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Acta Crystallogr Sect E Struct Rep Online. 2010 June 1; 66(Pt 6): m612–m613.
Published online 2010 May 8. doi:  10.1107/S1600536810015837
PMCID: PMC2979368

Tetra­aqua­bis(orotato-κO)cobalt(II) dihydrate

Abstract

In the title CoII complex, [Co(C5H3N2O4)2(H2O)4]·2H2O, the CoII ion is located on an inversion center and is coordinated by two orotate (2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylate) anions and four water mol­ecules in a slightly distorted octa­hedral geometry. The dihedral angle between the carboxyl­ate group and the attached orotate ring is 1.2 (3)°. In the crystal structure, inter­molecular O—H(...)O, N—H(...)O and C—H(...)O hydrogen bonds link the mol­ecules into a three-dimensional network. π–π contacts between the orotate rings [centroid–centroid distances = 3.439 (2) and 3.438 (2) Å] further stabilize the structure.

Related literature

For orotic acid, see: Doody et al. (1996 [triangle]); Köse et al. (2008 [triangle]); Levine et al. (1974 [triangle]); Nelson & Michael (2000 [triangle]); Smith & Baker (1959 [triangle]). For applications of metal–orotate complexes and their derivatives, see: Schmidbaur et al. (1990 [triangle]); Castan et al. (1990 [triangle]); Köse et al. (2006 [triangle]). For related structures, see: Ha et al. (1999 [triangle]); Icbudak et al. (2003 [triangle]); Karipides & Thomas (1986 [triangle]); Kumberger et al. (1991 [triangle]); Mutikainen (1987 [triangle]); Mutikainen et al. (1996 [triangle]); Nepveu et al. (1995 [triangle]); Platter et al. (2002 [triangle]); Sabat et al. (1980 [triangle]); Solbakk (1971 [triangle]); Sun et al. (2002 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-0m612-scheme1.jpg

Experimental

Crystal data

  • [Co(C5H3N2O4)2(H2O)4]·2H2O
  • M r = 477.21
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0m612-efi1.jpg
  • a = 9.8715 (5) Å
  • b = 13.1514 (7) Å
  • c = 6.7281 (3) Å
  • β = 92.224 (3)°
  • V = 872.81 (8) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 1.07 mm−1
  • T = 100 K
  • 0.35 × 0.20 × 0.15 mm

Data collection

  • Bruker Kappa APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.775, T max = 0.851
  • 6413 measured reflections
  • 2006 independent reflections
  • 1905 reflections with I > 2σ(I)
  • R int = 0.024

Refinement

  • R[F 2 > 2σ(F 2)] = 0.056
  • wR(F 2) = 0.168
  • S = 1.11
  • 2006 reflections
  • 164 parameters
  • 11 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 1.99 e Å−3
  • Δρmin = −0.49 e Å−3

Data collection: APEX2 (Bruker, 2007 [triangle]); cell refinement: SAINT (Bruker, 2007 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: Mercury (Macrae et al., 2006 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]) and PLATON (Spek, 2009 [triangle]).

Table 1
Selected bond lengths (Å)
Table 2
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810015837/xu2754sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810015837/xu2754Isup2.hkl

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

supplementary crystallographic information

Comment

Orotic acid (6-uracilic acid, vitamin B13, H3Or) is an essential vitamin in the syntheses of pyrimidine bases of nucleic acids, since it is the first pyridine product of an enzymatic step in normal blood cells (Nelson & Michael, 2000; Smith & Baker, 1959; Levine et al., 1974). Metal orotate complexes and their derivatives not only found applications in curing syndromes but also they have encouraging studies as therapeutic agents for cancer (Schmidbaur et al., 1990; Castan et al., 1990; Köse et al., 2006). Orotic acid is an interesting ligand because it has multiple coordination sites at low and neutral pH, it is coordinated from the carboxylic acid group monodentately in ketonic form but at higher pH values bidentate coordination occurs in enolic form, the tautomerism between the ketonic and enolic structures makes multiform coordinations possible (Doody et al., 1996; Köse et al., 2008). Mononuclear crystal structures of Co, Cu, Mg, Ni and Zn complexes were reported, where bidentate orotate dianions (HOr2-) found in the molecules (Mutikainen, 1987; Mutikainen et al., 1996; Icbudak et al., 2003; Sabat et al., 1980; Karipides & Thomas, 1986; Platter et al., 2002; Kumberger et al., 1991). Dianionic form of the acid (HOr2-) can also act as a polydentate ligand in its polymeric complexes with Cu, Ni and Mn metals (Nepveu et al., 1995; Ha et al., 1999; Platter et al., 2002; Sun et al., 2002). Relatively limited number of monoanionic orotate complex crystal studies are found in the literature. The metal orotate structures including Mg, Ni and Zn have (H2Or-) ions located in the outer coordination sphere and the monoanion does not enter the inner coordination sphere of the aquated metal, M(II), cations (Solbakk, 1971). The title compound was synthesized and its crystal structure is reported herein.

