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Acta Crystallogr Sect E Struct Rep Online. 2009 September 1; 65(Pt 9): o2203.
Published online 2009 August 22. doi:  10.1107/S1600536809032528
PMCID: PMC2969923

6,12-Dihydro­dipyrido[1,2-a:1′,2′-d]pyrazinium bis­(perchlorate)

Abstract

In the title compound, C12H12N2 2+·2ClO4 , the dihedral angle between the two outer pyridine rings of the dication is 44.8 (1)°. In the crystal, weak intermolecular C—H(...)O hydrogen bonds occur.

Related literature

For the crystal structure of (C12H12N2)Br2, see: Bryce et al. (1985 [triangle]). For a MNDO (modified neglect of diatomic overlap) study of dipyridopyrazinium and related cations, see: Eaves et al. (1986 [triangle]).

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Object name is e-65-o2203-scheme1.jpg

Experimental

Crystal data

  • C12H12N2 2+·2ClO4
  • M r = 383.14
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2203-efi1.jpg
  • a = 8.1632 (8) Å
  • b = 13.9396 (14) Å
  • c = 13.5903 (13) Å
  • β = 96.023 (2)°
  • V = 1537.9 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.47 mm−1
  • T = 296 K
  • 0.22 × 0.16 × 0.10 mm

Data collection

  • Bruker SMART 1000 CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2000 [triangle]) T min = 0.646, T max = 0.954
  • 11269 measured reflections
  • 3809 independent reflections
  • 1871 reflections with I > 2σ(I)
  • R int = 0.068

Refinement

  • R[F 2 > 2σ(F 2)] = 0.058
  • wR(F 2) = 0.163
  • S = 1.06
  • 3809 reflections
  • 217 parameters
  • H-atom parameters constrained
  • Δρmax = 0.39 e Å−3
  • Δρmin = −0.48 e Å−3

Data collection: SMART (Bruker, 2000 [triangle]); cell refinement: SAINT (Bruker, 2000 [triangle]); data reduction: SAINT; 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]) and PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809032528/om2266sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809032528/om2266Isup2.hkl

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

Acknowledgments

This work was supported by the Korea Research Foundation Grant funded by the Korean Government (MOEHRD) (KRF-2007–412-J02001).

supplementary crystallographic information

Comment

The asymmetric unit of the title compound, C12H12N22+.2ClO4-, consists of a 6,12-dihydrodipyrido[1,2-a:1',2'-d]pyrazinium dication and two perchlorate counter-anions (Fig. 1). In the dication, two pyridine rings are linked by two methylene groups and the bridgehead N atoms are disposed on the opposite side of the central six-membered ring which adopts an eclipsed boat conforamtion. The two methylene C atoms (C6 and C12) lie practically on the pyridine ring planes with the largest deviations 0.046 (6) Å (C6) and 0.023 (6) Å (C12) from the respective least-squares planes, and the dihedral angles between these planes is 44.8 (1)°. The geometry of the ClO4- anions is nearly tetrahedral with the O—Cl—O bond angles of 107.4 (2)°–112.5 (2)°, and the Cl—O bond distances are almost equal (1.416 (3)–1.426 (3) Å). The compound displays intermolecular C—H···O hydrogen bonds (Table 1 and Fig. 2). There may also be weak intermolecular π-π interactions between adjacent pyridine rings, with a shortest centroid-centroid distance of 5.057 (2) Å.

Experimental

Single crystals of the title compound were unexpectedly obtained as a byproduct of an attempted preparation of an Mn(II) complex by reacting 2-(chloromethyl)pyridine hydrochloride (0.99 g, 6.04 mmol), 1,6-diaminohexane (0.17 g, 1.46 mmol), NaOH (for adjustment of pH 7–8) and Mn(ClO4)2.6H2O (0.37 g, 1.02 mmol) in EtOH (10 ml) and H2O (5 ml) for 2 h at 60 °C. Crystals suitable for X-ray analysis were obtained by slow evaporation from a CH3CN solution of the orange reaction product.

Refinement

H atoms were positioned geometrically and allowed to ride on their respective carrier atoms [C—H = 0.93 (sp2) or 0.97 Å (sp3) and Uiso(H) = 1.2Ueq(C)].

