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Acta Cryst. (2011). E67, o2558    [ doi:10.1107/S1600536811034982 ]

2,2'-Bipyrimidine-1,1'-diium bis(triiodide)-2,2'-bipyrimidine-water (1/2/2)

K. Ha

Abstract top

In the crystal of the title compound, C8H8N42+·2I3-·2C8H6N4·2H2O, inversion centres are located at the centroids of the central C-C bonds of the cation and the bpym molecules, as well as at the central I atoms of both anions. Intermolecular O-H...N and N-H...O hydrogen bonds are observed in the crystal structure.

Comment top

The title compound, (C8H8N4)2+(I3-)2.2C8H6N4 × 2 H2O, consists of a diprotonated 2,2'-bipyrimidinium cation, two discrete I3- anions, two 2,2'-bipyrimidine (bpym) and two water solvent molecules (Fig. 1). Single crystals of the compound were unexpectedly obtained as a byproduct from the reaction of MnI2 with 2,2'-bipyrimidine (Ha, 2011), and the structure is related to that of the compounds (C8H8N4)[ReCl6].2H2O (Kochel, 2005) and (C10H9N2)(I3) (Fialho De Assis et al., 1996).

The asymmetric unit contains one half of the formula unit. Inversion centres are located at the centroids of the central carbon carbon bond of the cation and the bpym molecules. Therefore the two pyrimidine rings in each moiety are exactly parallel. The central I atoms (I1 and I3) of the anions also occupy crystallographic inversion centres: the anions are linear and the I—I distances are almost equal. Intermolecular O—H···N and N—H···O hydrogen bonds stabilize the crystal structure and the cation reveals short intramolecular N—H···N hydrogen bonds (Fig. 2 and Table 1). Moreover, there are weak intermolecular π-π interactions between pyrimidine rings, with a shortest ring centroid-centroid distance of 5.239 (6) Å.

Related literature top

For related structures, see: Fialho De Assis et al. (1996); Kochel (2005). For the synthesis and crystal structure of [Mn(C8H6N4)3](I3)2.CH3NO2, see: Ha (2011).

Experimental top

The title compound was unexpectedly obtained as a byproduct from the reaction of MnI2 (0.3086 g, 1.000 mmol) with 2,2'-bipyrimidine (0.1588 g, 1.004 mmol) in acetone (30 ml). After stirring of the reaction mixture for 3 h at room temperature and addition of pentane (30 ml), the formed precipitate was separated by filtration, washed with EtOH and ether, to give a brown powder (0.3621 g) (Ha, 2011). Single crystals of the title compound suitable for X-ray analysis were obtained by slow evaporation from the brown filtrate.

Refinement top

H atoms at nitrogen were observed in the Fourier maps but were nevertheless as H atoms at carbon positioned geometrically and allowed to ride on their respective parent atoms [C—H = 0.95 Å (CH) or 0.88 Å (NH) and Uiso(H) = 1.2Ueq(C, N)]. The H atoms of the solvent water molecules were located from the difference Fourier map then allowed to ride on their parent O atoms in the final cycles of refinement with O—H = 0.84 Å and Uiso(H) = 1.5 Ueq(O). The highest peak (1.29 e Å-3) and the deepest hole (-1.67 e Å-3) in the difference Fourier map are located 1.38 Å and 0.93 Å from the atoms I2 and I1, respectively.