The title complex, (I), is a crystallographically centrosymmetric mononuclear complex, consisting of two orotate, (Or), ligands, four coordinated and one uncoordinated water molecules (Fig. 1). Or ligands are monodentate. The four O atoms (O5, O6, and the symmetry-related atoms, O5', O6') in the equatorial plane around the Co atom form a slightly distorted square-planar arrangement, while the slightly distorted octahedral coordination is completed by the two O atoms of the Or ligands (O1, O1') in the axial positions (Fig. 1).

The near equality of the C1—O1 [1.269 (4) Å] and C1—O2 [1.224 (5) Å] bonds in the carboxylate group indicates a delocalized bonding arrangement, rather than localized single and double bonds. The average Co—O bond length is 2.095 (3) Å (Table 1), and the Co atom is displaced out of the least-squares plane of the carboxylate group (O1/C1/O2) by 0.6042 (1) Å. The dihedral angle between the planar carboxylate group and the Or ring A (N1/N2/C2—C5) is 1.15 (31)°. Atoms O1, O2, O3, O4 and C1 are -0.064 (3), -0.027 (4), -0.069 (3), 0.040 (3) and -0.039 (4) Å away from the plane of the Or ring, respectively.

In the crystal structure, intramolecular O—H···O and intermolecular O—H···O, N—H···O and C—H···O hydrogen bonds (Table 2) link the molecules into a three-dimensional network, in which they may be effective in the stabilization of the structure. The π–π contacts between the Or rings, Cg1—Cg1i and Cg1—Cg1ii [symmetry codes: (i) x, 1/2 - y, z - 1/2; (ii) x, 1/2 - y, z + 1/2, where Cg1 is the centroid of the ring (N1/N2/C2—C5)] may further stabilize the structure, with centroid-centroid distances of 3.439 (2) and 3.438 (2) Å, respectively.

Experimental

The title compound was prepared by the reaction of NH4H2Or (0.96 g, 5 mmol) in H2O (100 ml) and nicotinamide (1.22 g, 10 mmol) in H2O (100 ml) with Co(NO3)2.6H2O (1.45 g, 5 mmol) in H2O (50 ml). The mixture was filtered and set aside to crystallize at ambient temperature for one week, giving pink single crystals.

Refinement

The highest peak and deepest hole in the final difference electron-density map were located 1.99 and 0.49 Å, respectively, from atom Co1. Atom H5 was positioned geometrically with C—H = 0.93 Å, for aromatic H atom and constrained to ride on its parent atom, with Uiso(H) = 1.2Ueq(C). Atoms H1, H2 (for NH), H51, H52, H61, H62, H71, H72 (for H2O) were located in difference Fourier maps and refined isotropically, with restrains of N1—H1 = 0.83 (2), N2—H2 = 0.84 (6), O5—H51 = 0.93 (2), O5—H52 = 0.91 (5), O6—H61 = 0.95 (2), O6—H62 = 0.92 (5), O7—H71 = 0.94 (5), O7—H72 = 0.97 (5) Å and H51-O5-H52 = 107 (4), H61-O6-H62 = 107 (4) and H71-O7-H72 = 107 (4)°.

Figures

Fig. 1.
The molecular structure of the title molecule with the atom-numbering scheme. Displacement ellipsoids are drawn at the 40% probability level. Primed atoms are generated by the symmetry operator:(') -x, -y, -z.

