Pyridine-3-carbonitrile–chloranilic acid–acetonitrile (2/1/2)

Gotoh, K.; Ishida, H.

doi:10.1107/S1600536809036605

organic compounds

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Volume 65| Part 10| October 2009| Page o2467

doi:10.1107/S1600536809036605

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Pyridine-3-carbonitrile–chloranilic acid–acetonitrile (2/1/2)

Kazuma Gotoh ^a and Hiroyuki Ishida ^a ^*

^aDepartment of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
^*Correspondence e-mail: ishidah@cc.okayama-u.ac.jp

(Received 7 September 2009; accepted 10 September 2009; online 16 September 2009)

In the crystal structure of the title compound, 2C₆H₄N₂·C₆H₂Cl₂O₄·2C₂H₃N, the two symmetry-related pyridine-3-carbonitrile molecules are linked to either side of a chloranilic acid (systematic name: 2,5-dichloro-3,6-dihydroxy-1,4-benzoquinone) molecule via intermolecular O—H⋯N hydrogen bonds, giving a centrosymmetric 2:1 unit. The dihedral angle between the pyridine ring and the chloranilic acid plane is 26.71 (6)°. In addition, the two acetonitrile molecules are linked to either side of the 2:1 unit through C—H⋯N hydrogen bonds, forming a 2:1:2 aggregate. These 2:1:2 aggregates are further linked by weak intermolecular C—H⋯N and C—H⋯O hydrogen bonds, forming a tape along the c axis.

Related literature

For related structures, see, for example: Gotoh et al. (2009 ); Gotoh, Asaji & Ishida (2008 ); Gotoh, Nagoshi & Ishida (2008 ).

Experimental

Crystal data

2C₆H₄N₂·C₆H₂Cl₂O₄·2C₂H₃N
M_r = 499.31
Triclinic, $[P \overline 1]$
a = 3.91269 (16) Å
b = 10.8937 (9) Å
c = 13.5966 (5) Å
α = 105.302 (4)°
β = 90.0058 (14)°
γ = 90.847 (5)°
V = 558.93 (6) Å³
Z = 1
Mo Kα radiation
μ = 0.33 mm⁻¹
T = 180 K
0.32 × 0.25 × 0.15 mm

Data collection

Rigaku RAXIS-RAPID II diffractometer
Absorption correction: numerical (ABSCOR; Higashi, 1995 ) T_min = 0.906, T_max = 0.951
7721 measured reflections
3232 independent reflections
2592 reflections with I > 2σ(I)
R_int = 0.031

Refinement

R[F² > 2σ(F²)] = 0.035
wR(F²) = 0.099
S = 1.07
3232 reflections
159 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.44 e Å⁻³
Δρ_min = −0.28 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H2⋯N1	0.92 (3)	1.75 (3)	2.6111 (17)	154 (3)
O2—H2⋯O1ⁱ	0.92 (3)	2.25 (3)	2.6824 (14)	108 (2)
C4—H4⋯N2ⁱⁱ	0.95	2.46	3.292 (2)	146
C6—H6⋯N3	0.95	2.57	3.385 (2)	144
C7—H7⋯O1ⁱⁱⁱ	0.95	2.48	3.4248 (18)	172
C11—H11A⋯N2	0.98	2.62	3.341 (2)	130
Symmetry codes: (i) -x+2, -y, -z; (ii) -x+1, -y+1, -z+1; (iii) x-1, y+1, z.

Data collection: PROCESS-AUTO (Rigaku/MSC, 2004 ); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997 ); software used to prepare material for publication: CrystalStructure and PLATON (Spek, 2009 ).

Supporting information

Crystal structure: contains datablocks General, I. DOI: 10.1107/S1600536809036605/lh2901sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809036605/lh2901Isup2.hkl

checkCIF report

Comment top

The title compound, (I), was prepared in order to extend our study on D—H···A hydrogen bonding (D = N, O, or C; A = N, O or Cl) in amine–chloranilic acid systems (Gotoh, Asaji & Ishida, 2008; Gotoh et al., 2009).

In the crystal structure of the title compound, two pyridine-3-carbonitrile molecules, one chloranilic acid molecule and two acetonitrile molecules are linked by O—H···N and C—H···N hydrogen bonds (Table 1) to afford a 2:1:2 aggregate (Fig. 1). The O···N distance [2.6111 (17) Å] between the acid and the base is comparable to that of 2.610 (3) Å in pyridine-4-carbonitrile–chloranilic acid (1/1), where the H atom in the O···H···N hydrogen bond is disordered (Gotoh, Nagoshi & Ishida, 2008), but in the title compound no distinct evidence of H disorder was observed in a difference Fourier map. The 2:1:2 aggregates are linked by weak intermolecular C—H···N and C—H···O hydrogen bonds, forming a tape along the c axis (Fig. 2). A short contact between the adjacent C≡N bonds of acetonitrile molecules is observed [C10···C10ⁱⁱⁱ 3.314 Å; symmetry code: (iii) -x - 1, -y + 2, -z + 1].

