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Acta Crystallogr Sect E Struct Rep Online. 2008 January 1; 64(Pt 1): m77.
Published online 2007 December 6. doi:  10.1107/S1600536807063258
PMCID: PMC2914955

Diaqua­bis(pyrimidine-2-carboxylic acid-κ2 N,O)cobalt(II) dichloride

Abstract

In the title salt, [Co(C5H4N2O2)2(H2O)2]Cl2, the CoII ion is located on an inversion center. It is chelated by two neutral pyrimidine-2-carboxylic acid molecules and is coordinated by two water mol­ecules in an octa­hedral coordination geometry. The cations and anions are linked via O—H(...)Cl hydrogen bonds into a layer structure; an intra­molecular O—H(...)N hydrogen bond connects the carboxylic acid group to the pyrimidine N atom.

Related literature

For general background, see: Cheng et al. (2000 [triangle]); Wu et al. (2003 [triangle]). For related structures, see: Rodriquez-Dieguez et al. (2007 [triangle]); Zhang et al. (2008 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-00m77-scheme1.jpg

Experimental

Crystal data

  • [Co(C5H4N2O2)2(H2O)2]Cl2
  • M r = 414.07
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-00m77-efi1.jpg
  • a = 6.2803 (8) Å
  • b = 10.361 (2) Å
  • c = 11.906 (2) Å
  • β = 95.254 (15)°
  • V = 771.5 (2) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 1.49 mm−1
  • T = 293 (2) K
  • 0.25 × 0.12 × 0.10 mm

Data collection

  • Rigaku R-AXIS RAPID IP diffractometer
  • Absorption correction: multi-scan (ABSCOR; Higashi, 1995 [triangle]) T min = 0.726, T max = 0.862
  • 7413 measured reflections
  • 1763 independent reflections
  • 1178 reflections with I > 2σ(I)
  • R int = 0.052

Refinement

  • R[F 2 > 2σ(F 2)] = 0.040
  • wR(F 2) = 0.119
  • S = 1.12
  • 1763 reflections
  • 107 parameters
  • H-atom parameters constrained
  • Δρmax = 0.70 e Å−3
  • Δρmin = −0.72 e Å−3

Data collection: PROCESS-AUTO (Rigaku, 1998 [triangle]); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002 [triangle]); program(s) used to solve structure: SIR92 (Altomare et al., 1993 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Selected geometric parameters (Å, °)
Table 2
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536807063258/ng2402sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536807063258/ng2402Isup2.hkl

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

Acknowledgments

The work was supported by the ZIJIN project of Zhejiang University, China.

supplementary crystallographic information

Comment

As part of our ongoing investigation on the nature of aromatic stacking (Cheng et al., 2000; Wu et al., 2003), the title CoII compound has recently been prepared and its crystal structure is presented here.

The molecular structure of the title compound is shown in Fig. 1. The crystal of the title compound consists of complex cations and Cl- anions. The CoII located on an inversion center is coordinated by two neutral pyrimidine-2-carboxylic acid and two water molecules with an octahedral geometry (Table 1). The Cl- anions link with the complex cations via O—H···Cl hydrogen bonding (Table 2 and Fig. 1). The charge balance indicates that the pyrimidine-2-carboxylic acid is a neutral ligand but not an anion; and the significant difference in C—O bond distances (Table 1) also suggests that the carboxyl group is not deprotonated. This is obviously owing to the acidified solution environment in the preparation of the compound (see _publ_section_exptl_prep). The intra-molecular O—H···N hydrogen bonding exsits between the carboxyl group and adjacent pyrimidine-N atom (Fig. 1). Thus the pyrimidine-2-carboxylic acid can not play a role of bridge ligand in this structure, contrast to that found in pyrimidine-2-carboxylate complex of Co(II) reported previously (Rodriquez-Dieguez et al., 2007).

