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Acta Crystallogr Sect E Struct Rep Online. 2010 October 1; 66(Pt 10): m1320–m1321.
Published online 2010 September 30. doi:  10.1107/S1600536810037736
PMCID: PMC2983271

Bis(2-amino-4-methyl­pyrimidin-3-ium) trans-diaqua­bis­(pyrazine-2,3-di­car­boxylato)cobaltate(II) hexa­hydrate

Abstract

In the crystal structure of the mononuclear title compound, (C5H8N3)2[Co(C6H2N2O4)2(H2O)2]·6H2O or (ampymH)2[Co(pyzdc)2(H2O)2]·6H2O (ampym = 2-amino-4-methyl pyrimidine, pyzdcH2 = pyrazine-2,3-dicarb­oxy­lic acid), the CoII ion is hexa­coordinated by two (pyzdc)2− groups in the equatorial plane and two water mol­ecules in axial positions, giving an N2CoO4 bound set. The (pyzdc)2− anion acts as a bidentate ligand through one carboxyl­ate group O atom and pyrazine ring N atom. There are diverse N—H(...) O and O—H(...)O and O—H(...)N hydrogen-bonding inter­actions, which lead to the formation of a three-dimensional supra­molecular architecture. Off-set or slipped π–π stacking inter­actions are also observed between adjacent pyrimidine rings with face-to-face distances of 3.6337 (9) Å.

Related literature

For the pyzdcH2 ligand, see: Aghabozorg et al. (2008 [triangle]). For the crystal structure of pyrazine-2,3-dicarb­oxy­lic acid (pyzdcH2), see: Takusagawa & Shimada (1973 [triangle]). For complexes of pyzdcH2 with zinc and manganese, see: Eshtiagh-Hosseini et al. (2010a [triangle],b [triangle],c [triangle],d [triangle],e [triangle]). The six uncoordinated water mol­ecules increase the number of hydrogen bonds and lead to the formation of (H2O)n clusters throughout the crystal, see: Aghabozorg et al. (2010 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-m1320-scheme1.jpg

Experimental

Crystal data

  • (C5H8N3)2[Co(C6H2N2O4)2(H2O)2]·6H2O
  • M r = 755.54
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-m1320-efi3.jpg
  • a = 6.5880 (4) Å
  • b = 8.0591 (5) Å
  • c = 15.0285 (8) Å
  • α = 98.085 (5)°
  • β = 96.940 (4)°
  • γ = 91.261 (5)°
  • V = 783.58 (8) Å3
  • Z = 1
  • Mo Kα radiation
  • μ = 0.64 mm−1
  • T = 120 K
  • 0.40 × 0.40 × 0.20 mm

Data collection

  • Oxford Diffraction Xcalibur diffractometer with Sapphire2 detector
  • Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2009 [triangle]) T min = 0.903, T max = 1.000
  • 5733 measured reflections
  • 2758 independent reflections
  • 2428 reflections with I > 2σ(I)
  • R int = 0.011

Refinement

  • R[F 2 > 2σ(F 2)] = 0.025
  • wR(F 2) = 0.064
  • S = 1.04
  • 2758 reflections
  • 256 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.30 e Å−3
  • Δρmin = −0.40 e Å−3

Data collection: CrysAlis CCD (Oxford Diffraction, 2009 [triangle]); cell refinement: CrysAlis RED (Oxford Diffraction, 2009 [triangle]); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: DIAMOND (Crystal Impact, 2009 [triangle]); software used to prepare material for publication: publCIF (Westrip, 2010 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, New_Global_Publ_Block. DOI: 10.1107/S1600536810037736/vm2043sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810037736/vm2043Isup2.hkl

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

Acknowledgments

The Ferdowsi University of Mashhad and Masaryk University are gratefully acknowledged by the authors.