Crystal data

[Co(C5H3N2O4)2(H2O)4]·2H2OF(000) = 490
Mr = 477.21Dx = 1.816 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2967 reflections
a = 9.8715 (5) Åθ = 2.2–24.3°
b = 13.1514 (7) ŵ = 1.07 mm1
c = 6.7281 (3) ÅT = 100 K
β = 92.224 (3)°Block, pink
V = 872.81 (8) Å30.35 × 0.20 × 0.15 mm
Z = 2

Data collection

Bruker Kappa APEXII CCD area-detector diffractometer2006 independent reflections
Radiation source: fine-focus sealed tube1905 reflections with I > 2σ(I)
graphiteRint = 0.024
[var phi] and ω scansθmax = 27.7°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −12→11
Tmin = 0.775, Tmax = 0.851k = −17→12
6413 measured reflectionsl = −8→8

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)] = 0.056Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.168H atoms treated by a mixture of independent and constrained refinement
S = 1.11w = 1/[σ2(Fo2) + (0.106P)2 + 1.3319P] where P = (Fo2 + 2Fc2)/3
2006 reflections(Δ/σ)max < 0.001
164 parametersΔρmax = 1.99 e Å3
11 restraintsΔρmin = −0.49 e Å3

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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
Co10.00000.00000.00000.0219 (3)
O1−0.1500 (2)0.0836 (2)0.1269 (4)0.0294 (6)
O2−0.3106 (3)−0.0336 (2)0.1649 (5)0.0388 (7)
O3−0.3502 (3)0.4086 (2)0.1788 (5)0.0387 (7)
O4−0.7136 (3)0.2040 (2)0.2605 (5)0.0388 (7)
O5−0.0640 (3)−0.1370 (2)0.1312 (4)0.0310 (6)
H51−0.158 (2)−0.137 (5)0.127 (9)0.067*
H52−0.038 (7)−0.200 (3)0.092 (12)0.09 (3)*
O60.1274 (3)0.0294 (2)0.2535 (4)0.0319 (6)
H610.175 (5)0.092 (2)0.259 (8)0.060 (18)*
H620.191 (5)−0.021 (3)0.278 (9)0.057 (18)*
O70.0502 (4)0.6880 (2)0.0068 (5)0.0399 (7)
H710.010 (7)0.656 (5)−0.106 (6)0.08 (2)*
H720.047 (8)0.639 (4)0.114 (7)0.09 (3)*
N1−0.3185 (3)0.2368 (2)0.1577 (5)0.0251 (6)
H1−0.240 (3)0.250 (5)0.127 (9)0.053 (16)*
N2−0.5297 (3)0.3038 (2)0.2173 (5)0.0269 (6)
H2−0.573 (7)0.358 (4)0.229 (12)0.09 (3)*
C1−0.2701 (3)0.0542 (3)0.1553 (5)0.0224 (7)
C2−0.3695 (3)0.1405 (3)0.1770 (5)0.0216 (6)
C3−0.3958 (3)0.3223 (3)0.1841 (5)0.0248 (7)
C4−0.5914 (3)0.2099 (3)0.2312 (5)0.0243 (7)
C5−0.5017 (3)0.1247 (3)0.2120 (5)0.0226 (7)
H5−0.53450.05880.22360.027*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Co10.0145 (4)0.0152 (4)0.0363 (4)0.00237 (19)0.0044 (3)−0.0016 (2)
O10.0167 (11)0.0196 (12)0.0525 (16)0.0007 (9)0.0096 (10)−0.0062 (10)
O20.0304 (15)0.0164 (14)0.071 (2)−0.0017 (11)0.0170 (13)0.0004 (13)
O30.0296 (14)0.0192 (13)0.0672 (19)−0.0064 (11)0.0013 (12)−0.0018 (12)
O40.0164 (12)0.0321 (15)0.068 (2)−0.0008 (10)0.0099 (12)−0.0026 (13)
O50.0220 (12)0.0229 (13)0.0488 (16)0.0000 (10)0.0085 (10)0.0044 (11)
O60.0227 (13)0.0267 (14)0.0460 (15)0.0023 (11)−0.0015 (10)−0.0024 (12)
O70.0453 (18)0.0282 (15)0.0462 (17)0.0016 (13)0.0007 (13)0.0015 (12)
N10.0180 (13)0.0189 (15)0.0389 (16)−0.0018 (11)0.0071 (11)−0.0014 (11)
N20.0189 (14)0.0178 (14)0.0441 (17)0.0032 (11)0.0045 (11)−0.0049 (12)
C10.0147 (14)0.0176 (15)0.0351 (16)0.0007 (12)0.0038 (11)−0.0011 (12)
C20.0180 (14)0.0195 (16)0.0276 (15)0.0025 (12)0.0042 (11)−0.0022 (12)
C30.0203 (16)0.0181 (16)0.0359 (17)−0.0002 (12)0.0001 (12)−0.0027 (12)
C40.0157 (14)0.0205 (16)0.0369 (17)−0.0008 (12)0.0046 (12)−0.0051 (13)
C50.0165 (14)0.0159 (15)0.0358 (17)0.0006 (11)0.0055 (12)0.0000 (12)