π-π stacking is not observed in this crystal structure, which is different from the situation in a related CuII complex with pyrimidine-2-carboxylate (Zhang et al., 2008). It may be due to extensive hydrogen bonding network involving coordinated water molecules and counter Cl- anions.

Experimental

2-Cyanopyrimidine (0.19 g, 1.8 mmol), CoCl2.6(H2O) (0.24 g, 1 mmol) were dissolved in a mixture solution of water (15 ml) and ethanol (5 ml), then hydrochloric acid solution (3 ml, 37%) was added into the solution. The solution was refluxed for 5 h. Single crystals of the title compound were obtained after about one month.

Refinement

Hydroxy and water H atoms were located in a difference Fourier map and refined as riding in as-found relative positions, with Uiso(H) = 1.5Ueq(O). Other H atoms were placed in calculated positions with C—H = 0.93 Å and refined in riding mode with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The molecular structure of the title compound with 30% probability displacement (arbitrary spheres for H atoms), dashed lines indicate hydrogen bonding [symmetry codes: (i) 1 - x,1 - y,1 - z].

Crystal data

[Co(C5H4N2O2)2(H2O)2]Cl2F000 = 418
Mr = 414.07Dx = 1.782 Mg m3
Monoclinic, P21/nMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 2668 reflections
a = 6.2803 (8) Åθ = 3.5–24.5º
b = 10.361 (2) ŵ = 1.49 mm1
c = 11.906 (2) ÅT = 293 (2) K
β = 95.254 (15)ºPrism, pink
V = 771.5 (2) Å30.25 × 0.12 × 0.10 mm
Z = 2

Data collection

Rigaku R-AXIS RAPID IP diffractometer1763 independent reflections
Radiation source: fine-focus sealed tube1178 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.052
Detector resolution: 10.0 pixels mm-1θmax = 27.4º
T = 291(2) Kθmin = 3.4º
ω scansh = −8→8
Absorption correction: multi-scan(ABSCOR; Higashi, 1995)k = −12→13
Tmin = 0.726, Tmax = 0.862l = −15→15
7413 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.040H-atom parameters constrained
wR(F2) = 0.119  w = 1/[σ2(Fo2) + (0.0359P)2 + 1.9784P] where P = (Fo2 + 2Fc2)/3
S = 1.12(Δ/σ)max < 0.001
1763 reflectionsΔρmax = 0.70 e Å3
107 parametersΔρmin = −0.72 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

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
Co0.50000.50000.50000.0257 (2)
Cl10.83609 (17)0.85016 (10)0.65401 (9)0.0367 (3)
N10.6455 (5)0.6498 (3)0.4186 (3)0.0250 (7)
N20.5891 (6)0.8696 (3)0.3695 (3)0.0340 (8)
O10.3012 (4)0.6537 (3)0.5310 (2)0.0329 (7)
O20.2425 (6)0.8657 (3)0.4995 (3)0.0541 (9)
H20.29930.92470.46740.081*
O30.7051 (5)0.5443 (3)0.6466 (3)0.0397 (7)
H3A0.70180.49510.71420.060*
H3B0.76420.62880.66490.060*
C10.3501 (6)0.7589 (3)0.4885 (3)0.0268 (8)
C20.5395 (6)0.7618 (4)0.4203 (3)0.0258 (8)
C30.7628 (8)0.8641 (5)0.3124 (4)0.0415 (11)
H30.80270.93740.27460.050*
C40.8852 (7)0.7540 (4)0.3075 (4)0.0381 (10)
H41.00580.75240.26770.046*
C50.8217 (6)0.6467 (4)0.3637 (3)0.0323 (9)
H50.90210.57130.36350.039*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Co0.0300 (4)0.0184 (4)0.0294 (4)0.0009 (3)0.0068 (3)0.0022 (3)
Cl10.0399 (6)0.0365 (6)0.0339 (6)−0.0014 (5)0.0045 (4)−0.0036 (4)
N10.0274 (16)0.0192 (15)0.0289 (17)−0.0015 (14)0.0056 (13)−0.0003 (13)
N20.0376 (19)0.0261 (18)0.039 (2)−0.0039 (16)0.0045 (16)0.0076 (15)
O10.0352 (15)0.0248 (14)0.0410 (17)0.0033 (13)0.0157 (13)0.0007 (13)
O20.058 (2)0.0387 (19)0.067 (3)0.0051 (18)0.0102 (19)−0.0011 (18)
O30.0529 (19)0.0332 (16)0.0317 (16)−0.0045 (15)−0.0028 (14)0.0010 (13)
C10.030 (2)0.0167 (17)0.034 (2)0.0004 (16)0.0038 (17)−0.0033 (16)
C20.031 (2)0.0210 (18)0.025 (2)−0.0024 (17)0.0017 (16)0.0000 (15)
C30.047 (3)0.037 (2)0.041 (3)−0.010 (2)0.007 (2)0.014 (2)
C40.037 (2)0.042 (3)0.037 (2)−0.007 (2)0.0124 (19)0.005 (2)
C50.028 (2)0.036 (2)0.033 (2)0.0004 (19)0.0047 (17)−0.0040 (18)