Figures

Fig. 1.
The structure of the title compound, with displacement ellipsoids drawn at the 30% probability level for non-H atoms.
Fig. 2.
View of the unit-cell contents of the title compound. Hydrogen-bond interactions are drawn with dashed lines.

Crystal data

C12H12N22+·2ClO4F(000) = 784
Mr = 383.14Dx = 1.655 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2227 reflections
a = 8.1632 (8) Åθ = 2.5–23.7°
b = 13.9396 (14) ŵ = 0.47 mm1
c = 13.5903 (13) ÅT = 296 K
β = 96.023 (2)°Block, colorless
V = 1537.9 (3) Å30.22 × 0.16 × 0.10 mm
Z = 4

Data collection

Bruker SMART 1000 CCD diffractometer3809 independent reflections
Radiation source: fine-focus sealed tube1871 reflections with I > 2σ(I)
graphiteRint = 0.068
[var phi] and ω scansθmax = 28.3°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2000)h = −10→10
Tmin = 0.646, Tmax = 0.954k = −18→16
11269 measured reflectionsl = −15→18

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)] = 0.058Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.163H-atom parameters constrained
S = 1.06w = 1/[σ2(Fo2) + (0.0561P)2 + 0.3329P] where P = (Fo2 + 2Fc2)/3
3809 reflections(Δ/σ)max < 0.001
217 parametersΔρmax = 0.39 e Å3
0 restraintsΔρmin = −0.48 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
N10.4245 (4)0.3340 (2)0.2124 (2)0.0413 (8)
N20.1643 (4)0.4419 (2)0.2709 (2)0.0424 (8)
C10.5777 (5)0.3093 (3)0.1934 (3)0.0512 (11)
H10.65170.28400.24350.061*
C20.6240 (6)0.3214 (3)0.1007 (3)0.0592 (12)
H20.72840.30250.08670.071*
C30.5151 (6)0.3618 (3)0.0275 (3)0.0584 (12)
H30.54650.3718−0.03560.070*
C40.3592 (5)0.3872 (3)0.0490 (3)0.0518 (11)
H40.28490.41440.00040.062*
C50.3140 (4)0.3723 (2)0.1422 (3)0.0360 (8)
C60.1484 (5)0.3943 (3)0.1727 (3)0.0486 (10)
H6A0.08920.43590.12400.058*
H6B0.08600.33530.17590.058*
C70.0714 (5)0.5186 (3)0.2886 (3)0.0528 (11)
H7−0.00360.54280.23860.063*
C80.0869 (6)0.5607 (3)0.3796 (3)0.0607 (12)
H80.02350.61400.39190.073*
C90.1978 (5)0.5233 (3)0.4535 (3)0.0582 (12)
H90.20830.55050.51630.070*
C100.2924 (5)0.4459 (3)0.4336 (3)0.0497 (10)
H100.36850.42110.48280.060*
C110.2753 (4)0.4047 (2)0.3413 (2)0.0334 (8)