supplementary crystallographic information

Comment

Many organic aromatic ligands and metal ions may aggregate into supramolecular networks using coordination and hydrogen bonds and π –π stacking interactions. Metal pyrazine-(di)carboxylates may possess versatile structural motifs, which finally aggregate to various supramolecular architectures with interesting properties. For the first time, Takusagawa & Shimada (1973) determined the structure of pyzdcH2. Until now, several proton transfer compounds with pyzdcH2 have been synthesized by our research group such as, (ampyH)2[M(pyzdc)2(H2O)2].6H2O (M = Co (1), Cu, Zn and ampy = 2-amino-4-methyl pyridine) (Eshtiagh-Hosseini et al., 2010b,cd). Continuing our previous work on the syntheses of coordination compounds via proton transfer mechanism, we planned the reaction between pyzdcH2, ampym and cobaltII chloride in order to provide a new coordination compound containing a proton transfer ligand. The title compound, (ampymH)2[Co(pyzdcH)2(H2O)2].6H2O, is analogous to previously synthesized compound 1 in which ampy was replaced by ampym (Fig. 1). The equatorial plane is occupied by two (pyzdc)2- ligands coordinating through the pyrazine nitrogen and one oxygen of the deprotonated carboxylate groups. The two coordinated water molecules occupy the axial plane. This compound consists of an anionic moiety, trans-[Co(pyzdc)2(H2O)2]2- complex, counter-ions, (ampymH)+, and six uncoordinated water molecules. The Co—O and Co—N bond distances related to the (pyzdc)2- ligand are 2.0445 (12) Å, and 2.1086 (14) Å, respectively. The intermolecular forces between the anionic, cationic parts, and uncoordinated water molecules consist of hydrogen bonding interactions. The hydrogen bond interactions cause further stabilization for crystalline network using two types of graph-sets namely R22(8) and R46(12) (Fig. 2). Indeed, the arrangement of anionic parts in the network resulted in the creation of anionic holes for entering cationic parts; this arrangement results in off-set or slipped π -π stacking interactions with the distance of 3.6337 (9) Å between the centroids of the rings (Fig. 3). Moreover, six uncoordinated water molecules increase the number of hydrogen bonds in the crystalline network and lead to the formation of (H2O)n clusters throughout the crystalline network (Aghabozorg et al. 2010).

Experimental

A solution of pyzdcH2 (0.60 mmol, 0.10 g), ampym (1.2 mmol, 0.13 g), and CoCl2.6H2O (0.02 mmol, 0.05 g) at 333 K lead to formation of (ampymH)2[Co(pyzdc)2(H2O)2].6H2O orange block crystals after slow evaporation of solvent at room temperature.

Refinement

Carbon and nitrogen bound hydrogen atoms were positioned geometrically and refined as riding using standard SHELXTL constraints, with their Uiso set to either 1.2Ueq or 1.5Ueq (methyl) of their parent atoms. The C-H distances were set to 0.95 and 0.98 \%A for aromatic and methyl groups, respectively, the N-H distances used were 0.88 \%A. Oxygen bound hydrogen atoms were located in a difference Fourier map and refined isotropically.

Figures

Fig. 1.
Molecular structure of (ampymH)2[Co(pyzdc)2(H2O)2].6H2O compound. Ellipsoids are drawn at the 50% probability level.
Fig. 2.
Schematic representation of the present R22(8) and R46(12) graph-sets in the crystalline network.
Fig. 3.
(a) Packing diagram along the a-axis. (b) The off-set or slipped π -π stacking interactions between aromatic rings of two (ampymH)+ fragments.

Crystal data

(C5H8N3)2[Co(C6H2N2O4)2(H2O)2]·6H2OZ = 1
Mr = 755.54F(000) = 393
Triclinic, P1Dx = 1.601 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.5880 (4) ÅCell parameters from 4417 reflections
b = 8.0591 (5) Åθ = 3.1–27.6°
c = 15.0285 (8) ŵ = 0.64 mm1
α = 98.085 (5)°T = 120 K
β = 96.940 (4)°Plate, pale orange
γ = 91.261 (5)°0.40 × 0.40 × 0.20 mm
V = 783.58 (8) Å3

