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Acta Crystallogr Sect E Struct Rep Online. 2009 October 1; 65(Pt 10): o2467.
Published online 2009 September 16. doi:  10.1107/S1600536809036605
PMCID: PMC2970440

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

Abstract

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 [triangle]); Gotoh, Asaji & Ishida (2008 [triangle]); Gotoh, Nagoshi & Ishida (2008 [triangle]).

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Object name is e-65-o2467-scheme1.jpg

Experimental

Crystal data

  • 2C6H4N2·C6H2Cl2O4·2C2H3N
  • M r = 499.31
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2467-efi1.jpg
  • 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 [triangle]) 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[F 2 > 2σ(F 2)] = 0.035
  • wR(F 2) = 0.099
  • S = 1.07
  • 3232 reflections
  • 159 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.44 e Å−3
  • Δρmin = −0.28 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

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

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

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

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

supplementary crystallographic information

Comment

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[equivalent]N bonds of acetonitrile molecules is observed [C10···C10iii 3.314 Å; symmetry code: (iii) -x - 1, -y + 2, -z + 1].

Experimental

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.

Refinement

C-bound H atoms were positioned geometrically (C—H = 0.95 or 0.98 Å) and refined as riding, allowing for free rotation of the methyl group. Uiso(H) values were set at 1.2Ueq(C) or 1.5Ueq(methyl C). The O-bound H atom was found in a difference Fourier map and refined isotropically. The refined O—H distance is 0.92 (3) Å.

Figures

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 ...
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 ...

Crystal data

2C6H4N2·C6H2Cl2O4·2C2H3NZ = 1
Mr = 499.31F(000) = 256.00
Triclinic, P1Dx = 1.483 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71075 Å
a = 3.91269 (16) ÅCell parameters from 6412 reflections
b = 10.8937 (9) Åθ = 3.1–30.1°
c = 13.5966 (5) ŵ = 0.33 mm1
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

Rigaku RAXIS-RAPID II diffractometer2592 reflections with I > 2σ(I)
Detector resolution: 10.00 pixels mm-1Rint = 0.031
ω scansθmax = 30.0°
Absorption correction: numerical (ABSCOR; Higashi, 1995)h = −5→5
Tmin = 0.906, Tmax = 0.951k = −15→15
7721 measured reflectionsl = −19→17
3232 independent reflections

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.099H atoms treated by a mixture of independent and constrained refinement
S = 1.07w = 1/[σ2(Fo2) + (0.0495P)2 + 0.1506P] where P = (Fo2 + 2Fc2)/3
3232 reflections(Δ/σ)max < 0.001
159 parametersΔρmax = 0.44 e Å3
0 restraintsΔρmin = −0.28 e Å3

Special details

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)

xyzUiso*/Ueq
Cl10.74850 (9)−0.11634 (3)0.17747 (2)0.02647 (10)
O11.1404 (3)−0.24034 (9)−0.00816 (7)0.0278 (2)
O20.6357 (3)0.14675 (10)0.16065 (7)0.0294 (2)
N10.4384 (3)0.38133 (11)0.18840 (9)0.0268 (2)
N20.2005 (4)0.63890 (12)0.52232 (10)0.0347 (3)
N3−0.2867 (4)0.85277 (13)0.41743 (11)0.0400 (3)
C11.0708 (3)−0.12968 (12)−0.00163 (9)0.0213 (2)
C20.8789 (3)−0.04984 (12)0.08193 (9)0.0208 (2)
C30.8076 (3)0.07272 (12)0.08605 (9)0.0215 (2)
C40.3922 (4)0.43073 (12)0.28796 (10)0.0254 (3)
H40.44230.38050.33350.031*
C50.2725 (3)0.55390 (12)0.32762 (10)0.0233 (3)
C60.1973 (4)0.62808 (13)0.26185 (10)0.0265 (3)
H60.11690.71240.28710.032*
C70.2431 (4)0.57525 (13)0.15812 (11)0.0281 (3)
H70.19220.62270.11060.034*
C80.3640 (4)0.45244 (13)0.12482 (10)0.0270 (3)
H80.39560.41710.05370.032*
C90.2324 (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−0.09330.84360.63320.055*
H11B−0.48460.88570.64060.055*
H11C−0.18690.98890.64320.055*
H20.596 (7)0.226 (3)0.152 (2)0.082 (9)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.03569 (18)0.02348 (16)0.02309 (16)0.00415 (12)0.00557 (12)0.01100 (11)
O10.0404 (5)0.0181 (4)0.0255 (5)0.0062 (4)0.0045 (4)0.0065 (4)
O20.0445 (6)0.0199 (5)0.0242 (5)0.0089 (4)0.0100 (4)0.0058 (4)
N10.0349 (6)0.0203 (5)0.0252 (5)0.0066 (4)0.0041 (5)0.0061 (4)
N20.0488 (8)0.0284 (6)0.0272 (6)0.0078 (5)0.0018 (5)0.0075 (5)
N30.0512 (8)0.0302 (7)0.0380 (7)0.0070 (6)0.0065 (6)0.0076 (5)
C10.0267 (6)0.0180 (5)0.0194 (5)0.0010 (4)−0.0019 (5)0.0053 (4)
C20.0272 (6)0.0186 (6)0.0174 (5)0.0009 (4)0.0006 (5)0.0060 (4)
C30.0268 (6)0.0188 (6)0.0188 (5)0.0017 (4)−0.0010 (5)0.0045 (4)
C40.0321 (7)0.0199 (6)0.0254 (6)0.0057 (5)0.0015 (5)0.0077 (5)
C50.0272 (6)0.0199 (6)0.0226 (6)0.0024 (5)0.0009 (5)0.0049 (5)
C60.0327 (7)0.0188 (6)0.0286 (7)0.0065 (5)0.0026 (5)0.0070 (5)
C70.0365 (7)0.0238 (6)0.0261 (6)0.0066 (5)0.0010 (5)0.0100 (5)
C80.0348 (7)0.0229 (6)0.0235 (6)0.0048 (5)0.0036 (5)0.0062 (5)
C90.0316 (7)0.0205 (6)0.0273 (6)0.0052 (5)0.0015 (5)0.0067 (5)
C100.0307 (7)0.0227 (6)0.0387 (8)0.0033 (5)0.0063 (6)0.0061 (5)
C110.0407 (8)0.0335 (8)0.0329 (8)0.0040 (6)0.0042 (6)0.0044 (6)