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as small circles of arbitrary radius. Unlabelled atoms are generated by the application of the inversion centres.
[Figure 2] Fig. 2. View of the unit-cell contents of the title compound. Hydrogen-bond interactions are drawn with dashed lines.
2,2'-Bipyrimidine-1,1'-diium bis(triiodide)–2,2'-bipyrimidine–water (1/2/2) top
Crystal data top
C8H8N42+·2I3·2C8H6N4·2H2OZ = 1
Mr = 1273.95F(000) = 586
Triclinic, P1Dx = 2.321 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 8.964 (2) ÅCell parameters from 3632 reflections
b = 9.013 (2) Åθ = 2.4–25.9°
c = 12.112 (3) ŵ = 5.15 mm1
α = 77.265 (5)°T = 200 K
β = 76.881 (5)°Block, redbrown
γ = 76.287 (4)°0.35 × 0.21 × 0.16 mm
V = 911.3 (4) Å3
Data collection top
Bruker SMART 1000 CCD
diffractometer
3505 independent reflections
Radiation source: fine-focus sealed tube2993 reflections with I > 2σ(I)
graphiteRint = 0.018
φ and ω scansθmax = 26.0°, θmin = 2.4°
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
h = 1011
Tmin = 0.769, Tmax = 1.000k = 1111
5688 measured reflectionsl = 1314
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.053Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.132H-atom parameters constrained
S = 1.31 w = 1/[σ2(Fo2) + (0.0114P)2 + 14.2699P]
where P = (Fo2 + 2Fc2)/3
3505 reflections(Δ/σ)max < 0.001
202 parametersΔρmax = 1.29 e Å3
0 restraintsΔρmin = 1.67 e Å3
Crystal data top
C8H8N42+·2I3·2C8H6N4·2H2Oγ = 76.287 (4)°
Mr = 1273.95V = 911.3 (4) Å3
Triclinic, P1Z = 1
a = 8.964 (2) ÅMo Kα radiation
b = 9.013 (2) ŵ = 5.15 mm1
c = 12.112 (3) ÅT = 200 K
α = 77.265 (5)°0.35 × 0.21 × 0.16 mm
β = 76.881 (5)°
Data collection top
Bruker SMART 1000 CCD
diffractometer
3505 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
2993 reflections with I > 2σ(I)
Tmin = 0.769, Tmax = 1.000Rint = 0.018
5688 measured reflectionsθmax = 26.0°
Refinement top
R[F2 > 2σ(F2)] = 0.053 w = 1/[σ2(Fo2) + (0.0114P)2 + 14.2699P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.132Δρmax = 1.29 e Å3
S = 1.31Δρmin = 1.67 e Å3
3505 reflectionsAbsolute structure: ?
202 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
H-atom parameters constrained
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
xyzUiso*/Ueq
I11.00000.00000.00000.0408 (3)
I20.74916 (11)0.26620 (10)0.03957 (9)0.0590 (3)
I30.00000.50000.50000.0465 (3)
I40.11198 (10)0.59729 (11)0.67614 (7)0.0543 (3)
N10.3970 (10)0.1722 (10)0.0778 (7)0.0340 (19)
H1N0.44760.16410.14820.041*
N20.3607 (9)0.0652 (9)0.1209 (7)0.0281 (18)
N30.4427 (9)0.6152 (9)0.3680 (7)0.0273 (17)
N40.4734 (10)0.3448 (10)0.4394 (7)0.0324 (19)
N50.1907 (9)0.0208 (9)0.5125 (7)0.0293 (18)
N60.0604 (10)0.0811 (10)0.6308 (7)0.0327 (19)