Data collection

Oxford Diffraction Xcalibur diffractometer with Sapphire2 (large Be window) detector2758 independent reflections
Radiation source: Enhance (Mo) X-ray Source2428 reflections with I > 2σ(I)
graphiteRint = 0.011
Detector resolution: 8.4353 pixels mm-1θmax = 25.0°, θmin = 3.1°
ω scanh = −7→7
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2009)k = −9→9
Tmin = 0.903, Tmax = 1.000l = −17→17
5733 measured 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)] = 0.025Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.064H atoms treated by a mixture of independent and constrained refinement
S = 1.04w = 1/[σ2(Fo2) + (0.0279P)2 + 0.458P] where P = (Fo2 + 2Fc2)/3
2758 reflections(Δ/σ)max < 0.001
256 parametersΔρmax = 0.30 e Å3
0 restraintsΔρmin = −0.40 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
Co20.50000.50000.50000.01426 (11)
O10.58615 (17)0.62856 (14)0.25548 (7)0.0143 (3)
O20.62546 (18)0.51362 (15)0.38308 (8)0.0167 (3)
O30.33723 (18)0.93937 (14)0.19964 (8)0.0163 (3)
O40.17222 (18)0.69382 (14)0.14483 (8)0.0144 (3)
O50.6551 (2)0.72932 (17)0.55885 (9)0.0201 (3)
H5A0.572 (4)0.793 (3)0.5817 (18)0.053 (8)*
H5B0.748 (4)0.733 (3)0.5952 (17)0.037 (8)*
N10.0477 (2)0.84612 (18)0.33031 (9)0.0150 (3)
N20.2829 (2)0.64620 (17)0.43486 (9)0.0136 (3)
N30.7241 (2)0.96452 (17)−0.03740 (9)0.0115 (3)
H3A0.71421.0023−0.08980.014*
N40.7962 (2)1.02237 (18)0.12227 (9)0.0142 (3)
N50.8275 (2)1.23050 (17)0.03349 (9)0.0132 (3)
H5C0.86541.30240.08270.016*
H5D0.81931.2640−0.02010.016*
C10.3367 (2)0.6769 (2)0.35513 (11)0.0111 (3)
C20.2154 (3)0.7745 (2)0.30243 (11)0.0114 (3)
C3−0.0026 (3)0.8140 (2)0.40958 (11)0.0154 (4)
H3−0.12120.86190.43110.018*
C40.1129 (3)0.7127 (2)0.46163 (11)0.0150 (4)
H40.07040.69030.51710.018*
C50.5328 (2)0.6005 (2)0.32850 (11)0.0115 (4)
C60.2498 (2)0.8028 (2)0.20784 (11)0.0123 (4)
C70.7832 (2)1.0727 (2)0.03993 (11)0.0115 (4)
C80.7472 (3)0.8626 (2)0.12403 (12)0.0157 (4)
H80.75180.82510.18140.019*
C90.6893 (3)0.7459 (2)0.04676 (12)0.0158 (4)
H90.65720.63220.05140.019*
C100.6801 (2)0.7997 (2)−0.03562 (12)0.0133 (4)
C110.6237 (3)0.6941 (2)−0.12543 (12)0.0174 (4)
H11A0.73090.7070−0.16410.026*