Geometric parameters (Å, °)

Co—O12.077 (3)O2—C11.309 (5)
Co—O1i2.077 (3)O2—H20.8200
Co—O3i2.123 (3)O3—H3A0.9545
Co—O32.123 (3)O3—H3B0.9674
Co—N1i2.085 (3)C1—C21.501 (5)
Co—N12.085 (3)C3—C41.379 (7)
N1—C51.337 (5)C3—H30.9300
N1—C21.338 (5)C4—C51.375 (6)
N2—C21.321 (5)C4—H40.9300
N2—C31.338 (6)C5—H50.9300
O1—C11.252 (5)
O1—Co—O1i180.00 (16)C1—O2—H2109.5
O1—Co—N1i101.08 (11)Co—O3—H3A121.3
O1i—Co—N1i78.92 (11)Co—O3—H3B124.9
O1—Co—N178.92 (11)H3A—O3—H3B109.3
O1i—Co—N1101.08 (11)O1—C1—O2123.2 (4)
N1i—Co—N1180.00 (11)O1—C1—C2118.2 (3)
O1—Co—O3i88.99 (12)O2—C1—C2118.6 (3)
O1i—Co—O3i91.01 (12)N2—C2—N1126.0 (4)
N1i—Co—O3i87.84 (12)N2—C2—C1119.7 (3)
N1—Co—O3i92.16 (12)N1—C2—C1114.3 (3)
O1—Co—O391.01 (12)N2—C3—C4122.7 (4)
O1i—Co—O388.99 (12)N2—C3—H3118.6
N1i—Co—O392.16 (12)C4—C3—H3118.6
N1—Co—O387.84 (12)C5—C4—C3117.4 (4)
O3i—Co—O3180.000 (1)C5—C4—H4121.3
C5—N1—C2117.6 (3)C3—C4—H4121.3
C5—N1—Co128.8 (3)N1—C5—C4120.5 (4)
C2—N1—Co113.5 (2)N1—C5—H5119.7
C2—N2—C3115.7 (4)C4—C5—H5119.7
C1—O1—Co115.0 (2)

Symmetry codes: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O2—H2···N20.822.322.784 (5)116
O3—H3A···Cl1ii0.952.203.140 (4)168
O3—H3B···Cl10.972.343.273 (3)161
C4—H4···Cl1iii0.932.793.670 (5)159

Symmetry codes: (ii) −x+3/2, y−1/2, −z+3/2; (iii) x+1/2, −y+3/2, z−1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: NG2402).

References

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  • Higashi, T. (1995). ABSCOR Rigaku Corporation, Tokyo, Japan.
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  • Rigaku/MSC (2002). CrystalStructure Version 3.00. Rigaku/MSC, The Woodlands, Texas, USA.
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Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography