metal-organic compounds
Tetraaqua(pyrimidine-4,6-dicarboxylato-κ2N1,O6)magnesium monohydrate
aInstitute of Nuclear Chemistry and Technology, ul.Dorodna 16, 03-195 Warszawa, Poland
*Correspondence e-mail: j.leciejewicz@ichtj.waw.pl
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.
Related literature
For the crystal structures of Mg 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
Crystal data
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Data collection
Refinement
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Data collection: KM-4 Software (Kuma, 1996); cell KM-4 Software; 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.
Supporting information
10.1107/S1600536813005850/su2567sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536813005850/su2567Isup2.hkl
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.
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).
Data collection: KM-4 Software (Kuma, 1996); cell
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).Fig. 1. A view of the molecular structure of the title compound, with atom labelling. Displacement ellipsoids are drawn at the 50% probability level. | |
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). |
[Mg(C6H2N2O4)(H2O)4]·H2O | F(000) = 584 |
Mr = 280.49 | Dx = 1.677 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 25 reflections |
a = 7.5633 (15) Å | θ = 6–15° |
b = 6.7977 (14) Å | µ = 0.21 mm−1 |
c = 21.605 (4) Å | T = 293 K |
β = 90.97 (3)° | Plates, colourless |
V = 1110.6 (4) Å3 | 0.25 × 0.23 × 0.09 mm |
Z = 4 |
Kuma KM-4 four-circle diffractometer | 2187 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.023 |
Graphite monochromator | θmax = 30.1°, θmin = 1.9° |
profile data from ω/2θ scans | h = −10→0 |
Absorption correction: analytical (CrysAlis RED; Oxford Diffraction, 2008) | k = 0→9 |
Tmin = 0.947, Tmax = 0.975 | l = −30→30 |
3485 measured reflections | 3 standard reflections every 200 reflections |
3246 independent reflections | intensity decay: 5.1% |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.036 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.125 | H 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 parameters | Δρmax = 0.47 e Å−3 |
0 restraints | Δρmin = −0.26 e Å−3 |
[Mg(C6H2N2O4)(H2O)4]·H2O | V = 1110.6 (4) Å3 |
Mr = 280.49 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 7.5633 (15) Å | µ = 0.21 mm−1 |
b = 6.7977 (14) Å | T = 293 K |
c = 21.605 (4) Å | 0.25 × 0.23 × 0.09 mm |
β = 90.97 (3)° |
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 = 0.975 | 3 standard reflections every 200 reflections |
3485 measured reflections | intensity decay: 5.1% |
3246 independent reflections |
R[F2 > 2σ(F2)] = 0.036 | 0 restraints |
wR(F2) = 0.125 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.01 | Δρmax = 0.47 e Å−3 |
3246 reflections | Δρmin = −0.26 e Å−3 |
