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In hexa­aqua­nickel bis(2,6-di­oxo-1,2,3,6-tetrahydro­pyrimidine-4-carboxyl­ate) dihydrate, [Ni(H2O)6](C5H3N2O4)2·2H2O, the nickel cation is coordinated by six aqua ligands and only associated with the two orotate ions through hydrogen bonds. The structure is isotypic with the magnesium and zinc analogues. The metal cation sits on a crystallographic center of inversion that relates the water mol­ecules and the organic anions. The orotate moieties form an unbonded one-dimensional chain mediated by a hydrogen-bonded self-recognition interaction. The hexa­aqua­nickel complex molecules bridge these chains laterally, acting as molecular clamps that bring neighboring layers nearer than expected. As a result of this three-dimensional arrangement, a short contact of 3.166 (5) Å is observed between two C atoms of two adjacent ribbons.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270103004773/ln1162sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270103004773/ln1162Isup2.hkl
Contains datablock I

CCDC reference: 211734

Comment top

Orotic acid (6-uracilic acid, OrH2) and some of its derivatives are of great importance in biological systems due to their role as precursors of pyrimidine nucleosides (Rawn, 1989), and they are found in the cells and body fluids of many living organisms. Metal orotates are widely applied in medicine, e.g. platinum, palladium and nickel orotates with a wide variety of substituents have been screened as therapeutic agents for cancer (Sabat et al., 1980; Karipides & Thomas, 1986; Castan et al., 1990). However, recent interest has focused on the proposed biological function of orotic acid as a carrier, which underlies the successful application of metal orotates in therapies for a variety of metal deficiencies, such as calcium, magnesium, zinc or iron.

OrH2 can act as a dibasic acid, depending on the pH range. The acid functions are the exocyclic carboxylate group (pK = 2.09) and the 1-imino position (pK = 9.28), so in the pH range of approximately 5–9, deprotonation of orotic acid yields orotate(1-) salts containing OrH (Kaneti & Golovinski, 1971). Only in very alkaline solutions or in the presence of strong coordination centers are orotate(2-) ions present in significant quantities.

A great number of orotate(2-) complexes have been characterized structurally (Mutikainen & Lumme, 1980; Mentzafos et al., 1987; Mutikainen, 1989; Hodgson & Asplund, 1990), but less has been written about the equally important complexes of orotate (1-). Some examples are the coordination compounds of lithium and magnesium orotate(1-) (Bach et al., 1990; Lutz, 2001) and the coordination complex of zinc orotate(1-) (Kumberger et al., 1993).

In this paper, we report the preparation and crystal structure of a water-rich nickel orotate(1-) complex, (I). The importance of this compound, as happens with the zinc and magnesium analogues, lies in its similarity to the metal–orotate species found in aqueous solution. Such structural similarity could enhance its possible pharmacological interest.

From our X-ray crystallographic analysis at 150 K we found that the nickel-containing compound is isotypic with the previously reported magnesium and zinc orotate(1-) compounds. The structure is formed by a cationic hexaaquanickel complex hydrogen bonded to two OrH counter-ions.

In (I), the nickel cation sits on a crystallographic center of inversion that relates the water molecules of the coordination shell, the orotate anions and the uncoordinated water molecules. The orotate anion is essentially planar, with a slight deviation from planarity arising from the small non-zero torsion angle between the carboxylate group and the ring [N1—C6—C7—O5 = 5.9 (4)°]. The angles formed at the amide CO group, N3—C2—O2 and N1—C2—O2, of the urea fragment are essentially equal, but as the chemical environment of the C4O4 carbonyl group is not symmetrical, the angles around it are quite different [N3—C4—O4 = 119.8 (3)° and C5—C4—O4 = 125.1 (3)°]. The same deviation from symmetry is observed in the structure of the ammonium salt of the orotate anion (Solbakk, 1971). The orotate moiety seems to have a degree of plasticity involving coordination to metal centers. In the Cu (Mutikainen & Lumme, 1980) and Ni (Sabat et al., 1980) complexes of OrH2−, the C2—N1—C6 angle is smaller [117.9 (2) and 118.3 (3)°, respectively] than that of 122.7 (2)° found in orotic acid (Takusagawa & Shimada, 1973) or in (I) [122.8 (3)°]. The carboxylate C—O distances also display some variability, depending upon their environment. When unligated or when bound to Ni or Li (Lutz, 2001), the two C—O distances are practically equal. When OrH is bound to uranium through a carboxylate O atom, however, the C—O bond involving the ligated O atom is longer [1.275 (5) versus 1.221 (6) Å], probably as a result of greater covalency in the U—O bond (Mentzafos et al., 1987).