C10.2819 (12)0.2904 (12)0.0578 (9)0.033 (2)
H10.25500.36890.12070.040*
C20.1989 (12)0.3036 (12)0.0521 (9)0.035 (2)
H20.11680.38950.06640.042*
C30.2421 (12)0.1847 (12)0.1401 (9)0.035 (2)
H30.18590.18800.21650.042*
C40.4339 (11)0.0663 (11)0.0113 (9)0.028 (2)
C50.4007 (12)0.5968 (13)0.2747 (8)0.033 (2)
H50.37290.68500.21840.039*
C60.3968 (13)0.4517 (14)0.2580 (9)0.041 (3)
H60.36980.43700.19030.049*
C70.4334 (14)0.3302 (13)0.3431 (10)0.042 (3)
H70.43030.22920.33350.051*
C80.4744 (11)0.4879 (11)0.4473 (8)0.026 (2)
C90.2583 (12)0.0653 (12)0.5860 (9)0.035 (2)
H90.36790.06070.57010.042*
C100.1691 (12)0.1169 (12)0.6831 (8)0.033 (2)
H100.21590.14370.73710.040*
C110.0077 (13)0.1291 (13)0.7005 (8)0.035 (2)
H110.05620.17290.76410.043*
C120.0361 (12)0.0280 (11)0.5389 (8)0.029 (2)
O10.5739 (8)0.0741 (8)0.6568 (6)0.0321 (16)
H1A0.57050.17000.64720.048*
H1B0.62490.01750.70610.048*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
I10.0539 (7)0.0402 (6)0.0341 (5)0.0204 (5)0.0139 (5)0.0004 (4)
I20.0621 (6)0.0466 (5)0.0748 (7)0.0098 (4)0.0217 (5)0.0159 (4)
I30.0351 (6)0.0436 (6)0.0406 (6)0.0054 (4)0.0029 (4)0.0102 (5)
I40.0437 (5)0.0571 (5)0.0466 (5)0.0078 (4)0.0030 (4)0.0018 (4)
N10.035 (5)0.032 (5)0.031 (5)0.003 (4)0.007 (4)0.001 (4)
N20.029 (4)0.028 (4)0.023 (4)0.006 (3)0.002 (3)0.002 (3)
N30.022 (4)0.030 (4)0.027 (4)0.000 (3)0.005 (3)0.005 (3)
N40.041 (5)0.026 (4)0.033 (5)0.005 (4)0.013 (4)0.008 (4)
N50.024 (4)0.027 (4)0.031 (4)0.004 (3)0.004 (3)0.005 (3)
N60.027 (4)0.043 (5)0.023 (4)0.007 (4)0.006 (3)0.006 (4)
C10.038 (6)0.027 (5)0.030 (5)0.008 (4)0.014 (4)0.013 (4)
C20.033 (5)0.026 (5)0.043 (6)0.001 (4)0.009 (5)0.005 (4)
C30.035 (6)0.034 (6)0.036 (6)0.011 (5)0.001 (4)0.009 (5)
C40.027 (5)0.027 (5)0.034 (5)0.012 (4)0.013 (4)0.001 (4)
C50.036 (6)0.042 (6)0.024 (5)0.013 (5)0.013 (4)0.000 (4)
C60.044 (7)0.054 (7)0.030 (6)0.013 (5)0.009 (5)0.015 (5)
C70.050 (7)0.035 (6)0.046 (7)0.016 (5)0.009 (5)0.008 (5)
C80.027 (5)0.025 (5)0.022 (5)0.004 (4)0.005 (4)0.000 (4)
C90.031 (5)0.042 (6)0.037 (6)0.010 (5)0.019 (5)0.002 (5)
C100.038 (6)0.044 (6)0.021 (5)0.013 (5)0.013 (4)0.001 (4)
C110.040 (6)0.050 (7)0.016 (5)0.001 (5)0.009 (4)0.010 (4)
C120.042 (6)0.025 (5)0.016 (4)0.010 (4)0.009 (4)0.009 (4)
O10.042 (4)0.028 (4)0.025 (4)0.010 (3)0.011 (3)0.004 (3)
Geometric parameters (Å, °) top
I1—I22.9158 (10)C2—C31.386 (15)
I1—I2i2.9158 (10)C2—H20.9500
I3—I42.9226 (11)C3—H30.9500
I3—I4ii2.9226 (11)C4—C4iii1.49 (2)
N1—C11.319 (13)C5—C61.376 (15)
N1—C41.320 (12)C5—H50.9500
N1—H1N0.8800C6—C71.363 (16)
N2—C41.339 (13)C6—H60.9500
N2—C31.342 (13)C7—H70.9500
N3—C51.324 (12)C8—C8iv1.525 (18)
N3—C81.342 (12)C9—C101.370 (15)
N4—C81.316 (12)C9—H90.9500
