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Acta Cryst. (2012). E68, m1478-m1479    [ doi:10.1107/S160053681204617X ]

Poly[[hexaaquabis([mu]3-pyrimidine-4,6-dicarboxylato)dicalcium] dihydrate]

W. Starosta and J. Leciejewicz

Abstract top

The polymeric structure of the title compound, {[Ca2(C6H2N2O4)2(H2O)6]·2H2O}n, is built up of molecular layers composed of CaII ions bridged by both ligand N and O atoms with one of the O atoms being bis-monodentate. Two adjacent CaII ions are bridged by these O atoms, forming a centrosymmetric dimer which is the building unit of the structure. The dimers are nodes of a cross-linked molecular layer parallel to (101). The CaII ion is coordinated by two bidentate ligands, one monodentate ligand and three water molecules in the form of a distorted polyhedron with a coordination number of eight. Solvate water molecules located between adjacent layers participate as donors and acceptors in a system of hydrogen bonds in which coordinating water molecules also act as donors and non-coordinating carboxylate O atoms act as acceptors.

Comment top

The asymmetric unit of the title compound contains one CaII ion, one fully deprotonated pyrimidine-4,6-diarboxylate ligand molecule, three water molecules coordinated to the metal ion and one solvation water molecule. The ligand molecule acts in µ3 mode and bridges Ca II ions using monodentate N and O atoms and another O atom which is bidentate. One of the O atoms in the carboxylate groups remains uncoordinated. Ca1 and Ca1ii ions are related by an inversion centre and bridged by bidentate carboxylato O1 and O1ii atoms to form a dimeric moiety (Fig.1). Due to the bridging action of the ligands the dimers are the nodes of a cross-linked two dimensional molecular network. The structure of the title compound can be thus visualized as built of molecular layers parallel to the crystal (101) plane (Fig.2). Solvation water molecules are located between adjacent layers. The CaII ion has a distorted eight coordinate geometry. The observed Ca—N and Ca—O bond distances are typical (Table 1). The pyrimidine ring is planar with an r.m.s. of 0.0079 (2) Å; carboxylate groups C7/O1/O2 and C8/O3/O4 make dihedral angles with the plane of 9.7 (1)° and 8.9 (1)°, respectively. Bond distances and bond angles within the pyrimidine ring do not differ from those reported for the parent acid (Beobide, et al., 2007). In a system of hydrogen bonds, which is responsible for structure stability, solvation and coordinated water molecules act as donors and as acceptors and coordination inactive carboxylato O atoms act as acceptors (Table 2). Centro-symmetric dimeric units in which two CaIIions are bridged by ligand bidentate carboxylato O atoms have been also observed in the structures of complexes with pyrazine-2,6-dicarboxylate and water ligands. In all, dimeric units bridged by pairs of coordinated aqua O atoms form "ladder" type molecular ribbons (Starosta, et al., 2003, 2004).

Related literature top

For the crystal structures of CaII complexes with pyrazine-2,6-dicarboxylate and water ligands, see: Starosta, et al. (2003, 2004). The crystal structure of pyrimidine-4,6-dicarboxylic acid dihydrate was reported by Beobide et al. (2007).

Experimental top

An aqueous solution containing 1 mmol of calcium acetate hydrate and 1 mmol of pyrimidine-4,6-diarboxylic acid dihydrate was refluxed with constant stirring for 6 h. After cooling to room temperature, the solution was left to evaporate. Well formed single-crystal blocks appeared overnight at the bottom of the reaction pot. They were separated from the mother liquid, washed with cold water and dried in air.