203 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
Mg1 | 0.32572 (6) | 0.46078 (8) | 0.15804 (2) | 0.01813 (14) | |
O1 | 0.05876 (14) | 0.42580 (19) | 0.14674 (5) | 0.0237 (2) | |
O3 | 0.00597 (16) | 0.06801 (19) | −0.12636 (5) | 0.0273 (3) | |
H82 | 0.667 (4) | 0.431 (4) | 0.1337 (12) | 0.043 (7)* | |
O2 | −0.16427 (15) | 0.3374 (2) | 0.08385 (6) | 0.0284 (3) | |
O5 | 0.36240 (18) | 0.1989 (2) | 0.20187 (7) | 0.0304 (3) | |
O7 | 0.30383 (16) | 0.59579 (19) | 0.24329 (5) | 0.0236 (2) | |
N1 | 0.29679 (17) | 0.3154 (2) | 0.06501 (6) | 0.0211 (3) | |
C7 | −0.00682 (19) | 0.3566 (2) | 0.09709 (7) | 0.0188 (3) | |
C2 | 0.12644 (18) | 0.2956 (2) | 0.04897 (7) | 0.0179 (3) | |
C3 | 0.07484 (19) | 0.2275 (2) | −0.00879 (7) | 0.0200 (3) | |
H3 | −0.0439 | 0.2128 | −0.0196 | 0.024* | |
C4 | 0.2075 (2) | 0.1819 (2) | −0.04993 (7) | 0.0195 (3) | |
O6 | 0.30977 (19) | 0.7335 (2) | 0.11370 (7) | 0.0312 (3) | |
O4 | 0.28320 (19) | 0.1211 (2) | −0.15411 (6) | 0.0355 (3) | |
C8 | 0.1616 (2) | 0.1171 (2) | −0.11589 (7) | 0.0217 (3) | |
N5 | 0.37836 (17) | 0.1979 (2) | −0.03413 (6) | 0.0242 (3) | |
C6 | 0.41441 (19) | 0.2628 (3) | 0.02291 (8) | 0.0247 (3) | |
H6 | 0.5331 | 0.2722 | 0.0344 | 0.030* | |
O9 | 0.12147 (16) | 0.9368 (2) | 0.24311 (6) | 0.0267 (3) | |
H51 | 0.290 (4) | 0.132 (5) | 0.2170 (13) | 0.052 (8)* | |
H61 | 0.389 (5) | 0.794 (5) | 0.1006 (15) | 0.067 (10)* | |
H62 | 0.216 (4) | 0.815 (4) | 0.1146 (12) | 0.046 (7)* | |
H81 | 0.629 (3) | 0.613 (4) | 0.1576 (11) | 0.040 (7)* | |
O8 | 0.58966 (15) | 0.4954 (2) | 0.15529 (6) | 0.0264 (3) | |
H71 | 0.282 (4) | 0.526 (4) | 0.2778 (13) | 0.043 (7)* | |
H52 | 0.452 (4) | 0.166 (5) | 0.2159 (13) | 0.050 (8)* | |
H91 | 0.069 (4) | 0.959 (5) | 0.2725 (15) | 0.063 (9)* | |
H92 | 0.061 (4) | 0.939 (5) | 0.2119 (14) | 0.052 (8)* | |
H72 | 0.241 (4) | 0.699 (4) | 0.2451 (11) | 0.038 (7)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Mg1 | 0.0142 (2) | 0.0234 (3) | 0.0168 (2) | −0.00041 (18) | 0.00078 (17) | −0.00113 (18) |
O1 | 0.0172 (5) | 0.0342 (6) | 0.0199 (5) | −0.0025 (4) | 0.0039 (4) | −0.0066 (4) |
O3 | 0.0225 (5) | 0.0341 (6) | 0.0251 (6) | 0.0008 (5) | −0.0041 (4) | −0.0043 (5) |
O2 | 0.0139 (5) | 0.0429 (7) | 0.0284 (6) | 0.0009 (5) | 0.0011 (4) | −0.0072 (5) |
O5 | 0.0223 (6) | 0.0293 (7) | 0.0396 (7) | −0.0006 (5) | −0.0016 (5) | 0.0119 (5) |
O7 | 0.0266 (5) | 0.0260 (6) | 0.0183 (5) | 0.0014 (5) | 0.0024 (4) | 0.0000 (5) |
N1 | 0.0157 (5) | 0.0284 (7) | 0.0192 (6) | −0.0001 (5) | 0.0009 (4) | −0.0028 (5) |
C7 | 0.0147 (6) | 0.0219 (7) | 0.0198 (6) | 0.0009 (5) | 0.0025 (5) | −0.0009 (5) |
C2 | 0.0148 (6) | 0.0204 (7) | 0.0185 (6) | 0.0000 (5) | 0.0014 (5) | −0.0007 (5) |
C3 | 0.0158 (6) | 0.0248 (7) | 0.0193 (7) | −0.0018 (5) | 0.0010 (5) | −0.0024 (5) |
C4 | 0.0199 (6) | 0.0223 (7) | 0.0165 (6) | −0.0017 (5) | 0.0015 (5) | −0.0018 (5) |