Geometric parameters (Å, °)

Co1—O12.056 (2)O6—H620.92 (5)
Co1—O1i2.056 (2)O7—H710.94 (5)
Co1—O52.113 (3)O7—H720.97 (5)
Co1—O5i2.113 (3)N1—C21.371 (4)
Co1—O62.115 (3)N1—C31.374 (5)
Co1—O6i2.115 (3)N1—H10.83 (2)
O1—C11.269 (4)N2—C31.371 (4)
O2—C11.224 (5)N2—C41.382 (4)
O3—C31.222 (5)N2—H20.84 (6)
O4—C41.232 (4)C2—C11.510 (4)
O5—H510.93 (2)C2—C51.351 (4)
O5—H520.91 (5)C5—C41.437 (5)
O6—H610.95 (2)C5—H50.9300
O1—Co1—O1i180.00 (14)H71—O7—H72107 (4)
O1—Co1—O592.89 (10)C2—N1—C3122.5 (3)
O1i—Co1—O587.11 (10)C2—N1—H1124 (4)
O1—Co1—O5i87.11 (10)C3—N1—H1113 (4)
O1i—Co1—O5i92.89 (10)C3—N2—C4126.8 (3)
O1—Co1—O689.00 (11)C3—N2—H2112 (6)
O1i—Co1—O691.00 (11)C4—N2—H2121 (6)
O1—Co1—O6i91.00 (11)O1—C1—C2113.6 (3)
O1i—Co1—O6i89.00 (11)O2—C1—O1127.2 (3)
O5i—Co1—O5180.00 (19)O2—C1—C2119.2 (3)
O5—Co1—O689.84 (11)N1—C2—C1116.3 (3)
O5i—Co1—O690.16 (11)C5—C2—N1121.3 (3)
O5—Co1—O6i90.16 (11)C5—C2—C1122.4 (3)
O5i—Co1—O6i89.84 (11)O3—C3—N1123.4 (3)
O6i—Co1—O6180.00 (10)O3—C3—N2121.8 (3)
C1—O1—Co1126.3 (2)N2—C3—N1114.8 (3)
Co1—O5—H51108 (4)O4—C4—N2120.2 (3)
Co1—O5—H52124 (5)O4—C4—C5125.2 (3)
H52—O5—H51107 (4)N2—C4—C5114.6 (3)
Co1—O6—H61118 (3)C2—C5—C4119.9 (3)
Co1—O6—H62113 (4)C2—C5—H5120.0
H61—O6—H62107 (4)C4—C5—H5120.0
O5—Co1—O1—C1−36.3 (3)C4—N2—C3—N11.7 (5)
O5i—Co1—O1—C1143.7 (3)C3—N2—C4—O4−179.6 (4)
O6—Co1—O1—C1−126.1 (3)C3—N2—C4—C51.3 (5)
O6i—Co1—O1—C153.9 (3)N1—C2—C1—O11.8 (5)
Co1—O1—C1—O221.4 (5)N1—C2—C1—O2−177.8 (3)
Co1—O1—C1—C2−158.2 (2)C5—C2—C1—O1−178.7 (3)
C3—N1—C2—C1−176.5 (3)C5—C2—C1—O21.8 (5)
C3—N1—C2—C53.9 (5)N1—C2—C5—C4−0.5 (5)
C2—N1—C3—O3175.6 (4)C1—C2—C5—C4180.0 (3)
C2—N1—C3—N2−4.4 (5)C2—C5—C4—O4179.0 (4)
C4—N2—C3—O3−178.3 (4)C2—C5—C4—N2−1.9 (5)

Symmetry codes: (i) −x, −y, −z.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O7ii0.83 (4)2.26 (4)3.073 (4)167 (5)
N2—H2···O2iii0.84 (6)1.98 (6)2.790 (4)162 (7)
O5—H51···O20.93 (2)2.05 (5)2.805 (4)137 (5)
O5—H52···O7iv0.91 (5)1.82 (5)2.710 (4)167 (6)
O6—H61···O4v0.95 (3)1.84 (4)2.781 (4)173 (5)
O6—H62···O3vi0.92 (5)1.84 (5)2.737 (4)164 (4)
O7—H71···O5vii0.94 (5)1.90 (5)2.808 (4)160 (6)
O7—H72···O1viii0.97 (5)2.11 (5)2.957 (4)145 (6)
O7—H72···O6viii0.97 (5)2.44 (7)3.201 (4)135 (6)
C5—H5···O3ix0.932.383.292 (5)165

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: XU2754).

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