The most important structural feature of (I) is the extensive network of hydrogen bonds, which not only connect the orotate(1-) anions to the nickel complex, but also relate adjacent anions through the O atoms of carbonyl and carboxylate groups and the two N atoms present in the ring. This self-recognition of the orotate ions leads to the formation of stacked ribbons which are propagated parallel to the b axis of the cell (Fig. 2). This pattern is also found in the structure of the ammonium salt of the orotate anion (Solbakk, 1971). In that compound, the orotate ribbons are interconnected through hydrogen bonds with the ammonium ions and water molecules. The hydrogen bonds linking the orotate ribbons in (I) follow a pattern of the type R22(9) (Bernstein et al., 1995). Adjacent ribbons are bridged laterally by [Ni(H2O)6]2+ cations, the aqua ligands of which act as hydrogen-bond donors to the carbonyl and carboxylate O atoms of the orotate anions, forming an R32(8) motif on one side of the ribbon and an R33(13) motif on the other (Fig. 3). The hexaaquanickel complex cations act as molecular clamps, which force the neighbouring ribbons to approach each other more closely than expected, producing a short contact between two C atoms of neighbouring layers [C6···C7i = 3.166 (5) Å; symmetry code: (i) x, 1/2 − y, −1/2 + z].

The differences in bond lengths and angles between this structure and the isotypic Mg- and Zn-containing structures can be attributed to the difference in size of the metal cations, and follow the pattern found for hexaaqua compounds of the first d-block series in the case of the complexes of nickel and zinc (Cotton et al., 1993). The structure found in these examples of divalent metal complexes differs notably from that of the lithium orotate monohydrate. In that compound, the orotate moiety binds directly to the metal cation. The Li+ cation is surrounded by a tetrahedral environment consisting of a water molecule and three orotate moieties displaying three coordination modes. Conversely, each orotate is ligated to three Li+ ions. The three-dimensional arrangement in that case consists of two-dimensional layers instead of ribbons, which are connected to each other by O—H···O and N—H···O hydrogen bonds, some of them bifurcated.

Experimental top

Crystals of (I) were grown from an aqueous mixture of NiCl2, orotic acid (purchased from Aldrich) and ammonium hydroxide in 1:2:2 molar ratio by slow evaporation at room temperature.

Refinement top

All of the H atoms were found in a difference Fourier map and, except for the orotate H5 atom, their positions were refined freely with Uiso(H) = 1.2Ueq(parent atom). Atom H5 was placed at a geometrically calculated position and refined as riding, with Uiso(H) = 1.2Ueq(C).

Computing details top

Data collection: CAD-4-PC (Enraf-Nonius, 1996); cell refinement: CAD-4-PC; data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Siemens, 1996); software used to prepare material for publication: SHELXL97.