H11B0.49360.7298−0.15420.026*
H11C0.60960.5762−0.11700.026*
O210.9070 (2)0.46146 (16)0.19544 (9)0.0162 (3)
O220.9951 (2)0.2292 (2)0.31495 (9)0.0216 (3)
O230.6098 (2)0.07554 (19)0.35418 (10)0.0228 (3)
H21A0.809 (4)0.516 (3)0.2147 (16)0.039 (7)*
H21B0.987 (4)0.530 (3)0.1837 (15)0.030 (6)*
H22A1.001 (4)0.142 (4)0.2846 (18)0.054 (9)*
H22B0.973 (4)0.300 (3)0.2803 (18)0.049 (8)*
H23A0.708 (4)0.136 (3)0.3438 (17)0.048 (8)*
H23B0.544 (4)0.039 (3)0.3088 (19)0.049 (9)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Co20.01444 (19)0.0194 (2)0.01064 (18)0.00400 (14)0.00278 (13)0.00658 (13)
O10.0159 (6)0.0177 (6)0.0109 (6)0.0020 (5)0.0042 (5)0.0054 (5)
O20.0164 (6)0.0223 (7)0.0138 (6)0.0075 (5)0.0041 (5)0.0085 (5)
O30.0210 (7)0.0146 (6)0.0137 (6)−0.0042 (5)−0.0001 (5)0.0054 (5)
O40.0175 (6)0.0148 (6)0.0108 (6)−0.0018 (5)0.0004 (5)0.0026 (5)
O50.0173 (7)0.0245 (8)0.0181 (7)0.0034 (6)0.0006 (6)0.0024 (6)
N10.0146 (7)0.0163 (8)0.0137 (7)0.0023 (6)0.0008 (6)0.0018 (6)
N20.0142 (7)0.0164 (8)0.0105 (7)0.0000 (6)0.0017 (6)0.0027 (6)
N30.0122 (7)0.0132 (7)0.0100 (7)0.0011 (6)0.0021 (6)0.0040 (6)
N40.0136 (7)0.0171 (8)0.0127 (7)0.0004 (6)0.0016 (6)0.0054 (6)
N50.0172 (8)0.0141 (8)0.0083 (7)−0.0014 (6)0.0001 (6)0.0030 (6)
C10.0128 (8)0.0110 (8)0.0095 (8)−0.0017 (6)0.0006 (7)0.0019 (6)
C20.0127 (8)0.0095 (8)0.0112 (8)−0.0025 (6)0.0005 (7)0.0003 (6)
C30.0141 (9)0.0179 (9)0.0139 (9)0.0023 (7)0.0028 (7)0.0002 (7)
C40.0153 (9)0.0193 (9)0.0109 (8)0.0003 (7)0.0042 (7)0.0018 (7)
C50.0128 (8)0.0101 (8)0.0113 (9)−0.0009 (7)0.0003 (7)0.0011 (7)
C60.0104 (8)0.0145 (9)0.0130 (9)0.0041 (7)0.0011 (7)0.0050 (7)
C70.0067 (8)0.0162 (9)0.0120 (8)0.0019 (7)0.0019 (7)0.0028 (7)
C80.0110 (8)0.0228 (10)0.0156 (9)0.0029 (7)0.0022 (7)0.0102 (7)
C90.0130 (9)0.0140 (9)0.0217 (10)0.0004 (7)0.0023 (7)0.0071 (7)
C100.0075 (8)0.0145 (9)0.0182 (9)0.0014 (7)0.0027 (7)0.0027 (7)
C110.0189 (9)0.0145 (9)0.0185 (9)0.0009 (7)0.0032 (7)0.0006 (7)
O210.0162 (7)0.0146 (7)0.0184 (7)−0.0007 (6)0.0054 (5)0.0013 (5)
O220.0257 (8)0.0183 (7)0.0198 (7)0.0030 (6)0.0000 (6)0.0018 (6)
O230.0199 (8)0.0266 (8)0.0198 (8)−0.0015 (6)0.0007 (6)−0.0016 (6)

