Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807054050/bt2564sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807054050/bt2564Isup2.hkl |
CCDC reference: 672581
A solution of CoCl2.6H2O (1.2 g, 1 mmol) in water (25 ml) was added to a solution of orotic acid (0.9 g, 1 mmol) in water (25 ml). The solution refluxed and stirred in a temperature-controlled bath. The mixture was then left for crystallization.
The H atom attached to the N atom was located in a difference Fourier map and refined isotropically. H atoms of coordinated water molecules were located in a difference Fourier map and refined isotropically with Uiso(H) = 1.5 Ueq(O). The N2—H2N and coordinated water H atoms were restrained to values of 0.85 (1) and 0.89 (1) Å, respectively. The H atom attached to the C atom was positioned geometrically and treated as riding on its parent C atom with C—H distance = 0.93 Å, and with Uiso(H) = 1.2Ueq(C). The O atoms of the uncoordinated water (O5W, O6W & O7W) molecules show high displacement parameters, but attempts to refine them as disordered were unsucessful. Hence, the O atoms were refined isotropically. The H atoms of O5W, O6W and O7W could not be located from electron density maps. These H atoms were not included in the calculations (although they are included in the emprical formula). A maximum (positive) residual density was observed 0.88 Å from atom O5W.
Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL/PC (Sheldrick, 1990) and PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997).
[Co(C5H2N2O4)(H2O)4]·2.5H2O | F(000) = 1360 |
Mr = 330.12 | Dx = 1.673 Mg m−3 |
Orthorhombic, Pbcn | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2n 2ab | Cell parameters from 7524 reflections |
a = 20.8700 (19) Å | θ = 2.4–24.3° |
b = 17.1153 (16) Å | µ = 1.36 mm−1 |
c = 7.3375 (7) Å | T = 293 K |
V = 2620.9 (4) Å3 | Block, brown |
Z = 8 | 0.16 × 0.11 × 0.05 mm |
Bruker SMART CCD area-detector diffractometer | 2321 independent reflections |
Radiation source: fine-focus sealed tube | 1971 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.038 |
ω scans | θmax = 25.0°, θmin = 1.5° |
Absorption correction: multi-scan (SADABS; Bruker, 2001) | h = −24→24 |
Tmin = 0.82, Tmax = 0.94 | k = −20→19 |
17563 measured reflections | l = −8→8 |
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)] = 0.063 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.199 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.12 | w = 1/[σ2(Fo2) + (0.1193P)2 + 6.0462P] where P = (Fo2 + 2Fc2)/3 |
2321 reflections | (Δ/σ)max = 0.001 |
183 parameters | Δρmax = 1.39 e Å−3 |
10 restraints | Δρmin = −0.71 e Å−3 |
[Co(C5H2N2O4)(H2O)4]·2.5H2O | V = 2620.9 (4) Å3 |
Mr = 330.12 | Z = 8 |
Orthorhombic, Pbcn | Mo Kα radiation |
a = 20.8700 (19) Å | µ = 1.36 mm−1 |
b = 17.1153 (16) Å | T = 293 K |