Related literature top

For related structures, see, for example: Gotoh et al. (2009); Gotoh, Asaji & Ishida (2008); Gotoh, Nagoshi & Ishida (2008).

Experimental top

Single crystals were obtained by slow evaporation from an acetonitrile solution (120 ml) of chloranilic acid (250 mg) and pyridine-3-carbonitrile (250 mg) at room temperature.

Computing details top

Data collection: PROCESS-AUTO (Rigaku/MSC, 2004); cell refinement: PROCESS-AUTO (Rigaku/MSC, 2004); data reduction: CrystalStructure (Rigaku/MSC, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: CrystalStructure (Rigaku/MSC, 2004) and PLATON (Spek, 2009).

Figures top

	Fig. 1. The molecular structure of the title compound, with the atom-labeling. Displacement ellipsoids of non-H atoms are drawn at the 50% probability level. The dashed lines indicate O—H···O, O—H···N and C—H···N hydrogen bonds. [Symmetry code: (i) -x + 2, -y, -z].
	Fig. 2. A packing diagram of (I), showing a molecular tape running along the c axis. The dashed lines indicate O—H···O, O—H···N, C—H···N and C—H···O hydrogen bonds.

Pyridine-3-carbonitrile–chloranilic acid–acetonitrile (2/1/2) top

Crystal data top

2C₆H₄N₂·C₆H₂Cl₂O₄·2C₂H₃N	Z = 1
M_r = 499.31	F(000) = 256.00
Triclinic, P1	D_x = 1.483 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71075 Å
a = 3.91269 (16) Å	Cell parameters from 6412 reflections
b = 10.8937 (9) Å	θ = 3.1–30.1°
c = 13.5966 (5) Å	µ = 0.33 mm⁻¹
α = 105.302 (4)°	T = 180 K
β = 90.0058 (14)°	Block, brown
γ = 90.847 (5)°	0.32 × 0.25 × 0.15 mm
V = 558.93 (6) Å³

Data collection top

Rigaku RAXIS-RAPID II diffractometer	2592 reflections with I > 2σ(I)
Detector resolution: 10.00 pixels mm^-1	R_int = 0.031
ω scans	θ_max = 30.0°
Absorption correction: numerical (ABSCOR; Higashi, 1995)	h = −5→5
T_min = 0.906, T_max = 0.951	k = −15→15
7721 measured reflections	l = −19→17
3232 independent reflections

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)] = 0.035	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.099	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	w = 1/[σ²(F_o²) + (0.0495P)² + 0.1506P] where P = (F_o² + 2F_c²)/3
3232 reflections	(Δ/σ)_max < 0.001
159 parameters	Δρ_max = 0.44 e Å⁻³
0 restraints	Δρ_min = −0.28 e Å⁻³

Crystal data top

2C₆H₄N₂·C₆H₂Cl₂O₄·2C₂H₃N	γ = 90.847 (5)°
M_r = 499.31	V = 558.93 (6) Å³
Triclinic, P1	Z = 1
a = 3.91269 (16) Å	Mo Kα radiation
b = 10.8937 (9) Å	µ = 0.33 mm⁻¹
c = 13.5966 (5) Å	T = 180 K
α = 105.302 (4)°	0.32 × 0.25 × 0.15 mm
β = 90.0058 (14)°