Figures top
[Figure 1] Fig. 1. Displacement ellipsoid plot of hexaaquanickel diorotate(1-) dihydrate. Non-H atoms are represented by 50% probability ellipsoids [symmetry code: (i) −x, 1 − y, −z].
[Figure 2] Fig. 2. The orientation inside the cell of the ribbons formed by orotate self-recognition.
[Figure 3] Fig. 3. Partial view of the packing, showing the stacking of the orotate ribbons and the connection through the hexaaquanickel complex cations.
hexaaquanickel bis(2,4-dihydroxypyrimidine-6-carboxylate) dihydrate top
Crystal data top
[Ni(H2O)6](C5H3N2O4)2·2H2OF(000) = 532
Mr = 513.03Dx = 1.810 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 25 reflections
a = 10.7908 (10) Åθ = 10.5–17.3°
b = 12.8626 (10) ŵ = 1.13 mm1
c = 6.8482 (10) ÅT = 150 K
β = 97.932 (12)°Plate, pale blue
V = 941.42 (18) Å30.20 × 0.11 × 0.02 mm
Z = 2
Data collection top
Nonius CAD-4
diffractometer
1562 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.038
Graphite monochromatorθmax = 27.5°, θmin = 2.5°
ωθ scansh = 1413
Absorption correction: ψ scan
(Kopfmann & Huber, 1968)
k = 160
Tmin = 0.906, Tmax = 0.993l = 08
2326 measured reflections3 standard reflections every 30 min
2148 independent reflections intensity decay: 8.0%
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)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.119H atoms treated by a mixture of independent and constrained refinement
S = 1.00 w = 1/[σ2(Fo2) + (0.045P)2]
where P = (Fo2 + 2Fc2)/3
2148 reflections(Δ/σ)max = 0.005
172 parametersΔρmax = 0.41 e Å3
0 restraintsΔρmin = 0.49 e Å3
Crystal data top
[Ni(H2O)6](C5H3N2O4)2·2H2OV = 941.42 (18) Å3
Mr = 513.03Z = 2
Monoclinic, P21/cMo Kα radiation
a = 10.7908 (10) ŵ = 1.13 mm1
b = 12.8626 (10) ÅT = 150 K
c = 6.8482 (10) Å0.20 × 0.11 × 0.02 mm
β = 97.932 (12)°
Data collection top
Nonius CAD-4
diffractometer
1562 reflections with I > 2σ(I)
Absorption correction: ψ scan
(Kopfmann & Huber, 1968)
Rint = 0.038
Tmin = 0.906, Tmax = 0.9933 standard reflections every 30 min
2326 measured reflections intensity decay: 8.0%
2148 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0470 restraints
wR(F2) = 0.119H atoms treated by a mixture of independent and constrained refinement
S = 1.00Δρmax = 0.41 e Å3
2148 reflectionsΔρmin = 0.49 e Å3
172 parameters
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
Ni10.00000.50000.00000.00961 (16)
O1W0.1754 (2)0.5099 (2)0.0687 (4)0.0137 (5)
H1B0.227 (4)0.451 (3)0.031 (6)0.016*
H1A0.208 (4)0.554 (3)0.020 (6)0.016*
O2W0.0248 (2)0.35856 (19)0.1457 (4)0.0139 (5)
H2B0.043 (4)0.324 (3)0.146 (6)0.017*
H2A0.064 (4)0.363 (3)0.257 (6)0.017*
O3W0.0514 (3)0.5749 (2)0.2661 (4)0.0161 (5)
H3B0.102 (4)0.624 (4)0.292 (6)0.019*
H3A0.005 (4)0.591 (3)0.324 (6)0.019*
O4W0.1357 (3)0.3390 (2)0.5356 (4)0.0174 (6)
H4B0.210 (4)0.355 (3)0.560 (7)0.021*
H4A0.129 (4)0.283 (4)0.559 (7)0.021*
N10.5132 (3)0.2954 (2)0.3016 (4)0.0114 (6)
H1N0.490 (4)0.239 (3)0.283 (6)0.014*
C20.4298 (3)0.3674 (3)0.2143 (5)0.0127 (7)
O20.3276 (2)0.3437 (2)0.1277 (4)0.0207 (6)
N30.4724 (3)0.4688 (2)0.2306 (5)0.0127 (6)
H3N0.418 (4)0.514 (3)0.166 (6)0.015*
C40.5863 (3)0.5024 (3)0.3265 (5)0.0115 (6)
O40.6113 (2)0.59625 (18)0.3324 (4)0.0154 (5)
C50.6672 (3)0.4214 (3)0.4165 (5)0.0112 (7)
H50.74700.43800.48620.013*
C60.6281 (3)0.3220 (3)0.4005 (5)0.0103 (7)
C70.7094 (3)0.2317 (3)0.4851 (5)0.0108 (7)
O50.6674 (2)0.14282 (18)0.4412 (4)0.0138 (5)
