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Acta Cryst. (2013). E69, m189    [ doi:10.1107/S1600536813005850 ]

Tetraaqua(pyrimidine-4,6-dicarboxylato-[kappa]2N1,O6)magnesium monohydrate

W. Starosta, J. Leciejewicz and K. Kiegiel

Abstract top

In the title compound, [Mg(C6H2N2O4)(H2O)4]·H2O, the MgII ion is coordinated by a fully deprotonated pyrimidine-4,6-dicarboxylate molecule, via a ring N and a carboxylate O atom, and by four water O atoms at the apices of a slightly distorted octahedron. In the crystal, molecules are linked by O-H...O and O-H...N hydrogen bonds, forming a three-dimensional network.

Comment top

Crystal structures of MgII complexes with diazine dicarboxylate molecules belong to three types. For example, the structure of a MgII complex with pyrazine-2,3-dicarboxylate and water ligands is a catenated polymer (Ptasiewicz-Bąk & Leciejewicz, 1997), while those with pyrazine-2,5-dicarboxylate (Ptasiewicz-Bąk & Leciejewicz, 1998) and pyrazine-2,6-dicarboxylate (Ptasiewicz-Bąk & Leciejewicz, 2003) are composed of hexaquamagnesium(II) cations and fully deprotonated organic molecules.

On the other hand, the MgII complex with a pyridazine-3,6-dicarboxylate molecule is built of anions in which the MgII ion is coordinated by two water O atoms and two fully deprotonated organic molecules with singly protonated hydrazine molecules as cations (Gryz et al., 2004).

The structure of the title compound, Fig. 1, is built of monomeric molecules in which a MgII ion is coordinated by one of the N,O bonding groups of a fully deprotonated pyrimidine-4,6-dicarboxylate molecule and four water O atoms. The coordination geometry of atom Mg1 is a slightly distorted octahedron with typical Mg-N and Mg—O distances [Mg1-N1 = 2.2472 (15) Å; the Mg1-O distances vary from 2.0120 (13) to 2.0896 (15) Å]. The carboxylic groups C7/O1/O2 and C8/O3/O4 are inclined to the pyrimidine ring by 3.5 (1)° and 14.9 (2)°, respectively.

In the crystal, the complexes interact via an extended network of O-H···O and O-H···N hydrogen bonds, in which coordinated and solvate water molecules are donors and the carboxylato O and hetero-ring N atoms act as acceptors, forming a three-dimensional network (Fig. 2 and Table 1).

Related literature top

For the crystal structures of MgII complexes with pyrazine-2,3-dicarboxylic acid, see: Ptasiewicz-Bąk & Leciejewicz (1997), with pyrazine-2,5-dicarboxylic acid, see: Ptasiewicz-Bąk & Leciejewicz (1998), with pyrazine-2,6-dicarboxylic acid, see: Ptasiewicz-Bąk & Leciejewicz (2003) and with pyridazine-3,6-dicarboxylic acid, see: Gryz et al. (2004).

Experimental top

An aqueous solution containing 1 mmol of magnesium acetate tetrahydrate and 1 mmol of pyrimidine-4,6-dicarboxylic acid dihydrate were refluxed with constant stirring for 2 h yielding a white precipitate which subsequently was filtered and redissolved in an excess of boiling water. Cooled to room temperature, the solution was left to evaporate. Colourless plate-like crystals deposited after a few days. They were washed with cold ethanol and dried in the air.

Refinement top

Water H atoms were located in a difference Fourier map and freely refined. The C-bound H atoms were positioned at calculated positions and treated as riding on the parent atoms: C—H = 0.93 Å with Uiso(H )= 1.2Ueq(C).