Data collection top

Rigaku RAXIS-RAPID II diffractometer	3232 independent reflections
Absorption correction: numerical (ABSCOR; Higashi, 1995)	2592 reflections with I > 2σ(I)
T_min = 0.906, T_max = 0.951	R_int = 0.031
7721 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.035	0 restraints
wR(F²) = 0.099	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	Δρ_max = 0.44 e Å⁻³
3232 reflections	Δρ_min = −0.28 e Å⁻³
159 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
Cl1	0.74850 (9)	−0.11634 (3)	0.17747 (2)	0.02647 (10)
O1	1.1404 (3)	−0.24034 (9)	−0.00816 (7)	0.0278 (2)
O2	0.6357 (3)	0.14675 (10)	0.16065 (7)	0.0294 (2)
N1	0.4384 (3)	0.38133 (11)	0.18840 (9)	0.0268 (2)
N2	0.2005 (4)	0.63890 (12)	0.52232 (10)	0.0347 (3)
N3	−0.2867 (4)	0.85277 (13)	0.41743 (11)	0.0400 (3)
C1	1.0708 (3)	−0.12968 (12)	−0.00163 (9)	0.0213 (2)
C2	0.8789 (3)	−0.04984 (12)	0.08193 (9)	0.0208 (2)
C3	0.8076 (3)	0.07272 (12)	0.08605 (9)	0.0215 (2)
C4	0.3922 (4)	0.43073 (12)	0.28796 (10)	0.0254 (3)
H4	0.4423	0.3805	0.3335	0.031*
C5	0.2725 (3)	0.55390 (12)	0.32762 (10)	0.0233 (3)
C6	0.1973 (4)	0.62808 (13)	0.26185 (10)	0.0265 (3)
H6	0.1169	0.7124	0.2871	0.032*
C7	0.2431 (4)	0.57525 (13)	0.15812 (11)	0.0281 (3)
H7	0.1922	0.6227	0.1106	0.034*
C8	0.3640 (4)	0.45244 (13)	0.12482 (10)	0.0270 (3)
H8	0.3956	0.4171	0.0537	0.032*
C9	0.2324 (4)	0.60218 (13)	0.43620 (10)	0.0263 (3)
C10	−0.2753 (4)	0.87366 (14)	0.50394 (12)	0.0310 (3)
C11	−0.2586 (4)	0.90013 (16)	0.61421 (12)	0.0365 (3)
H11A	−0.0933	0.8436	0.6332	0.055*
H11B	−0.4846	0.8857	0.6406	0.055*
H11C	−0.1869	0.9889	0.6432	0.055*
H2	0.596 (7)	0.226 (3)	0.152 (2)	0.082 (9)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.03569 (18)	0.02348 (16)	0.02309 (16)	0.00415 (12)	0.00557 (12)	0.01100 (11)
O1	0.0404 (5)	0.0181 (4)	0.0255 (5)	0.0062 (4)	0.0045 (4)	0.0065 (4)
O2	0.0445 (6)	0.0199 (5)	0.0242 (5)	0.0089 (4)	0.0100 (4)	0.0058 (4)
N1	0.0349 (6)	0.0203 (5)	0.0252 (5)	0.0066 (4)	0.0041 (5)	0.0061 (4)
N2	0.0488 (8)	0.0284 (6)	0.0272 (6)	0.0078 (5)	0.0018 (5)	0.0075 (5)
N3	0.0512 (8)	0.0302 (7)	0.0380 (7)	0.0070 (6)	0.0065 (6)	0.0076 (5)
C1	0.0267 (6)	0.0180 (5)	0.0194 (5)	0.0010 (4)	−0.0019 (5)	0.0053 (4)
C2	0.0272 (6)	0.0186 (6)	0.0174 (5)	0.0009 (4)	0.0006 (5)	0.0060 (4)
C3	0.0268 (6)	0.0188 (6)	0.0188 (5)	0.0017 (4)	−0.0010 (5)	0.0045 (4)
C4	0.0321 (7)	0.0199 (6)	0.0254 (6)	0.0057 (5)	0.0015 (5)	0.0077 (5)
C5	0.0272 (6)	0.0199 (6)	0.0226 (6)	0.0024 (5)	0.0009 (5)	0.0049 (5)
C6	0.0327 (7)	0.0188 (6)	0.0286 (7)	0.0065 (5)	0.0026 (5)	0.0070 (5)
C7	0.0365 (7)	0.0238 (6)	0.0261 (6)	0.0066 (5)	0.0010 (5)	0.0100 (5)
C8	0.0348 (7)	0.0229 (6)	0.0235 (6)	0.0048 (5)	0.0036 (5)	0.0062 (5)
C9	0.0316 (7)	0.0205 (6)	0.0273 (6)	0.0052 (5)	0.0015 (5)	0.0067 (5)
C10	0.0307 (7)	0.0227 (6)	0.0387 (8)	0.0033 (5)	0.0063 (6)	0.0061 (5)
C11	0.0407 (8)	0.0335 (8)	0.0329 (8)	0.0040 (6)	0.0042 (6)	0.0044 (6)

Geometric parameters (Å, º) top

Cl1—C2	1.7200 (13)	C4—H4	0.9500
O1—C1	1.2201 (15)	C5—C6	1.3884 (18)
O2—C3	1.3099 (15)	C5—C9	1.4399 (18)
O2—H2	0.91 (3)	C6—C7	1.3883 (19)
N1—C4	1.3316 (17)	C6—H6	0.9500
N1—C8	1.3387 (18)	C7—C8	1.3848 (19)
N2—C9	1.1406 (18)	C7—H7	0.9500
N3—C10	1.138 (2)	C8—H8	0.9500
C1—C2	1.4521 (17)	C10—C11	1.451 (2)
C1—C3ⁱ	1.5153 (18)	C11—H11A	0.9800
C2—C3	1.3546 (17)	C11—H11B	0.9800
C3—C1ⁱ	1.5153 (18)	C11—H11C	0.9800
C4—C5	1.3955 (18)