Refinement top

Hydrogen atoms attached to water molecules were located in a difference map and refined isotropically, while two H atoms attached to pyrimidine C atoms were located at a calculated positions and treated as riding on the parent atoms with C—H=0.93 Å and

Computing details top

Data collection: KM-4 Software (Kuma, 1996); cell refinement: KM-4 Software (Kuma, 1996); data reduction: DATAPROC (Kuma, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. A fragment of the molecular layer showing a dimeric moiety with atom labelling scheme and 50% probability displacement ellipsoids. Symmetry code: i -x + 1/2, y - 1/2, -z + 3/2; ii -x, -y,-z + 1; iii x - 1/2, -y + 1/2, z + 1/2.
[Figure 2] Fig. 2. The alignment of molecular layers in the structure of a CaII complex with pyrimidine-4,6-carboxylate and water ligands viewed along [010].
Poly[[hexaaquabis(µ3-pyrimidine-4,6-dicarboxylato)dicalcium] dihydrate] top
Crystal data top
[Ca2(C6H2N2O4)2(H2O)6]·2H2OF(000) = 576
Mr = 278.24Dx = 1.762 Mg m−3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 25 reflections
a = 7.7053 (15) Åθ = 6–15°
b = 11.432 (2) ŵ = 0.64 mm−1
c = 11.916 (2) ÅT = 293 K
β = 92.16 (3)°Blocks, colourless
V = 1048.9 (4) Å30.10 × 0.04 × 0.03 mm
Z = 4
Data collection top
Kuma KM-4 four-circle
diffractometer		1709 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.049
Graphite monochromatorθmax = 30.1°, θmin = 2.5°
profile data from ω/2θ scansh = 0→10
Absorption correction: analytical
(CrysAlis RED; Oxford Diffraction, 2008)		k = −16→0
Tmin = 0.968, Tmax = 0.982l = −16→16
3274 measured reflections3 standard reflections every 200 reflections
3065 independent reflections intensity decay: 2.9%
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)] = 0.033Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.107H atoms treated by a mixture of independent and constrained refinement
S = 1.01 w = 1/[σ2(Fo2) + (0.0572P)2 + 0.0532P]
where P = (Fo2 + 2Fc2)/3
3065 reflections(Δ/σ)max = 0.001
186 parametersΔρmax = 0.44 e Å−3
0 restraintsΔρmin = −0.59 e Å−3
Crystal data top
[Ca2(C6H2N2O4)2(H2O)6]·2H2OV = 1048.9 (4) Å3
Mr = 278.24Z = 4
Monoclinic, P21/nMo Kα radiation
a = 7.7053 (15) ŵ = 0.64 mm−1
b = 11.432 (2) ÅT = 293 K
c = 11.916 (2) Å0.10 × 0.04 × 0.03 mm
β = 92.16 (3)°
Data collection top
Kuma KM-4 four-circle
diffractometer		1709 reflections with I > 2σ(I)