c = 7.3375 (7) Å | 0.16 × 0.11 × 0.05 mm |
Bruker SMART CCD area-detector diffractometer | 2321 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2001) | 1971 reflections with I > 2σ(I) |
Tmin = 0.82, Tmax = 0.94 | Rint = 0.038 |
17563 measured reflections |
R[F2 > 2σ(F2)] = 0.063 | 10 restraints |
wR(F2) = 0.199 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.12 | Δρmax = 1.39 e Å−3 |
2321 reflections | Δρmin = −0.71 e Å−3 |
183 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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.7263 (2) | 0.3856 (3) | 0.3371 (7) | 0.0385 (12) | |
C2 | 0.6732 (2) | 0.4366 (3) | 0.2594 (7) | 0.0309 (10) | |
C3 | 0.6769 (2) | 0.5154 (3) | 0.2676 (7) | 0.0338 (11) | |
H3 | 0.7118 | 0.5399 | 0.3216 | 0.041* | |
C4 | 0.6257 (2) | 0.5599 (3) | 0.1911 (6) | 0.0312 (11) | |
C5 | 0.5743 (2) | 0.4364 (3) | 0.1159 (6) | 0.0286 (10) | |
Co1 | 0.63880 (3) | 0.27419 (4) | 0.18230 (9) | 0.0331 (3) | |
N1 | 0.62351 (19) | 0.3957 (2) | 0.1868 (5) | 0.0299 (9) | |
N2 | 0.57606 (18) | 0.5165 (2) | 0.1237 (5) | 0.0292 (9) | |
H2N | 0.5431 (16) | 0.542 (3) | 0.090 (7) | 0.039 (15)* | |
O5 | 0.71873 (17) | 0.3129 (2) | 0.3242 (5) | 0.0435 (9) | |
O6 | 0.77339 (19) | 0.4172 (2) | 0.4090 (7) | 0.0578 (12) | |
O7 | 0.62424 (19) | 0.6324 (2) | 0.1820 (5) | 0.0397 (9) | |
O8 | 0.52739 (15) | 0.40450 (19) | 0.0404 (5) | 0.0360 (8) | |
O1W | 0.6869 (2) | 0.2836 (3) | −0.0659 (6) | 0.0688 (15) | |
H1W | 0.674 (5) | 0.306 (5) | −0.169 (7) | 0.108* | |
H2W | 0.715 (4) | 0.252 (5) | −0.120 (13) | 0.108* | |
O2W | 0.5526 (2) | 0.2518 (2) | 0.0408 (6) | 0.0525 (10) | |
H3W | 0.534 (3) | 0.298 (2) | 0.030 (10) | 0.073* | |
H4W | 0.548 (4) | 0.221 (4) | 0.137 (6) | 0.073* | |
O3W | 0.6630 (3) | 0.1565 (3) | 0.1854 (6) | 0.0619 (13) | |
H5W | 0.686 (5) | 0.142 (7) | 0.089 (10) | 0.144* | |
H6W | 0.680 (5) | 0.144 (7) | 0.293 (8) | 0.144* | |
O4W | 0.5907 (2) | 0.2568 (2) | 0.4340 (5) | 0.0452 (9) | |
H7W | 0.589 (4) | 0.3028 (18) | 0.491 (8) | 0.082* | |
H8W | 0.608 (4) | 0.216 (2) | 0.491 (8) | 0.082* | |
O5W | 0.6640 (5) | 0.0575 (6) | 0.4756 (14) | 0.148 (3)* | |
O6W | 0.5927 (4) | 0.1499 (6) | 0.7340 (14) | 0.141 (3)* | |
O7W | 0.5000 | 0.1145 (14) | 0.2500 | 0.251 (9)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.029 (2) | 0.045 (3) | 0.042 (3) | 0.004 (2) | −0.005 (2) | 0.010 (2) |
C2 | 0.024 (2) | 0.039 (3) | 0.030 (2) | 0.0022 (19) | −0.0005 (19) | 0.005 (2) |
C3 | 0.027 (2) | 0.040 (3) | 0.035 (2) | −0.003 (2) | −0.007 (2) | 0.005 (2) |
C4 | 0.032 (2) | 0.035 (3) | 0.027 (2) | 0.003 (2) | −0.0020 (19) | 0.0046 (19) |
C5 | 0.025 (2) | 0.031 (2) | 0.029 (2) | 0.0065 (18) | 0.0007 (19) | −0.0014 (19) |
Co1 | 0.0328 (5) | 0.0306 (5) | 0.0359 (5) | 0.0094 (2) | 0.0009 (3) | −0.0006 (3) |
N1 | 0.0249 (19) | 0.029 (2) | 0.035 (2) | 0.0053 (16) | −0.0030 (16) | 0.0001 (16) |
