.0423 (4)
H7A	0.6284	−0.0657	0.3300	0.051*
H7B	0.4520	−0.0912	0.2152	0.051*
C8	0.6889 (2)	0.00837 (15)	0.18096 (15)	0.0383 (3)
H8A	0.6417	−0.0323	0.0831	0.046*
C9	0.8847 (2)	0.02844 (14)	0.23367 (14)	0.0360 (3)
C10	0.9652 (2)	−0.01886 (17)	0.15183 (16)	0.0453 (4)
H10A	0.8993	−0.0647	0.0605	0.054*
C11	1.1434 (2)	0.00199 (19)	0.20588 (19)	0.0542 (4)
H11A	1.2002	−0.0286	0.1516	0.065*
C12	1.2357 (2)	0.06803 (18)	0.34003 (19)	0.0555 (5)
H12A	1.3565	0.0834	0.3795	0.067*
C13	1.1469 (2)	0.11107 (19)	0.41502 (18)	0.0544 (4)
H13A	1.2104	0.1557	0.5068	0.065*
C14	0.6836 (2)	0.15105 (16)	0.21789 (16)	0.0433 (4)
H14A	0.5566	0.1351	0.1969	0.052*
H14B	0.7474	0.1990	0.3136	0.052*
C15	0.7697 (2)	0.24470 (16)	0.14624 (15)	0.0417 (4)
C16	0.8333 (2)	0.40088 (16)	0.20360 (15)	0.0416 (4)
C17	0.8833 (3)	0.48560 (18)	0.12857 (18)	0.0564 (5)
H17A	0.8748	0.4463	0.0418	0.068*
C18	0.9460 (3)	0.62891 (19)	0.1835 (2)	0.0691 (6)
H18A	0.9799	0.6887	0.1347	0.083*
C19	0.9575 (3)	0.68178 (19)	0.3110 (2)	0.0690 (6)
H19A	0.9998	0.7787	0.3511	0.083*
C20	0.9062 (3)	0.59109 (19)	0.3790 (2)	0.0690 (6)
H20A	0.9167	0.6290	0.4667	0.083*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0827 (9)	0.0397 (7)	0.0708 (9)	0.0201 (6)	0.0441 (7)	0.0133 (6)
O2	0.0957 (10)	0.0497 (7)	0.0500 (7)	0.0367 (7)	0.0365 (7)	0.0185 (6)
N1	0.0529 (9)	0.0523 (9)	0.0566 (9)	0.0150 (7)	0.0204 (7)	0.0205 (7)
N2	0.0775 (10)	0.0419 (8)	0.0516 (9)	0.0264 (7)	0.0299 (8)	0.0148 (7)
N3	0.0463 (8)	0.0487 (8)	0.0425 (8)	0.0206 (6)	0.0123 (6)	0.0094 (6)
C1	0.0720 (13)	0.0758 (15)	0.0686 (13)	0.0214 (11)	0.0322 (11)	0.0367 (11)
C2	0.0843 (15)	0.0638 (14)	0.0990 (18)	0.0202 (12)	0.0395 (14)	0.0501 (13)
C3	0.1021 (18)	0.0452 (11)	0.1096 (19)	0.0241 (12)	0.0468 (15)	0.0376 (12)
C4	0.0813 (14)	0.0426 (10)	0.0817 (14)	0.0249 (10)	0.0372 (11)	0.0238 (10)
C5	0.0383 (8)	0.0394 (9)	0.0525 (10)	0.0130 (7)	0.0130 (7)	0.0162 (7)
C6	0.0394 (8)	0.0369 (8)	0.0507 (10)	0.0137 (7)	0.0159 (7)	0.0116 (7)
C7	0.0408 (8)	0.0378 (8)	0.0492 (9)	0.0171 (7)	0.0183 (7)	0.0145 (7)
C8	0.0416 (8)	0.0340 (8)	0.0394 (8)	0.0174 (7)	0.0143 (7)	0.0113 (6)
C9	0.0417 (8)	0.0261 (7)	0.0396 (8)	0.0133 (6)	0.0156 (7)	0.0122 (6)
C10	0.0515 (9)	0.0423 (9)	0.0436 (9)	0.0210 (8)	0.0204 (7)	0.0133 (7)
C11	0.0514 (10)	0.0532 (10)	0.0703 (12)	0.0281 (9)	0.0328 (9)	0.0222 (9)
C12	0.0428 (9)	0.0536 (10)	0.0694 (12)	0.0219 (8)	0.0165 (9)	0.0226 (9)
C13	0.0492 (10)	0.0532 (10)	0.0482 (10)	0.0195 (8)	0.0070 (8)	0.0114 (8)
C14	0.0481 (9)	0.0390 (8)	0.0500 (9)	0.0231 (7)	0.0212 (7)	0.0175 (7)
C15	0.0473 (9)	0.0408 (9)	0.0398 (9)	0.0233 (7)	0.0138 (7)	0.0143 (7)
C16	0.0464 (9)	0.0387 (8)	0.0425 (9)	0.0211 (7)	0.0155 (7)	0.0153 (7)
C17	0.0724 (12)	0.0475 (10)	0.0527 (10)	0.0242 (9)	0.0280 (9)	0.0210 (8)
C18	0.0915 (15)	0.0420 (10)	0.0781 (14)	0.0245 (10)	0.0367 (12)	0.0298 (10)
C19	0.0864 (15)	0.0355 (10)	0.0810 (14)	0.0229 (10)	0.0340 (12)	0.0145 (10)
C20	0.1003 (16)	0.0443 (11)	0.0637 (12)	0.0304 (11)	0.0393 (11)	0.0116 (9)