Absorption correction: analytical
(CrysAlis RED; Oxford Diffraction, 2008)		Rint = 0.049
Tmin = 0.968, Tmax = 0.982θmax = 30.1°
3274 measured reflections3 standard reflections every 200 reflections
3065 independent reflections intensity decay: 2.9%
Refinement top
R[F2 > 2σ(F2)] = 0.033H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.107Δρmax = 0.44 e Å−3
S = 1.01Δρmin = −0.59 e Å−3
3065 reflectionsAbsolute structure: ?
186 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
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
Ca10.03092 (6)0.05117 (4)0.65920 (3)0.01409 (11)
O10.0060 (2)0.12495 (14)0.46120 (13)0.0195 (3)
O20.0320 (3)0.27178 (16)0.33877 (13)0.0261 (4)
N10.1313 (3)0.26241 (16)0.63011 (14)0.0163 (4)
C60.1190 (3)0.30679 (18)0.52650 (17)0.0148 (4)
C50.1834 (3)0.41685 (18)0.50185 (18)0.0174 (4)
H50.17050.44870.43020.021*
C70.0438 (3)0.22887 (19)0.43434 (18)0.0165 (4)
O40.3231 (3)0.64500 (15)0.48018 (14)0.0313 (5)
O7−0.2529 (3)0.14194 (19)0.6459 (2)0.0342 (5)
O6−0.1678 (3)−0.08219 (17)0.76038 (16)0.0267 (4)
N30.2839 (3)0.43217 (16)0.69222 (14)0.0169 (4)
O50.3228 (3)0.0407 (2)0.59679 (18)0.0348 (5)
C20.2132 (3)0.32771 (19)0.70832 (18)0.0180 (4)
H20.22160.29740.78070.022*
C40.2679 (3)0.47703 (19)0.58880 (17)0.0152 (4)
C80.3517 (3)0.59611 (18)0.57191 (18)0.0170 (4)
O80.9331 (3)0.35726 (19)0.89833 (19)0.0303 (4)
H510.390 (5)−0.010 (4)0.601 (3)0.047 (11)*
O30.4436 (2)0.63449 (14)0.65273 (13)0.0199 (3)
H71−0.285 (4)0.187 (3)0.600 (3)0.031 (9)*
H62−0.174 (5)−0.090 (3)0.824 (3)0.038 (10)*
H520.358 (5)0.081 (4)0.540 (3)0.055 (12)*
H820.882 (6)0.384 (5)0.847 (4)0.076 (16)*
H810.957 (5)0.293 (3)0.888 (3)0.036 (9)*
H61−0.120 (6)−0.146 (4)0.743 (4)0.081 (16)*
H72−0.324 (8)0.138 (5)0.693 (5)0.10 (2)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Ca10.0198 (2)0.01036 (17)0.01203 (17)−0.00052 (18)−0.00070 (13)−0.00012 (16)
O10.0290 (9)0.0126 (7)0.0168 (7)−0.0043 (6)−0.0002 (6)−0.0028 (6)
O20.0448 (10)0.0193 (8)0.0135 (7)−0.0052 (8)−0.0076 (7)0.0006 (6)
N10.0223 (9)0.0135 (8)0.0131 (8)−0.0017 (7)−0.0013 (7)−0.0006 (7)
C60.0180 (10)0.0128 (9)0.0135 (9)−0.0005 (8)−0.0010 (8)−0.0012 (7)
C50.0266 (11)0.0124 (9)0.0130 (8)−0.0024 (8)−0.0019 (8)0.0011 (7)
C70.0205 (10)0.0135 (9)0.0155 (9)−0.0016 (8)−0.0009 (8)−0.0038 (8)
O40.0595 (14)0.0183 (8)0.0154 (8)−0.0108 (9)−0.0070 (8)0.0064 (6)