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 view of the molecular structure of the title compound, with atom labelling. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. A view along the a axis of the crystal packing of the title compound. The hydrogen bonds are shown as dashed lines (see Table 1 for details).
Tetraaqua(pyrimidine-4,6-dicarboxylato-κ2N1,O6)magnesium monohydrate top
Crystal data top
[Mg(C6H2N2O4)(H2O)4]·H2OF(000) = 584
Mr = 280.49Dx = 1.677 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 25 reflections
a = 7.5633 (15) Åθ = 6–15°
b = 6.7977 (14) ŵ = 0.21 mm1
c = 21.605 (4) ÅT = 293 K
β = 90.97 (3)°Plates, colourless
V = 1110.6 (4) Å30.25 × 0.23 × 0.09 mm
Z = 4
Data collection top
Kuma KM-4 four-circle
diffractometer
2187 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.023
Graphite monochromatorθmax = 30.1°, θmin = 1.9°
profile data from ω/2θ scansh = 100
Absorption correction: analytical
(CrysAlis RED; Oxford Diffraction, 2008)
k = 09
Tmin = 0.947, Tmax = 0.975l = 3030
3485 measured reflections3 standard reflections every 200 reflections
3246 independent reflections intensity decay: 5.1%
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)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.125H atoms treated by a mixture of independent and constrained refinement
S = 1.01 w = 1/[σ2(Fo2) + (0.0833P)2 + 0.2045P]
where P = (Fo2 + 2Fc2)/3
3246 reflections(Δ/σ)max < 0.001
203 parametersΔρmax = 0.47 e Å3
0 restraintsΔρmin = 0.26 e Å3
Crystal data top
[Mg(C6H2N2O4)(H2O)4]·H2OV = 1110.6 (4) Å3
Mr = 280.49Z = 4
Monoclinic, P21/cMo Kα radiation
a = 7.5633 (15) ŵ = 0.21 mm1
b = 6.7977 (14) ÅT = 293 K
c = 21.605 (4) Å0.25 × 0.23 × 0.09 mm
β = 90.97 (3)°
Data collection top
Kuma KM-4 four-circle
diffractometer
2187 reflections with I > 2σ(I)
Absorption correction: analytical
(CrysAlis RED; Oxford Diffraction, 2008)
Rint = 0.023
Tmin = 0.947, Tmax = 0.975θmax = 30.1°
3485 measured reflections3 standard reflections every 200 reflections
3246 independent reflections intensity decay: 5.1%
Refinement top
R[F2 > 2σ(F2)] = 0.036H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.125Δρmax = 0.47 e Å3
S = 1.01Δρmin = 0.26 e Å3
3246 reflectionsAbsolute structure: ?
203 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
Mg10.32572 (6)0.46078 (8)0.15804 (2)0.01813 (14)
O10.05876 (14)0.42580 (19)0.14674 (5)0.0237 (2)
O30.00597 (16)0.06801 (19)0.12636 (5)0.0273 (3)
H820.667 (4)0.431 (4)0.1337 (12)0.043 (7)*
O20.16427 (15)0.3374 (2)0.08385 (6)0.0284 (3)
O50.36240 (18)0.1989 (2)0.20187 (7)0.0304 (3)
O70.30383 (16)0.59579 (19)0.24329 (5)0.0236 (2)
N10.29679 (17)0.3154 (2)0.06501 (6)0.0211 (3)