N4—C71.336 (14)C10—C111.395 (15)
N5—C121.339 (13)C10—H100.9500
N5—C91.355 (13)C11—H110.9500
N6—C111.339 (13)C12—C12v1.484 (19)
N6—C121.348 (13)O1—H1A0.8400
C1—C21.385 (15)O1—H1B0.8400
C1—H10.9500
I2—I1—I2i180.00 (3)C6—C5—H5119.5
I4—I3—I4ii180.0C7—C6—C5116.9 (10)
C1—N1—C4117.8 (9)C7—C6—H6121.5
C1—N1—H1N121.1C5—C6—H6121.5
C4—N1—H1N121.1N4—C7—C6123.8 (10)
C4—N2—C3116.1 (8)N4—C7—H7118.1
C5—N3—C8117.3 (9)C6—C7—H7118.1
C8—N4—C7114.8 (9)N4—C8—N3126.2 (9)
C12—N5—C9117.8 (9)N4—C8—C8iv117.6 (10)
C11—N6—C12115.7 (9)N3—C8—C8iv116.1 (10)
N1—C1—C2121.9 (9)N5—C9—C10120.3 (9)
N1—C1—H1119.0N5—C9—H9119.9
C2—C1—H1119.0C10—C9—H9119.9
C1—C2—C3116.5 (10)C9—C10—C11118.1 (9)
C1—C2—H2121.8C9—C10—H10121.0
C3—C2—H2121.8C11—C10—H10121.0
N2—C3—C2122.0 (10)N6—C11—C10122.3 (9)
N2—C3—H3119.0N6—C11—H11118.9
C2—C3—H3119.0C10—C11—H11118.9
N1—C4—N2125.6 (9)N5—C12—N6125.6 (9)
N1—C4—C4iii117.7 (11)N5—C12—C12v117.6 (11)
N2—C4—C4iii116.6 (10)N6—C12—C12v116.8 (11)
N3—C5—C6120.9 (10)H1A—O1—H1B116.6
N3—C5—H5119.5
C4—N1—C1—C21.3 (15)C7—N4—C8—N31.5 (15)
N1—C1—C2—C30.8 (16)C7—N4—C8—C8iv177.5 (11)
C4—N2—C3—C20.8 (14)C5—N3—C8—N42.7 (15)
C1—C2—C3—N21.8 (16)C5—N3—C8—C8iv178.8 (10)
C1—N1—C4—N22.5 (15)C12—N5—C9—C100.5 (14)
C1—N1—C4—C4iii179.0 (10)N5—C9—C10—C113.0 (15)
C3—N2—C4—N11.5 (14)C12—N6—C11—C103.5 (15)
C3—N2—C4—C4iii179.9 (10)C9—C10—C11—N65.2 (16)
C8—N3—C5—C62.8 (15)C9—N5—C12—N62.4 (14)
N3—C5—C6—C71.9 (16)C9—N5—C12—C12v177.1 (10)
C8—N4—C7—C60.4 (16)C11—N6—C12—N50.4 (14)
C5—C6—C7—N40.6 (18)C11—N6—C12—C12v179.1 (10)
Symmetry codes: (i) −x+2, −y, −z; (ii) −x, −y+1, −z+1; (iii) −x+1, −y, −z; (iv) −x+1, −y+1, −z+1; (v) −x, −y, −z+1.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···N3iv0.841.882.721 (11)178.
O1—H1B···N2vi0.842.092.837 (10)149.
N1—H1N···O1vii0.882.593.450 (11)166.
Symmetry codes: (iv) −x+1, −y+1, −z+1; (vi) −x+1, −y, −z+1; (vii) x, y, z−1.
Table 1
Hydrogen-bond geometry (Å, °)
top
D—H···AD—HH···AD···AD—H···A
O1—H1A···N3i0.841.882.721 (11)178.
O1—H1B···N2ii0.842.092.837 (10)149.
N1—H1N···O1iii0.882.593.450 (11)166.
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+1, −y, −z+1; (iii) x, y, z−1.
Acknowledgements top

This work was supported by the Priority Research Centers Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (2010–0029626).

references
References top

Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.

Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.

Fialho De Assis, E., Howie, R. A. & Wardell, J. L. (1996). Acta Cryst. C52, 955–957.

Ha, K. (2011). Z. Kristallogr. New Cryst. Struct. 226, 365–367.

Kochel, A. (2005). Acta Cryst. E61, m759–m760.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Spek, A. L. (2009). Acta Cryst. D65, 148–155.