Geometric parameters (Å, º) top

O1—C6	1.2078 (19)	C8—C14	1.523 (2)
O2—C15	1.2066 (18)	C8—H8A	0.9800
N1—C5	1.329 (2)	C9—C10	1.374 (2)
N1—C1	1.336 (2)	C10—C11	1.372 (2)
N2—C16	1.325 (2)	C10—H10A	0.9300
N2—C20	1.334 (2)	C11—C12	1.360 (3)
N3—C9	1.332 (2)	C11—H11A	0.9300
N3—C13	1.334 (2)	C12—C13	1.360 (2)
C1—C2	1.362 (3)	C12—H12A	0.9300
C1—H1B	0.9300	C13—H13A	0.9300
C2—C3	1.351 (3)	C14—C15	1.494 (2)
C2—H2B	0.9300	C14—H14A	0.9700
C3—C4	1.364 (3)	C14—H14B	0.9700
C3—H3B	0.9300	C15—C16	1.495 (2)
C4—C5	1.371 (2)	C16—C17	1.373 (2)
C4—H4A	0.9300	C17—C18	1.369 (2)
C5—C6	1.495 (2)	C17—H17A	0.9300
C6—C7	1.496 (2)	C18—C19	1.358 (3)
C7—C8	1.520 (2)	C18—H18A	0.9300
C7—H7A	0.9700	C19—C20	1.358 (3)
C7—H7B	0.9700	C19—H19A	0.9300
C8—C9	1.510 (2)	C20—H20A	0.9300

C5—N1—C1	116.29 (17)	C11—C10—C9	119.52 (16)
C16—N2—C20	116.38 (15)	C11—C10—H10A	120.2
C9—N3—C13	117.34 (14)	C9—C10—H10A	120.2
N1—C1—C2	123.4 (2)	C12—C11—C10	118.97 (16)
N1—C1—H1B	118.3	C12—C11—H11A	120.5
C2—C1—H1B	118.3	C10—C11—H11A	120.5
C3—C2—C1	119.29 (19)	C13—C12—C11	118.30 (16)
C3—C2—H2B	120.4	C13—C12—H12A	120.9
C1—C2—H2B	120.4	C11—C12—H12A	120.9
C2—C3—C4	118.8 (2)	N3—C13—C12	124.06 (17)
C2—C3—H3B	120.6	N3—C13—H13A	118.0
C4—C3—H3B	120.6	C12—C13—H13A	118.0
C3—C4—C5	118.7 (2)	C15—C14—C8	112.94 (13)
C3—C4—H4A	120.6	C15—C14—H14A	109.0
C5—C4—H4A	120.6	C8—C14—H14A	109.0
N1—C5—C4	123.38 (16)	C15—C14—H14B	109.0
N1—C5—C6	116.83 (14)	C8—C14—H14B	109.0
C4—C5—C6	119.79 (16)	H14A—C14—H14B	107.8
O1—C6—C5	119.43 (14)	O2—C15—C14	121.65 (14)
O1—C6—C7	121.65 (14)	O2—C15—C16	119.61 (14)
C5—C6—C7	118.90 (14)	C14—C15—C16	118.74 (13)
C6—C7—C8	112.50 (13)	N2—C16—C17	123.20 (15)
C6—C7—H7A	109.1	N2—C16—C15	117.27 (14)
C8—C7—H7A	109.1	C17—C16—C15	119.52 (14)
C6—C7—H7B	109.1	C18—C17—C16	118.98 (17)
C8—C7—H7B	109.1	C18—C17—H17A	120.5
H7A—C7—H7B	107.8	C16—C17—H17A	120.5
C9—C8—C7	110.17 (12)	C19—C18—C17	118.47 (18)
C9—C8—C14	110.11 (13)	C19—C18—H18A	120.8
C7—C8—C14	111.77 (12)	C17—C18—H18A	120.8
C9—C8—H8A	108.2	C20—C19—C18	119.05 (17)
C7—C8—H8A	108.2	C20—C19—H19A	120.5
C14—C8—H8A	108.2	C18—C19—H19A	120.5
N3—C9—C10	121.81 (14)	N2—C20—C19	123.91 (18)
N3—C9—C8	115.90 (13)	N2—C20—H20A	118.0
C10—C9—C8	122.28 (14)	C19—C20—H20A	118.0

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C4—H4A···O1ⁱ	0.93	2.51	3.322 (3)	146
C11—H11A···O2ⁱⁱ	0.93	2.55	3.415 (2)	155
C14—H14B···N2	0.97	2.48	2.836 (2)	101
C14—H14B···N3	0.97	2.56	2.908 (2)	101

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

Experimental details

Crystal data
Chemical formula	C₂₀H₁₇N₃O₂
M_r	331.37
Crystal system, space group	Triclinic, P1
Temperature (K)	295
a, b, c (Å)	8.3830 (17), 10.750 (2), 10.950 (2)
α, β, γ (°)	101.92 (3), 104.71 (3), 111.51 (3)
V (Å³)	837.3 (3)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.20 × 0.15 × 0.11

Data collection
Diffractometer	Enraf–Nonius CAD-4 diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	4623, 3084, 2353
R_int	0.018
(sin θ/λ)_max (Å⁻¹)	0.606

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.044, 0.113, 1.04
No. of reflections	3084
No. of parameters	226
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.13, −0.21

Computer programs: CAD-4 Software (Enraf–Nonius, 1989), NRCVAX (Gabe et al., 1989), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL/PC (Sheldrick, 1990), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C4—H4A···O1ⁱ	0.93	2.51	3.322 (3)	145.5
C11—H11A···O2ⁱⁱ	0.93	2.55	3.415 (2)	154.9
C14—H14B···N2	0.97	2.48	2.836 (2)	101.1
C14—H14B···N3	0.97	2.56	2.908 (2)	101.3

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

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