C70.00682 (19)0.3566 (2)0.09709 (7)0.0188 (3)
C20.12644 (18)0.2956 (2)0.04897 (7)0.0179 (3)
C30.07484 (19)0.2275 (2)0.00879 (7)0.0200 (3)
H30.04390.21280.01960.024*
C40.2075 (2)0.1819 (2)0.04993 (7)0.0195 (3)
O60.30977 (19)0.7335 (2)0.11370 (7)0.0312 (3)
O40.28320 (19)0.1211 (2)0.15411 (6)0.0355 (3)
C80.1616 (2)0.1171 (2)0.11589 (7)0.0217 (3)
N50.37836 (17)0.1979 (2)0.03413 (6)0.0242 (3)
C60.41441 (19)0.2628 (3)0.02291 (8)0.0247 (3)
H60.53310.27220.03440.030*
O90.12147 (16)0.9368 (2)0.24311 (6)0.0267 (3)
H510.290 (4)0.132 (5)0.2170 (13)0.052 (8)*
H610.389 (5)0.794 (5)0.1006 (15)0.067 (10)*
H620.216 (4)0.815 (4)0.1146 (12)0.046 (7)*
H810.629 (3)0.613 (4)0.1576 (11)0.040 (7)*
O80.58966 (15)0.4954 (2)0.15529 (6)0.0264 (3)
H710.282 (4)0.526 (4)0.2778 (13)0.043 (7)*
H520.452 (4)0.166 (5)0.2159 (13)0.050 (8)*
H910.069 (4)0.959 (5)0.2725 (15)0.063 (9)*
H920.061 (4)0.939 (5)0.2119 (14)0.052 (8)*
H720.241 (4)0.699 (4)0.2451 (11)0.038 (7)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Mg10.0142 (2)0.0234 (3)0.0168 (2)0.00041 (18)0.00078 (17)0.00113 (18)
O10.0172 (5)0.0342 (6)0.0199 (5)0.0025 (4)0.0039 (4)0.0066 (4)
O30.0225 (5)0.0341 (6)0.0251 (6)0.0008 (5)0.0041 (4)0.0043 (5)
O20.0139 (5)0.0429 (7)0.0284 (6)0.0009 (5)0.0011 (4)0.0072 (5)
O50.0223 (6)0.0293 (7)0.0396 (7)0.0006 (5)0.0016 (5)0.0119 (5)
O70.0266 (5)0.0260 (6)0.0183 (5)0.0014 (5)0.0024 (4)0.0000 (5)
N10.0157 (5)0.0284 (7)0.0192 (6)0.0001 (5)0.0009 (4)0.0028 (5)
C70.0147 (6)0.0219 (7)0.0198 (6)0.0009 (5)0.0025 (5)0.0009 (5)
C20.0148 (6)0.0204 (7)0.0185 (6)0.0000 (5)0.0014 (5)0.0007 (5)
C30.0158 (6)0.0248 (7)0.0193 (7)0.0018 (5)0.0010 (5)0.0024 (5)
C40.0199 (6)0.0223 (7)0.0165 (6)0.0017 (5)0.0015 (5)0.0018 (5)
O60.0238 (6)0.0307 (6)0.0394 (7)0.0042 (5)0.0085 (5)0.0103 (5)
O40.0368 (7)0.0463 (8)0.0238 (6)0.0141 (6)0.0110 (5)0.0125 (6)
C80.0257 (7)0.0215 (7)0.0178 (6)0.0013 (6)0.0006 (5)0.0028 (5)
N50.0170 (6)0.0340 (8)0.0217 (6)0.0011 (5)0.0021 (5)0.0051 (5)
C60.0134 (6)0.0383 (9)0.0225 (7)0.0000 (6)0.0009 (5)0.0052 (6)
O90.0203 (5)0.0387 (7)0.0210 (6)0.0009 (5)0.0008 (4)0.0008 (5)
O80.0154 (5)0.0310 (6)0.0329 (6)0.0015 (4)0.0042 (4)0.0036 (5)
Geometric parameters (Å, º) top
Mg1—O82.0120 (13)C7—C21.518 (2)
Mg1—O52.0331 (15)C2—C31.381 (2)
Mg1—O12.0436 (13)C3—C41.387 (2)
Mg1—O72.0671 (13)C3—H30.9300
Mg1—O62.0896 (15)C4—N51.335 (2)
Mg1—N12.2472 (15)C4—C81.526 (2)
O1—C71.2650 (19)O6—H610.78 (4)
O3—C81.241 (2)O6—H620.90 (3)
O2—C71.2270 (19)O4—C81.247 (2)
O5—H510.79 (3)N5—C61.333 (2)
O5—H520.77 (3)C6—H60.9300
O7—H710.90 (3)O9—H910.77 (3)
O7—H720.85 (3)O9—H920.81 (3)
N1—C61.332 (2)O8—H820.87 (3)
N1—C21.3353 (19)O8—H810.86 (3)
O8—Mg1—O589.34 (6)O2—C7—C2117.67 (13)