O60.8097 (2)0.25358 (19)0.5912 (4)0.0145 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Ni10.0079 (3)0.0077 (3)0.0126 (3)0.0007 (2)0.0010 (2)0.0004 (3)
O1W0.0088 (11)0.0106 (12)0.0211 (13)0.0007 (10)0.0003 (10)0.0001 (11)
O2W0.0123 (13)0.0118 (12)0.0164 (13)0.0029 (10)0.0022 (10)0.0025 (10)
O3W0.0131 (12)0.0154 (12)0.0197 (13)0.0043 (10)0.0019 (11)0.0050 (11)
O4W0.0163 (13)0.0116 (12)0.0232 (14)0.0023 (11)0.0012 (11)0.0017 (11)
N10.0116 (14)0.0061 (13)0.0161 (14)0.0006 (11)0.0008 (12)0.0015 (12)
C20.0138 (17)0.0113 (16)0.0131 (17)0.0019 (12)0.0027 (14)0.0015 (13)
O20.0140 (12)0.0139 (12)0.0311 (15)0.0015 (10)0.0077 (11)0.0034 (12)
N30.0123 (14)0.0090 (13)0.0162 (15)0.0013 (11)0.0002 (12)0.0002 (12)
C40.0091 (14)0.0122 (14)0.0140 (15)0.0006 (14)0.0039 (12)0.0003 (15)
O40.0175 (13)0.0066 (11)0.0218 (13)0.0027 (9)0.0019 (11)0.0006 (10)
C50.0103 (16)0.0104 (15)0.0121 (15)0.0008 (12)0.0013 (13)0.0013 (13)
C60.0116 (16)0.0118 (16)0.0077 (15)0.0013 (12)0.0015 (12)0.0009 (12)
C70.0117 (16)0.0103 (15)0.0108 (15)0.0001 (12)0.0033 (13)0.0036 (13)
O50.0121 (12)0.0104 (11)0.0174 (13)0.0013 (9)0.0030 (10)0.0003 (10)
O60.0127 (12)0.0117 (11)0.0178 (12)0.0019 (10)0.0032 (10)0.0015 (10)
Geometric parameters (Å, º) top
Ni1—O1W2.016 (2)N1—H1N0.78 (4)
Ni1—O3W2.068 (3)C2—O21.217 (4)
Ni1—O2W2.074 (2)C2—N31.382 (4)
O1W—H1B0.95 (4)N3—C41.381 (4)
O1W—H1A0.73 (4)N3—H3N0.90 (4)
O2W—H2B0.86 (4)C4—O41.236 (4)
O2W—H2A0.82 (4)C4—C51.442 (4)
O3W—H3B0.83 (5)C5—C61.347 (5)
O3W—H3A0.80 (5)C5—H50.9500
O4W—H4B0.82 (5)C6—C71.522 (4)
O4W—H4A0.74 (4)C7—O61.250 (4)
N1—C21.370 (4)C7—O51.251 (4)
N1—C61.372 (4)
O1Wi—Ni1—O1W180.0C2—N1—H1N113 (3)
O1Wi—Ni1—O3W95.08 (11)C6—N1—H1N124 (3)
O1W—Ni1—O3W84.92 (11)O2—C2—N1122.7 (3)
O3W—Ni1—O3Wi180.0O2—C2—N3123.0 (3)
O1W—Ni1—O2Wi89.66 (10)N1—C2—N3114.3 (3)
O3W—Ni1—O2Wi90.94 (10)C4—N3—C2126.8 (3)
O1W—Ni1—O2W90.34 (10)C4—N3—H3N120 (3)
O3W—Ni1—O2W89.06 (10)C2—N3—H3N113 (3)
O3Wi—Ni1—O2W90.95 (10)O4—C4—N3119.8 (3)
O2Wi—Ni1—O2W180.0O4—C4—C5125.1 (3)
Ni1—O1W—H1B115 (2)N3—C4—C5115.1 (3)
Ni1—O1W—H1A111 (3)C6—C5—C4119.2 (3)
H1B—O1W—H1A105 (4)C6—C5—H5120.4
Ni1—O2W—H2B114 (3)C4—C5—H5120.4
Ni1—O2W—H2A114 (3)C5—C6—N1121.9 (3)
H2B—O2W—H2A111 (4)C5—C6—C7122.5 (3)
Ni1—O3W—H3B129 (3)N1—C6—C7115.6 (3)
Ni1—O3W—H3A115 (3)O6—C7—O5127.0 (3)
H3B—O3W—H3A103 (4)O6—C7—C6117.2 (3)
H4B—O4W—H4A109 (4)O5—C7—C6115.8 (3)
C2—N1—C6122.8 (3)
C6—N1—C2—O2179.5 (3)C4—C5—C6—N10.3 (5)
C6—N1—C2—N31.3 (5)C4—C5—C6—C7177.9 (3)
O2—C2—N3—C4179.6 (3)C2—N1—C6—C50.7 (5)
N1—C2—N3—C41.2 (5)C2—N1—C6—C7179.0 (3)
C2—N3—C4—O4178.7 (3)C5—C6—C7—O68.1 (5)
C2—N3—C4—C50.4 (5)N1—C6—C7—O6173.7 (3)
O4—C4—C5—C6179.4 (3)C5—C6—C7—O5172.4 (3)
N3—C4—C5—C60.4 (5)N1—C6—C7—O55.9 (4)
Symmetry code: (i) x, y+1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3W—H3B···O6ii0.83 (5)1.96 (5)2.769 (4)164 (4)
O4W—H4B···O4ii0.82 (5)2.06 (5)2.878 (4)170 (4)
N3—H3N···O5iii0.90 (4)1.99 (4)2.860 (4)164 (4)
O2W—H2B···O6iv0.86 (4)1.87 (4)2.714 (3)168 (4)
O1W—H1B···O5iv0.95 (4)1.72 (4)2.663 (3)172 (4)
O3W—H3A···O4Wv0.80 (5)2.03 (5)2.812 (4)168 (4)
O2W—H2A···O4W0.82 (4)1.98 (4)2.782 (4)165 (4)
O4W—H4A···O2Wvi0.74 (4)2.26 (4)2.952 (4)154 (4)
O1W—H1A···O2i0.73 (4)2.01 (4)2.728 (4)169 (5)
N1—H1N···O4vii0.78 (4)2.22 (4)2.978 (4)165 (4)
Symmetry codes: (i) x, y+1, z; (ii) x+1, y+1, z+1; (iii) x+1, y+1/2, z+1/2; (iv) x1, y+1/2, z1/2; (v) x, y+1, z+1; (vi) x, y+1/2, z+1/2; (vii) x+1, y1/2, z+1/2.