O6 | 0.0238 (6) | 0.0307 (6) | 0.0394 (7) | 0.0042 (5) | 0.0085 (5) | 0.0103 (5) |
O4 | 0.0368 (7) | 0.0463 (8) | 0.0238 (6) | −0.0141 (6) | 0.0110 (5) | −0.0125 (6) |
C8 | 0.0257 (7) | 0.0215 (7) | 0.0178 (6) | −0.0013 (6) | 0.0006 (5) | −0.0028 (5) |
N5 | 0.0170 (6) | 0.0340 (8) | 0.0217 (6) | −0.0011 (5) | 0.0021 (5) | −0.0051 (5) |
C6 | 0.0134 (6) | 0.0383 (9) | 0.0225 (7) | 0.0000 (6) | 0.0009 (5) | −0.0052 (6) |
O9 | 0.0203 (5) | 0.0387 (7) | 0.0210 (6) | 0.0009 (5) | 0.0008 (4) | 0.0008 (5) |
O8 | 0.0154 (5) | 0.0310 (6) | 0.0329 (6) | −0.0015 (4) | 0.0042 (4) | −0.0036 (5) |
Mg1—O8 | 2.0120 (13) | C7—C2 | 1.518 (2) |
Mg1—O5 | 2.0331 (15) | C2—C3 | 1.381 (2) |
Mg1—O1 | 2.0436 (13) | C3—C4 | 1.387 (2) |
Mg1—O7 | 2.0671 (13) | C3—H3 | 0.9300 |
Mg1—O6 | 2.0896 (15) | C4—N5 | 1.335 (2) |
Mg1—N1 | 2.2472 (15) | C4—C8 | 1.526 (2) |
O1—C7 | 1.2650 (19) | O6—H61 | 0.78 (4) |
O3—C8 | 1.241 (2) | O6—H62 | 0.90 (3) |
O2—C7 | 1.2270 (19) | O4—C8 | 1.247 (2) |
O5—H51 | 0.79 (3) | N5—C6 | 1.333 (2) |
O5—H52 | 0.77 (3) | C6—H6 | 0.9300 |
O7—H71 | 0.90 (3) | O9—H91 | 0.77 (3) |
O7—H72 | 0.85 (3) | O9—H92 | 0.81 (3) |
N1—C6 | 1.332 (2) | O8—H82 | 0.87 (3) |
N1—C2 | 1.3353 (19) | O8—H81 | 0.86 (3) |
O8—Mg1—O5 | 89.34 (6) | O2—C7—C2 | 117.67 (13) |
O8—Mg1—O1 | 171.45 (6) | O1—C7—C2 | 115.28 (13) |
O5—Mg1—O1 | 94.62 (6) | N1—C2—C3 | 121.66 (13) |
O8—Mg1—O7 | 93.95 (6) | N1—C2—C7 | 116.35 (13) |
O5—Mg1—O7 | 89.20 (6) | C3—C2—C7 | 121.98 (13) |
O1—Mg1—O7 | 93.69 (6) | C2—C3—C4 | 117.23 (13) |
O8—Mg1—O6 | 86.12 (6) | C2—C3—H3 | 121.4 |
O5—Mg1—O6 | 175.43 (6) | C4—C3—H3 | 121.4 |
O1—Mg1—O6 | 89.95 (6) | N5—C4—C3 | 121.71 (14) |
O7—Mg1—O6 | 90.56 (6) | N5—C4—C8 | 117.78 (13) |
O8—Mg1—N1 | 96.12 (6) | C3—C4—C8 | 120.49 (13) |
O5—Mg1—N1 | 92.41 (6) | Mg1—O6—H61 | 126 (3) |
O1—Mg1—N1 | 76.17 (5) | Mg1—O6—H62 | 125.1 (17) |
O7—Mg1—N1 | 169.82 (5) | H61—O6—H62 | 107 (3) |
O6—Mg1—N1 | 88.64 (6) | O3—C8—O4 | 126.41 (15) |
C7—O1—Mg1 | 121.14 (10) | O3—C8—C4 | 116.62 (14) |
Mg1—O5—H51 | 128 (2) | O4—C8—C4 | 116.96 (14) |
Mg1—O5—H52 | 123 (2) | C6—N5—C4 | 116.43 (13) |
H51—O5—H52 | 106 (3) | N1—C6—N5 | 126.29 (14) |
Mg1—O7—H71 | 121.5 (17) | N1—C6—H6 | 116.9 |
Mg1—O7—H72 | 117.5 (17) | N5—C6—H6 | 116.9 |
H71—O7—H72 | 107 (2) | H91—O9—H92 | 113 (3) |
C6—N1—C2 | 116.64 (13) | Mg1—O8—H82 | 129.2 (18) |
C6—N1—Mg1 | 132.29 (11) | Mg1—O8—H81 | 117.0 (18) |
C2—N1—Mg1 | 110.81 (10) | H82—O8—H81 | 105 (3) |
O2—C7—O1 | 127.04 (14) |
D—H···A | D—H | H···A | D···A | D—H···A |
O8—H82···O2i | 0.87 (3) | 1.80 (3) | 2.6640 (18) | 171 (3) |
O5—H51···O9ii | 0.79 (3) | 1.93 (3) | 2.7102 (19) | 170 (3) |
O6—H61···N5iii | 0.78 (4) | 2.29 (4) | 2.979 (2) | 147 (3) |
O6—H62···O3iv | 0.90 (3) | 1.88 (3) | 2.7603 (19) | 166 (3) |
O8—H81···O4iii | 0.86 (3) | 1.93 (3) | 2.779 (2) | 174 (2) |
O7—H71···O4v | 0.90 (3) | 1.78 (3) | 2.6690 (18) | 169 (3) |
O5—H52···O7vi | 0.77 (3) | 2.09 (3) | 2.8577 (19) | 176 (3) |