C120.3709 (5)0.3198 (3)0.3127 (3)0.0444 (10)
H12A0.46670.31070.36040.053*
H12B0.30310.26270.31300.053*
Cl10.93531 (13)0.21962 (7)0.40847 (7)0.0483 (3)
O10.7805 (4)0.2646 (2)0.4167 (2)0.0735 (9)
O21.0582 (4)0.2624 (3)0.4763 (3)0.1006 (13)
O30.9764 (4)0.2311 (2)0.3100 (2)0.0798 (10)
O40.9247 (4)0.1204 (2)0.4313 (2)0.0759 (10)
Cl20.38056 (13)0.06673 (7)0.22970 (8)0.0508 (3)
O50.5488 (4)0.0854 (3)0.2602 (3)0.0955 (12)
O60.2971 (4)0.0624 (3)0.3163 (2)0.0988 (13)
O70.3618 (4)−0.0210 (2)0.1771 (2)0.0821 (11)
O80.3058 (5)0.1403 (2)0.1684 (2)0.0844 (11)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.047 (2)0.0404 (18)0.0363 (17)−0.0034 (15)0.0031 (15)−0.0021 (14)
N20.0370 (18)0.053 (2)0.0378 (17)−0.0020 (15)0.0059 (15)0.0048 (15)
C10.048 (3)0.052 (3)0.054 (3)0.0070 (19)0.006 (2)−0.007 (2)
C20.054 (3)0.078 (3)0.048 (3)0.002 (2)0.020 (2)−0.012 (2)
C30.065 (3)0.068 (3)0.044 (2)−0.011 (2)0.014 (2)−0.011 (2)
C40.063 (3)0.060 (3)0.031 (2)−0.009 (2)0.000 (2)0.0016 (19)
C50.038 (2)0.040 (2)0.0285 (18)−0.0069 (17)0.0014 (16)−0.0012 (15)
C60.048 (3)0.061 (3)0.036 (2)−0.006 (2)−0.0005 (19)−0.0014 (19)
C70.044 (3)0.062 (3)0.053 (3)0.015 (2)0.010 (2)0.009 (2)
C80.065 (3)0.059 (3)0.061 (3)0.018 (2)0.021 (3)−0.003 (2)
C90.067 (3)0.065 (3)0.044 (2)−0.001 (2)0.015 (2)−0.007 (2)
C100.057 (3)0.057 (3)0.034 (2)0.004 (2)0.0051 (19)−0.0004 (19)
C110.034 (2)0.0347 (19)0.0311 (18)−0.0020 (15)0.0029 (16)0.0035 (15)
C120.054 (3)0.044 (2)0.035 (2)0.0008 (19)0.0062 (19)0.0034 (17)
Cl10.0477 (6)0.0519 (6)0.0458 (6)0.0002 (5)0.0080 (5)−0.0004 (5)
O10.062 (2)0.088 (2)0.073 (2)0.0230 (18)0.0171 (17)0.0126 (18)
O20.086 (3)0.098 (3)0.108 (3)−0.009 (2)−0.035 (2)−0.029 (2)
O30.103 (3)0.083 (2)0.061 (2)−0.001 (2)0.046 (2)0.0076 (18)
O40.106 (3)0.0527 (19)0.071 (2)0.0025 (18)0.020 (2)0.0110 (16)
Cl20.0563 (7)0.0471 (6)0.0472 (6)0.0066 (5)−0.0020 (5)−0.0077 (5)
O50.055 (2)0.120 (3)0.107 (3)−0.005 (2)−0.015 (2)−0.016 (2)
O60.085 (3)0.166 (4)0.048 (2)0.000 (2)0.0160 (19)−0.012 (2)
O70.117 (3)0.0503 (19)0.072 (2)0.0157 (18)−0.021 (2)−0.0168 (16)
O80.120 (3)0.0476 (18)0.078 (2)0.0072 (18)−0.026 (2)0.0011 (16)