Experimental details

Crystal data
Chemical formula[Ni(H2O)6](C5H3N2O4)2·2H2O
Mr513.03
Crystal system, space groupMonoclinic, P21/c
Temperature (K)150
a, b, c (Å)10.7908 (10), 12.8626 (10), 6.8482 (10)
β (°) 97.932 (12)
V3)941.42 (18)
Z2
Radiation typeMo Kα
µ (mm1)1.13
Crystal size (mm)0.20 × 0.11 × 0.02
Data collection
DiffractometerNonius CAD-4
diffractometer
Absorption correctionψ scan
(Kopfmann & Huber, 1968)
Tmin, Tmax0.906, 0.993
No. of measured, independent and
observed [I > 2σ(I)] reflections
2326, 2148, 1562
Rint0.038
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.047, 0.119, 1.00
No. of reflections2148
No. of parameters172
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.41, 0.49

Computer programs: CAD-4-PC (Enraf-Nonius, 1996), CAD-4-PC, XCAD4 (Harms & Wocadlo, 1995), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Siemens, 1996), SHELXL97.

Selected geometric parameters (Å, º) top
Ni1—O1W2.016 (2)Ni1—O2W2.074 (2)
Ni1—O3W2.068 (3)
O1W—Ni1—O3W84.92 (11)O3W—Ni1—O2W89.06 (10)
O1W—Ni1—O2W90.34 (10)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3W—H3B···O6i0.83 (5)1.96 (5)2.769 (4)164 (4)
O4W—H4B···O4i0.82 (5)2.06 (5)2.878 (4)170 (4)
N3—H3N···O5ii0.90 (4)1.99 (4)2.860 (4)164 (4)
O2W—H2B···O6iii0.86 (4)1.87 (4)2.714 (3)168 (4)
O1W—H1B···O5iii0.95 (4)1.72 (4)2.663 (3)172 (4)
O3W—H3A···O4Wiv0.80 (5)2.03 (5)2.812 (4)168 (4)
O2W—H2A···O4W0.82 (4)1.98 (4)2.782 (4)165 (4)
O4W—H4A···O2Wv0.74 (4)2.26 (4)2.952 (4)154 (4)
O1W—H1A···O2vi0.73 (4)2.01 (4)2.728 (4)169 (5)
N1—H1N···O4vii0.78 (4)2.22 (4)2.978 (4)165 (4)
Symmetry codes: (i) x+1, y+1, z+1; (ii) x+1, y+1/2, z+1/2; (iii) x1, y+1/2, z1/2; (iv) x, y+1, z+1; (v) x, y+1/2, z+1/2; (vi) x, y+1, z; (vii) x+1, y1/2, z+1/2.
 

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