O9—H91···O1vii | 0.77 (3) | 2.02 (3) | 2.7635 (18) | 162 (4) |
O9—H92···O3iv | 0.81 (3) | 1.91 (3) | 2.6852 (18) | 161 (3) |
O7—H72···O9 | 0.85 (3) | 1.85 (3) | 2.6971 (19) | 174 (3) |
Symmetry codes: (i) x+1, y, z; (ii) x, y−1, z; (iii) −x+1, −y+1, −z; (iv) −x, −y+1, −z; (v) x, −y+1/2, z+1/2; (vi) −x+1, y−1/2, −z+1/2; (vii) −x, y+1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | [Mg(C6H2N2O4)(H2O)4]·H2O |
Mr | 280.49 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 293 |
a, b, c (Å) | 7.5633 (15), 6.7977 (14), 21.605 (4) |
β (°) | 90.97 (3) |
V (Å3) | 1110.6 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.21 |
Crystal size (mm) | 0.25 × 0.23 × 0.09 |
Data collection | |
Diffractometer | Kuma KM-4 four-circle diffractometer |
Absorption correction | Analytical (CrysAlis RED; Oxford Diffraction, 2008) |
Tmin, Tmax | 0.947, 0.975 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3485, 3246, 2187 |
Rint | 0.023 |
(sin θ/λ)max (Å−1) | 0.706 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.125, 1.01 |
No. of reflections | 3246 |
No. of parameters | 203 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.47, −0.26 |
Computer programs: KM-4 Software (Kuma, 1996), DATAPROC (Kuma, 2001), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
O8—H82···O2i | 0.87 (3) | 1.80 (3) | 2.6640 (18) | 171 (3) |
O5—H51···O9ii | 0.79 (3) | 1.93 (3) | 2.7102 (19) | 170 (3) |
O6—H61···N5iii | 0.78 (4) | 2.29 (4) | 2.979 (2) | 147 (3) |
O6—H62···O3iv | 0.90 (3) | 1.88 (3) | 2.7603 (19) | 166 (3) |
O8—H81···O4iii | 0.86 (3) | 1.93 (3) | 2.779 (2) | 174 (2) |
O7—H71···O4v | 0.90 (3) | 1.78 (3) | 2.6690 (18) | 169 (3) |
O5—H52···O7vi | 0.77 (3) | 2.09 (3) | 2.8577 (19) | 176 (3) |
O9—H91···O1vii | 0.77 (3) | 2.02 (3) | 2.7635 (18) | 162 (4) |
O9—H92···O3iv | 0.81 (3) | 1.91 (3) | 2.6852 (18) | 161 (3) |
O7—H72···O9 | 0.85 (3) | 1.85 (3) | 2.6971 (19) | 174 (3) |
Symmetry codes: (i) x+1, y, z; (ii) x, y−1, z; (iii) −x+1, −y+1, −z; (iv) −x, −y+1, −z; (v) x, −y+1/2, z+1/2; (vi) −x+1, y−1/2, −z+1/2; (vii) −x, y+1/2, −z+1/2. |
References
Gryz, M., Starosta, W. & Leciejewicz, J. (2004). J. Coord. Chem. 57, 917–922. Web of Science CSD CrossRef CAS Google Scholar
Kuma (1996). KM-4 Software. Kuma Diffraction Ltd. Wrocław, Poland. Google Scholar
Kuma (2001). DATAPROC. Kuma Diffraction Ltd. Wrocław, Poland. Google Scholar
Oxford Diffraction (2008). CrysAlis RED. Oxford Diffraction Ltd., Yarnton, England. Google Scholar
Ptasiewicz-Bąk, H. & Leciejewicz, J. (1997). Pol. J. Chem. 71, 493–500. Google Scholar
Ptasiewicz-Bąk, H. & Leciejewicz, J. (1998). J. Coord. Chem. 44, 299–309. CAS Google Scholar
Ptasiewicz-Bąk, H. & Leciejewicz, J. (2003). J. Coord. Chem. 56, 173–180. Web of Science CSD CrossRef CAS Google Scholar
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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).