O70.0323 (11)0.0327 (11)0.0378 (11)0.0116 (9)0.0063 (9)0.0124 (9)
O60.0394 (11)0.0236 (9)0.0172 (8)−0.0052 (8)0.0030 (8)0.0011 (7)
N30.0241 (9)0.0149 (9)0.0117 (7)−0.0054 (7)0.0003 (7)0.0005 (6)
O50.0301 (10)0.0360 (12)0.0389 (11)0.0114 (9)0.0109 (8)0.0158 (9)
C20.0264 (12)0.0164 (10)0.0112 (8)−0.0030 (9)−0.0013 (8)0.0013 (8)
C40.0206 (10)0.0123 (9)0.0125 (9)−0.0006 (8)0.0001 (8)−0.0001 (7)
C80.0257 (12)0.0116 (9)0.0136 (9)−0.0029 (9)0.0013 (8)−0.0012 (7)
O80.0296 (10)0.0219 (10)0.0392 (11)0.0042 (8)0.0005 (8)−0.0076 (8)
O30.0298 (9)0.0132 (7)0.0164 (7)−0.0064 (7)−0.0026 (6)−0.0015 (6)
Geometric parameters (Å, º) top
Ca1—O52.398 (2)C5—H50.9300
Ca1—O72.420 (2)O4—C81.240 (3)
Ca1—O3i2.4361 (17)O7—H710.79 (4)
Ca1—O1ii2.4823 (16)O7—H720.80 (6)
Ca1—O62.502 (2)O6—H620.77 (4)
Ca1—O12.5061 (17)O6—H610.85 (5)
Ca1—N12.563 (2)N3—C21.330 (3)
Ca1—N3i2.6133 (19)N3—C41.336 (3)
Ca1—Ca1ii3.9817 (11)N3—Ca1iii2.6133 (19)
Ca1—H612.74 (5)O5—H510.78 (4)
O1—C71.267 (3)O5—H520.87 (4)
O1—Ca1ii2.4823 (16)C2—H20.9300
O2—C71.240 (3)C4—C81.523 (3)
N1—C21.334 (3)C8—O31.253 (3)
N1—C61.335 (3)O8—H820.77 (5)
C6—C51.388 (3)O8—H810.76 (4)
C6—C71.512 (3)O3—Ca1iii2.4361 (17)
C5—C41.385 (3)
O5—Ca1—O7148.95 (7)N1—Ca1—H61163.4 (11)
O5—Ca1—O3i105.11 (8)N3i—Ca1—H6163.5 (11)
O7—Ca1—O3i86.21 (7)Ca1ii—Ca1—H6193.9 (11)
O5—Ca1—O1ii82.45 (7)C7—O1—Ca1ii129.56 (14)
O7—Ca1—O1ii103.09 (7)C7—O1—Ca1122.89 (13)
O3i—Ca1—O1ii148.46 (6)Ca1ii—O1—Ca1105.91 (6)
O5—Ca1—O6135.80 (7)C2—N1—C6116.67 (19)
O7—Ca1—O674.03 (7)C2—N1—Ca1124.75 (14)
O3i—Ca1—O679.90 (6)C6—N1—Ca1118.15 (14)
O1ii—Ca1—O674.06 (6)N1—C6—C5121.77 (19)
O5—Ca1—O176.37 (7)N1—C6—C7117.37 (19)
O7—Ca1—O175.95 (7)C5—C6—C7120.70 (19)
O3i—Ca1—O1137.32 (5)C4—C5—C6116.97 (19)
O1ii—Ca1—O174.09 (6)C4—C5—H5121.5
O6—Ca1—O1129.21 (6)C6—C5—H5121.5
O5—Ca1—N173.37 (7)O2—C7—O1126.4 (2)
O7—Ca1—N182.17 (7)O2—C7—C6116.52 (19)
O3i—Ca1—N175.03 (6)O1—C7—C6117.02 (19)
O1ii—Ca1—N1135.61 (6)Ca1—O7—H71126 (2)
O6—Ca1—N1146.35 (7)Ca1—O7—H72125 (4)
O1—Ca1—N164.43 (5)H71—O7—H72109 (5)
O5—Ca1—N3i71.93 (7)Ca1—O6—H62127 (3)
O7—Ca1—N3i137.41 (7)Ca1—O6—H6197 (3)
O3i—Ca1—N3i63.72 (6)H62—O6—H61101 (4)
O1ii—Ca1—N3i90.98 (6)C2—N3—C4116.97 (18)
O6—Ca1—N3i71.62 (7)C2—N3—Ca1iii125.87 (14)
O1—Ca1—N3i146.45 (6)C4—N3—Ca1iii117.02 (14)
N1—Ca1—N3i114.97 (6)Ca1—O5—H51131 (3)
O5—Ca1—Ca1ii76.69 (6)Ca1—O5—H52122 (3)
O7—Ca1—Ca1ii89.33 (6)H51—O5—H52103 (4)
O3i—Ca1—Ca1ii173.73 (4)N3—C2—N1126.0 (2)