Geometric parameters (Å, °)

N1—C11.348 (5)C7—H70.9300
N1—C51.352 (4)C8—C91.382 (6)
N1—C121.488 (4)C8—H80.9300
N2—C71.346 (5)C9—C101.370 (5)
N2—C111.351 (4)C9—H90.9300
N2—C61.484 (5)C10—C111.372 (5)
C1—C21.364 (6)C10—H100.9300
C1—H10.9300C11—C121.492 (5)
C2—C31.383 (6)C12—H12A0.9700
C2—H20.9300C12—H12B0.9700
C3—C41.382 (6)Cl1—O21.420 (3)
C3—H30.9300Cl1—O41.421 (3)
C4—C51.371 (5)Cl1—O31.423 (3)
C4—H40.9300Cl1—O11.426 (3)
C5—C61.487 (5)Cl2—O51.416 (3)
C6—H6A0.9700Cl2—O71.417 (3)
C6—H6B0.9700Cl2—O81.418 (3)
C7—C81.363 (6)Cl2—O61.421 (3)
C1—N1—C5122.0 (3)C7—C8—C9119.2 (4)
C1—N1—C12120.6 (3)C7—C8—H8120.4
C5—N1—C12117.4 (3)C9—C8—H8120.4
C7—N2—C11121.7 (3)C10—C9—C8119.6 (4)
C7—N2—C6121.3 (3)C10—C9—H9120.2
C11—N2—C6117.0 (3)C8—C9—H9120.2
N1—C1—C2119.8 (4)C9—C10—C11120.3 (4)
N1—C1—H1120.1C9—C10—H10119.9
C2—C1—H1120.1C11—C10—H10119.9
C1—C2—C3119.7 (4)N2—C11—C10118.9 (3)
C1—C2—H2120.1N2—C11—C12116.7 (3)
C3—C2—H2120.1C10—C11—C12124.4 (3)
C4—C3—C2119.3 (4)N1—C12—C11110.2 (3)
C4—C3—H3120.4N1—C12—H12A109.6
C2—C3—H3120.4C11—C12—H12A109.6
C5—C4—C3120.0 (4)N1—C12—H12B109.6
C5—C4—H4120.0C11—C12—H12B109.6
C3—C4—H4120.0H12A—C12—H12B108.1
N1—C5—C4119.2 (3)O2—Cl1—O4108.8 (2)
N1—C5—C6116.3 (3)O2—Cl1—O3110.1 (2)
C4—C5—C6124.5 (4)O4—Cl1—O3109.87 (19)
N2—C6—C5110.3 (3)O2—Cl1—O1109.6 (2)
N2—C6—H6A109.6O4—Cl1—O1109.6 (2)
C5—C6—H6A109.6O3—Cl1—O1108.8 (2)
N2—C6—H6B109.6O5—Cl2—O7110.9 (2)
C5—C6—H6B109.6O5—Cl2—O8112.5 (2)
H6A—C6—H6B108.1O7—Cl2—O8108.15 (19)
N2—C7—C8120.3 (4)O5—Cl2—O6107.4 (2)
N2—C7—H7119.8O7—Cl2—O6110.2 (2)
C8—C7—H7119.8O8—Cl2—O6107.6 (2)
C5—N1—C1—C2−1.1 (6)C11—N2—C7—C8−0.4 (6)
C12—N1—C1—C2179.0 (3)C6—N2—C7—C8179.4 (4)
N1—C1—C2—C32.1 (6)N2—C7—C8—C9−0.5 (6)
C1—C2—C3—C4−1.6 (6)C7—C8—C9—C101.2 (6)
C2—C3—C4—C50.1 (6)C8—C9—C10—C11−1.1 (6)
C1—N1—C5—C4−0.5 (5)C7—N2—C11—C100.5 (5)
C12—N1—C5—C4179.5 (3)C6—N2—C11—C10−179.2 (3)
C1—N1—C5—C6178.8 (3)C7—N2—C11—C12−179.9 (3)
C12—N1—C5—C6−1.3 (5)C6—N2—C11—C120.3 (4)
C3—C4—C5—N10.9 (6)C9—C10—C11—N20.2 (6)
C3—C4—C5—C6−178.2 (4)C9—C10—C11—C12−179.3 (4)
C7—N2—C6—C5136.2 (4)C1—N1—C12—C11137.8 (3)
C11—N2—C6—C5−44.1 (4)C5—N1—C12—C11−42.2 (4)
N1—C5—C6—N244.5 (4)N2—C11—C12—N142.6 (4)
C4—C5—C6—N2−136.4 (4)C10—C11—C12—N1−137.9 (4)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C1—H1···O10.932.493.358 (6)156
C2—H2···O1i0.932.573.160 (5)122
C4—H4···O6i0.932.543.228 (5)132
C6—H6B···O3ii0.972.563.343 (5)137
C7—H7···O6iii0.932.453.249 (5)144
C9—H9···O7iv0.932.443.190 (5)138

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: OM2266).

References

  • Bruker (2000). SADABS, SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Bryce, M. R., Eaves, J. G., Parker, D., Howard, J. A. K. & Johnson, O. (1985). J. Chem. Soc. Perkin Trans. 2, pp. 433–436.
  • Eaves, J. G., Parker, D. & Rudgewick-Brown, N. (1986). Can. J. Chem.64, 1711–1713.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • 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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