O8—Mg1—O1171.45 (6)O1—C7—C2115.28 (13)
O5—Mg1—O194.62 (6)N1—C2—C3121.66 (13)
O8—Mg1—O793.95 (6)N1—C2—C7116.35 (13)
O5—Mg1—O789.20 (6)C3—C2—C7121.98 (13)
O1—Mg1—O793.69 (6)C2—C3—C4117.23 (13)
O8—Mg1—O686.12 (6)C2—C3—H3121.4
O5—Mg1—O6175.43 (6)C4—C3—H3121.4
O1—Mg1—O689.95 (6)N5—C4—C3121.71 (14)
O7—Mg1—O690.56 (6)N5—C4—C8117.78 (13)
O8—Mg1—N196.12 (6)C3—C4—C8120.49 (13)
O5—Mg1—N192.41 (6)Mg1—O6—H61126 (3)
O1—Mg1—N176.17 (5)Mg1—O6—H62125.1 (17)
O7—Mg1—N1169.82 (5)H61—O6—H62107 (3)
O6—Mg1—N188.64 (6)O3—C8—O4126.41 (15)
C7—O1—Mg1121.14 (10)O3—C8—C4116.62 (14)
Mg1—O5—H51128 (2)O4—C8—C4116.96 (14)
Mg1—O5—H52123 (2)C6—N5—C4116.43 (13)
H51—O5—H52106 (3)N1—C6—N5126.29 (14)
Mg1—O7—H71121.5 (17)N1—C6—H6116.9
Mg1—O7—H72117.5 (17)N5—C6—H6116.9
H71—O7—H72107 (2)H91—O9—H92113 (3)
C6—N1—C2116.64 (13)Mg1—O8—H82129.2 (18)
C6—N1—Mg1132.29 (11)Mg1—O8—H81117.0 (18)
C2—N1—Mg1110.81 (10)H82—O8—H81105 (3)
O2—C7—O1127.04 (14)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O8—H82···O2i0.87 (3)1.80 (3)2.6640 (18)171 (3)
O5—H51···O9ii0.79 (3)1.93 (3)2.7102 (19)170 (3)
O6—H61···N5iii0.78 (4)2.29 (4)2.979 (2)147 (3)
O6—H62···O3iv0.90 (3)1.88 (3)2.7603 (19)166 (3)
O8—H81···O4iii0.86 (3)1.93 (3)2.779 (2)174 (2)
O7—H71···O4v0.90 (3)1.78 (3)2.6690 (18)169 (3)
O5—H52···O7vi0.77 (3)2.09 (3)2.8577 (19)176 (3)
O9—H91···O1vii0.77 (3)2.02 (3)2.7635 (18)162 (4)
O9—H92···O3iv0.81 (3)1.91 (3)2.6852 (18)161 (3)
O7—H72···O90.85 (3)1.85 (3)2.6971 (19)174 (3)
Symmetry codes: (i) x+1, y, z; (ii) x, y1, z; (iii) x+1, y+1, z; (iv) x, y+1, z; (v) x, y+1/2, z+1/2; (vi) x+1, y1/2, z+1/2; (vii) x, y+1/2, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O8—H82···O2i0.87 (3)1.80 (3)2.6640 (18)171 (3)
O5—H51···O9ii0.79 (3)1.93 (3)2.7102 (19)170 (3)
O6—H61···N5iii0.78 (4)2.29 (4)2.979 (2)147 (3)
O6—H62···O3iv0.90 (3)1.88 (3)2.7603 (19)166 (3)
O8—H81···O4iii0.86 (3)1.93 (3)2.779 (2)174 (2)
O7—H71···O4v0.90 (3)1.78 (3)2.6690 (18)169 (3)
O5—H52···O7vi0.77 (3)2.09 (3)2.8577 (19)176 (3)
O9—H91···O1vii0.77 (3)2.02 (3)2.7635 (18)162 (4)
O9—H92···O3iv0.81 (3)1.91 (3)2.6852 (18)161 (3)
O7—H72···O90.85 (3)1.85 (3)2.6971 (19)174 (3)
Symmetry codes: (i) x+1, y, z; (ii) x, y1, z; (iii) x+1, y+1, z; (iv) x, y+1, z; (v) x, y+1/2, z+1/2; (vi) x+1, y1/2, z+1/2; (vii) x, y+1/2, z+1/2.
Acknowledgements top

none

references
References top

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Kuma (2001). DATAPROC. Kuma Diffraction Ltd. Wrocław, Poland.

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Ptasiewicz-Bąk, H. & Leciejewicz, J. (1998). J. Coord. Chem. 44, 299–309.

Ptasiewicz-Bąk, H. & Leciejewicz, J. (2003). J. Coord. Chem. 56, 173–180.

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