O1ii—Ca1—Ca1ii37.25 (4)N3—C2—H2117.0
O6—Ca1—Ca1ii103.10 (5)N1—C2—H2117.0
O1—Ca1—Ca1ii36.84 (4)N3—C4—C5121.6 (2)
N1—Ca1—Ca1ii100.01 (4)N3—C4—C8116.09 (18)
N3i—Ca1—Ca1ii122.36 (5)C5—C4—C8122.31 (18)
O5—Ca1—H61119.2 (10)O4—C8—O3126.6 (2)
O7—Ca1—H6188.9 (10)O4—C8—C4117.21 (19)
O3i—Ca1—H6190.5 (11)O3—C8—C4116.20 (18)
O1ii—Ca1—H6160.1 (11)H82—O8—H81112 (4)
O6—Ca1—H6117.9 (10)C8—O3—Ca1iii126.43 (14)
O1—Ca1—H61126.9 (11)
Symmetry codes: (i) −x+1/2, y−1/2, −z+3/2; (ii) −x, −y, −z+1; (iii) −x+1/2, y+1/2, −z+3/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O7—H72···O2iv0.80 (6)2.34 (6)3.048 (3)149 (6)
O6—H61···O2ii0.85 (5)1.88 (5)2.698 (3)163 (5)
O8—H81···O3v0.76 (4)2.04 (4)2.793 (3)170 (4)
O8—H82···O6iii0.77 (5)2.09 (5)2.818 (3)157 (5)
O5—H52···O8vi0.87 (4)1.94 (4)2.798 (3)169 (4)
O6—H62···O4iv0.77 (4)1.96 (4)2.719 (2)167 (4)
O7—H71···O4vii0.79 (4)2.16 (4)2.902 (3)158 (3)
O5—H51···O8v0.78 (4)2.04 (4)2.816 (3)176 (4)
Symmetry codes: (ii) −x, −y, −z+1; (iii) −x+1/2, y+1/2, −z+3/2; (iv) x−1/2, −y+1/2, z+1/2; (v) −x+3/2, y−1/2, −z+3/2; (vi) x−1/2, −y+1/2, z−1/2; (vii) −x, −y+1, −z+1.
Selected bond lengths (Å) top
Ca1—O52.398 (2)Ca1—O62.502 (2)
Ca1—O72.420 (2)Ca1—O12.5061 (17)
Ca1—O3i2.4361 (17)Ca1—N12.563 (2)
Ca1—O1ii2.4823 (16)Ca1—N3i2.6133 (19)
Symmetry codes: (i) −x+1/2, y−1/2, −z+3/2; (ii) −x, −y, −z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O7—H72···O2iii0.80 (6)2.34 (6)3.048 (3)149 (6)
O6—H61···O2ii0.85 (5)1.88 (5)2.698 (3)163 (5)
O8—H81···O3iv0.76 (4)2.04 (4)2.793 (3)170 (4)
O8—H82···O6v0.77 (5)2.09 (5)2.818 (3)157 (5)
O5—H52···O8vi0.87 (4)1.94 (4)2.798 (3)169 (4)
O6—H62···O4iii0.77 (4)1.96 (4)2.719 (2)167 (4)
O7—H71···O4vii0.79 (4)2.16 (4)2.902 (3)158 (3)
O5—H51···O8iv0.78 (4)2.04 (4)2.816 (3)176 (4)
Symmetry codes: (ii) −x, −y, −z+1; (iii) x−1/2, −y+1/2, z+1/2; (iv) −x+3/2, y−1/2, −z+3/2; (v) −x+1/2, y+1/2, −z+3/2; (vi) x−1/2, −y+1/2, z−1/2; (vii) −x, −y+1, −z+1.
Acknowledgements top

No acknowledgments

references
References top

Beobide, G., Castillo, O., Luque, A., Garcia-Couceiro, U., Garcia-Teran, J. P. & Roman, P. (2007). Dalton Trans. pp. 2668–2680.

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

Starosta, W., Ptasiewicz-Bąk, H. & Leciejewicz, J. (2003). J. Coord. Chem. 56, 677–682.

Starosta, W., Ptasiewicz-Bąk, H. & Leciejewicz, J. (2004). J. Coord. Chem. 57, 167–173.