Geometric parameters (Å, °)

Co2—O2i2.0455 (12)N5—H5C0.8800
Co2—O22.0455 (12)N5—H5D0.8800
Co2—N2i2.1101 (14)C1—C21.390 (2)
Co2—N22.1101 (14)C1—C51.517 (2)
Co2—O5i2.1167 (14)C2—C61.513 (2)
Co2—O52.1167 (14)C3—C41.386 (2)
O1—C51.240 (2)C3—H30.9500
O2—C51.263 (2)C4—H40.9500
O3—C61.259 (2)C8—C91.396 (2)
O4—C61.249 (2)C8—H80.9500
O5—H5A0.83 (3)C9—C101.363 (2)
O5—H5B0.77 (3)C9—H90.9500
N1—C31.332 (2)C10—C111.492 (2)
N1—C21.342 (2)C11—H11A0.9800
N2—C41.334 (2)C11—H11B0.9800
N2—C11.343 (2)C11—H11C0.9800
N3—C101.358 (2)O21—H21A0.85 (3)
N3—C71.361 (2)O21—H21B0.81 (2)
N3—H3A0.8800O22—H22A0.79 (3)
N4—C81.325 (2)O22—H22B0.83 (3)
N4—C71.349 (2)O23—H23A0.85 (3)
N5—C71.318 (2)O23—H23B0.78 (3)
O2i—Co2—O2180.0C1—C2—C6124.49 (15)
O2i—Co2—N2i80.00 (5)N1—C3—C4121.94 (16)
O2—Co2—N2i100.00 (5)N1—C3—H3119.0
O2i—Co2—N2100.00 (5)C4—C3—H3119.0
O2—Co2—N280.00 (5)N2—C4—C3120.86 (16)
N2i—Co2—N2180.000 (1)N2—C4—H4119.6
O2i—Co2—O5i89.61 (5)C3—C4—H4119.6
O2—Co2—O5i90.39 (5)O1—C5—O2126.40 (15)
N2i—Co2—O5i86.62 (6)O1—C5—C1117.16 (14)
N2—Co2—O5i93.38 (6)O2—C5—C1116.44 (14)
O2i—Co2—O590.39 (5)O4—C6—O3126.31 (15)
O2—Co2—O589.61 (5)O4—C6—C2116.05 (14)
N2i—Co2—O593.38 (6)O3—C6—C2117.32 (14)
N2—Co2—O586.62 (6)N5—C7—N4119.64 (15)
O5i—Co2—O5180.00 (7)N5—C7—N3118.68 (15)
C5—O2—Co2116.20 (10)N4—C7—N3121.68 (15)
Co2—O5—H5A108.8 (19)N4—C8—C9124.00 (16)
Co2—O5—H5B121.8 (18)N4—C8—H8118.0
H5A—O5—H5B105 (3)C9—C8—H8118.0
C3—N1—C2116.87 (15)C10—C9—C8118.16 (16)
C4—N2—C1118.22 (14)C10—C9—H9120.9
C4—N2—Co2130.55 (12)C8—C9—H9120.9
C1—N2—Co2111.19 (11)N3—C10—C9117.89 (15)
C10—N3—C7121.63 (14)N3—C10—C11116.07 (15)
C10—N3—H3A119.2C9—C10—C11126.04 (16)
C7—N3—H3A119.2C10—C11—H11A109.5
C8—N4—C7116.59 (15)C10—C11—H11B109.5
C7—N5—H5C120.0H11A—C11—H11B109.5
C7—N5—H5D120.0C10—C11—H11C109.5
H5C—N5—H5D120.0H11A—C11—H11C109.5
N2—C1—C2120.13 (15)H11B—C11—H11C109.5
N2—C1—C5116.11 (14)H21A—O21—H21B106 (2)
C2—C1—C5123.75 (14)H22A—O22—H22B107 (3)
N1—C2—C1121.91 (15)H23A—O23—H23B110 (3)
N1—C2—C6113.51 (14)

Symmetry codes: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N3—H3A···O3ii0.881.772.6487 (17)172
N5—H5C···O21iii0.881.962.8350 (18)172
N5—H5D···O4ii0.881.962.8310 (18)171
O21—H21B···O4iv0.81 (2)1.97 (3)2.7777 (18)175 (2)
O21—H21A···O10.85 (3)1.86 (3)2.7093 (18)177 (2)
O5—H5B···O22v0.77 (3)2.02 (3)2.784 (2)172 (2)
O5—H5A···O23i0.83 (3)1.88 (3)2.706 (2)173 (3)
O23—H23B···O3vi0.78 (3)2.06 (3)2.8302 (19)172 (3)
O22—H22B···O210.83 (3)1.97 (3)2.794 (2)177 (3)
O23—H23A···O220.85 (3)2.13 (3)2.959 (2)165 (2)
O22—H22A···N1vii0.79 (3)2.59 (3)3.152 (2)130 (2)
O22—H22A···N4vi0.79 (3)2.68 (3)3.242 (2)130 (2)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: VM2043).

References

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