C3—O2—H2	114.0 (17)	C7—C6—C5	117.96 (12)
C4—N1—C8	118.49 (11)	C7—C6—H6	121.0
O1—C1—C2	123.93 (12)	C5—C6—H6	121.0
O1—C1—C3ⁱ	117.75 (11)	C8—C7—C6	119.07 (12)
C2—C1—C3ⁱ	118.31 (10)	C8—C7—H7	120.5
C3—C2—C1	121.90 (11)	C6—C7—H7	120.5
C3—C2—Cl1	120.77 (10)	N1—C8—C7	122.88 (13)
C1—C2—Cl1	117.33 (9)	N1—C8—H8	118.6
O2—C3—C2	123.08 (12)	C7—C8—H8	118.6
O2—C3—C1ⁱ	117.14 (11)	N2—C9—C5	179.14 (15)
C2—C3—C1ⁱ	119.78 (11)	N3—C10—C11	179.69 (18)
N1—C4—C5	122.13 (12)	C10—C11—H11A	109.5
N1—C4—H4	118.9	C10—C11—H11B	109.5
C5—C4—H4	118.9	H11A—C11—H11B	109.5
C6—C5—C4	119.46 (12)	C10—C11—H11C	109.5
C6—C5—C9	121.20 (12)	H11A—C11—H11C	109.5
C4—C5—C9	119.34 (12)	H11B—C11—H11C	109.5

O1—C1—C2—C3	179.96 (13)	C8—N1—C4—C5	−0.6 (2)
C3ⁱ—C1—C2—C3	−0.1 (2)	N1—C4—C5—C6	0.2 (2)
O1—C1—C2—Cl1	0.78 (18)	N1—C4—C5—C9	−179.19 (13)
C3ⁱ—C1—C2—Cl1	−179.23 (9)	C4—C5—C6—C7	0.4 (2)
C1—C2—C3—O2	−179.86 (12)	C9—C5—C6—C7	179.82 (13)
Cl1—C2—C3—O2	−0.72 (19)	C5—C6—C7—C8	−0.6 (2)
C1—C2—C3—C1ⁱ	0.1 (2)	C4—N1—C8—C7	0.4 (2)
Cl1—C2—C3—C1ⁱ	179.21 (9)	C6—C7—C8—N1	0.3 (2)

Symmetry code: (i) −x+2, −y, −z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2···N1	0.92 (3)	1.75 (3)	2.6111 (17)	154 (3)
O2—H2···O1ⁱ	0.92 (3)	2.25 (3)	2.6824 (14)	108 (2)
C4—H4···N2ⁱⁱ	0.95	2.46	3.292 (2)	146
C6—H6···N3	0.95	2.57	3.385 (2)	144
C7—H7···O1ⁱⁱⁱ	0.95	2.48	3.4248 (18)	172
C11—H11A···N2	0.98	2.62	3.341 (2)	130

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

Experimental details

Crystal data
Chemical formula	2C₆H₄N₂·C₆H₂Cl₂O₄·2C₂H₃N
M_r	499.31
Crystal system, space group	Triclinic, P1
Temperature (K)	180
a, b, c (Å)	3.91269 (16), 10.8937 (9), 13.5966 (5)
α, β, γ (°)	105.302 (4), 90.0058 (14), 90.847 (5)
V (Å³)	558.93 (6)
Z	1
Radiation type	Mo Kα
µ (mm⁻¹)	0.33
Crystal size (mm)	0.32 × 0.25 × 0.15

Data collection
Diffractometer	Rigaku RAXIS-RAPID II diffractometer
Absorption correction	Numerical (ABSCOR; Higashi, 1995)
T_min, T_max	0.906, 0.951
No. of measured, independent and observed [I > 2σ(I)] reflections	7721, 3232, 2592
R_int	0.031
(sin θ/λ)_max (Å⁻¹)	0.704

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.035, 0.099, 1.07
No. of reflections	3232
No. of parameters	159
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.44, −0.28

Computer programs: PROCESS-AUTO (Rigaku/MSC, 2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997), CrystalStructure (Rigaku/MSC, 2004) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2···N1	0.92 (3)	1.75 (3)	2.6111 (17)	154 (3)
O2—H2···O1ⁱ	0.92 (3)	2.25 (3)	2.6824 (14)	108 (2)
C4—H4···N2ⁱⁱ	0.95	2.46	3.292 (2)	146
C6—H6···N3	0.95	2.57	3.385 (2)	144
C7—H7···O1ⁱⁱⁱ	0.95	2.48	3.4248 (18)	172
C11—H11A···N2	0.98	2.62	3.341 (2)	130

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

Acknowledgements

This work was supported by a Grant-in-Aid for Scientific Research (C) (No. 19550018) from the Japanese Society for the Promotion of Science.

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