Geometric parameters (Å, °)

Cl1—C21.7200 (13)C4—H40.9500
O1—C11.2201 (15)C5—C61.3884 (18)
O2—C31.3099 (15)C5—C91.4399 (18)
O2—H20.91 (3)C6—C71.3883 (19)
N1—C41.3316 (17)C6—H60.9500
N1—C81.3387 (18)C7—C81.3848 (19)
N2—C91.1406 (18)C7—H70.9500
N3—C101.138 (2)C8—H80.9500
C1—C21.4521 (17)C10—C111.451 (2)
C1—C3i1.5153 (18)C11—H11A0.9800
C2—C31.3546 (17)C11—H11B0.9800
C3—C1i1.5153 (18)C11—H11C0.9800
C4—C51.3955 (18)
C3—O2—H2114.0 (17)C7—C6—C5117.96 (12)
C4—N1—C8118.49 (11)C7—C6—H6121.0
O1—C1—C2123.93 (12)C5—C6—H6121.0
O1—C1—C3i117.75 (11)C8—C7—C6119.07 (12)
C2—C1—C3i118.31 (10)C8—C7—H7120.5
C3—C2—C1121.90 (11)C6—C7—H7120.5
C3—C2—Cl1120.77 (10)N1—C8—C7122.88 (13)
C1—C2—Cl1117.33 (9)N1—C8—H8118.6
O2—C3—C2123.08 (12)C7—C8—H8118.6
O2—C3—C1i117.14 (11)N2—C9—C5179.14 (15)
C2—C3—C1i119.78 (11)N3—C10—C11179.69 (18)
N1—C4—C5122.13 (12)C10—C11—H11A109.5
N1—C4—H4118.9C10—C11—H11B109.5
C5—C4—H4118.9H11A—C11—H11B109.5
C6—C5—C4119.46 (12)C10—C11—H11C109.5
C6—C5—C9121.20 (12)H11A—C11—H11C109.5
C4—C5—C9119.34 (12)H11B—C11—H11C109.5
O1—C1—C2—C3179.96 (13)C8—N1—C4—C5−0.6 (2)
C3i—C1—C2—C3−0.1 (2)N1—C4—C5—C60.2 (2)
O1—C1—C2—Cl10.78 (18)N1—C4—C5—C9−179.19 (13)
C3i—C1—C2—Cl1−179.23 (9)C4—C5—C6—C70.4 (2)
C1—C2—C3—O2−179.86 (12)C9—C5—C6—C7179.82 (13)
Cl1—C2—C3—O2−0.72 (19)C5—C6—C7—C8−0.6 (2)
C1—C2—C3—C1i0.1 (2)C4—N1—C8—C70.4 (2)
Cl1—C2—C3—C1i179.21 (9)C6—C7—C8—N10.3 (2)

Symmetry codes: (i) −x+2, −y, −z.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O2—H2···N10.92 (3)1.75 (3)2.6111 (17)154 (3)
O2—H2···O1i0.92 (3)2.25 (3)2.6824 (14)108 (2)
C4—H4···N2ii0.952.463.292 (2)146
C6—H6···N30.952.573.385 (2)144
C7—H7···O1iii0.952.483.4248 (18)172
C11—H11A···N20.982.623.341 (2)130

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH2901).

References

  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Gotoh, K., Asaji, T. & Ishida, H. (2008). Acta Cryst. C64, o550–o553. [PubMed]
  • Gotoh, K., Nagoshi, H. & Ishida, H. (2008). Acta Cryst. E64, o1260. [PMC free article] [PubMed]
  • Gotoh, K., Nagoshi, H. & Ishida, H. (2009). Acta Cryst. C65, o273–o277. [PubMed]
  • Higashi, T. (1995). ABSCOR Rigaku Corporation, Tokyo, Japan.
  • Rigaku/MSC. (2004). PROCESS-AUTO and CrystalStructure Rigaku/MSC Inc., The Woodlands, Texas, USA.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]

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