N2 | 0.027 (2) | 0.027 (2) | 0.034 (2) | 0.0063 (15) | −0.0047 (17) | 0.0012 (17) |
O5 | 0.0367 (19) | 0.038 (2) | 0.056 (2) | 0.0099 (16) | −0.0112 (16) | 0.0036 (16) |
O6 | 0.039 (2) | 0.050 (2) | 0.085 (3) | −0.0030 (18) | −0.027 (2) | 0.015 (2) |
O7 | 0.050 (2) | 0.0253 (19) | 0.044 (2) | −0.0024 (15) | −0.0124 (16) | 0.0031 (15) |
O8 | 0.0307 (17) | 0.0303 (17) | 0.047 (2) | 0.0050 (13) | −0.0119 (15) | −0.0028 (15) |
O1W | 0.072 (3) | 0.087 (3) | 0.047 (3) | 0.053 (3) | 0.023 (2) | 0.021 (2) |
O2W | 0.049 (2) | 0.044 (2) | 0.065 (3) | 0.0031 (19) | −0.011 (2) | −0.008 (2) |
O3W | 0.096 (4) | 0.039 (2) | 0.051 (3) | 0.028 (2) | 0.020 (2) | 0.0046 (19) |
O4W | 0.054 (2) | 0.0392 (19) | 0.042 (2) | −0.0014 (18) | 0.0065 (18) | −0.0056 (17) |
C1—O6 | 1.240 (6) | Co1—O1W | 2.086 (4) |
C1—O5 | 1.258 (7) | Co1—N1 | 2.104 (4) |
C1—C2 | 1.521 (7) | Co1—O2W | 2.112 (4) |
C2—C3 | 1.352 (7) | Co1—O4W | 2.123 (4) |
C2—N1 | 1.360 (6) | N2—H2N | 0.85 (4) |
C3—C4 | 1.427 (7) | O1W—H1W | 0.89 (6) |
C3—H3 | 0.9300 | O1W—H2W | 0.89 (8) |
C4—O7 | 1.243 (6) | O2W—H3W | 0.88 (4) |
C4—N2 | 1.367 (6) | O2W—H4W | 0.89 (5) |
C5—O8 | 1.249 (6) | O3W—H5W | 0.89 (9) |
C5—N1 | 1.347 (6) | O3W—H6W | 0.89 (7) |
C5—N2 | 1.374 (6) | O4W—H7W | 0.89 (4) |
Co1—O5 | 2.075 (4) | O4W—H8W | 0.89 (5) |
Co1—O3W | 2.078 (4) | ||
O6—C1—O5 | 124.2 (5) | O5—Co1—O4W | 89.33 (15) |
O6—C1—C2 | 119.1 (5) | O3W—Co1—O4W | 88.23 (16) |
O5—C1—C2 | 116.6 (4) | O1W—Co1—O4W | 176.33 (17) |
C3—C2—N1 | 125.0 (4) | N1—Co1—O4W | 93.08 (15) |
C3—C2—C1 | 121.0 (4) | O2W—Co1—O4W | 89.99 (17) |
N1—C2—C1 | 114.0 (4) | C5—N1—C2 | 117.8 (4) |
C2—C3—C4 | 118.3 (4) | C5—N1—Co1 | 128.4 (3) |
C2—C3—H3 | 120.9 | C2—N1—Co1 | 113.6 (3) |
C4—C3—H3 | 120.9 | C4—N2—C5 | 125.3 (4) |
O7—C4—N2 | 120.2 (4) | C4—N2—H2N | 116 (4) |
O7—C4—C3 | 125.0 (5) | C5—N2—H2N | 118 (4) |
N2—C4—C3 | 114.8 (4) | C1—O5—Co1 | 117.0 (3) |
O8—C5—N1 | 122.9 (4) | Co1—O1W—H1W | 130 (7) |
O8—C5—N2 | 118.4 (4) | Co1—O1W—H2W | 131 (7) |
N1—C5—N2 | 118.7 (4) | H1W—O1W—H2W | 94 (8) |
O5—Co1—O3W | 96.2 (2) | Co1—O2W—H3W | 105 (5) |
O5—Co1—O1W | 91.51 (19) | Co1—O2W—H4W | 79 (5) |
O3W—Co1—O1W | 88.13 (17) | H3W—O2W—H4W | 123 (7) |
O5—Co1—N1 | 78.39 (15) | Co1—O3W—H5W | 113 (8) |
O3W—Co1—N1 | 174.4 (2) | Co1—O3W—H6W | 109 (8) |
O1W—Co1—N1 | 90.59 (17) | H5W—O3W—H6W | 115 (10) |
O5—Co1—O2W | 171.62 (15) | Co1—O4W—H7W | 108 (5) |
O3W—Co1—O2W | 92.1 (2) | Co1—O4W—H8W | 109 (5) |
O1W—Co1—O2W | 89.7 (2) | H7W—O4W—H8W | 119 (5) |
N1—Co1—O2W | 93.31 (16) | ||
O6—C1—C2—C3 | 0.1 (8) | O1W—Co1—N1—C5 | 88.8 (4) |
O5—C1—C2—C3 | 179.7 (5) | O2W—Co1—N1—C5 | −0.9 (4) |
O6—C1—C2—N1 | −179.0 (5) | O4W—Co1—N1—C5 | −91.1 (4) |
O5—C1—C2—N1 | 0.6 (7) | O5—Co1—N1—C2 | 5.7 (3) |
N1—C2—C3—C4 | −1.5 (8) | O1W—Co1—N1—C2 | −85.7 (4) |
C1—C2—C3—C4 | 179.6 (4) | O2W—Co1—N1—C2 | −175.4 (3) |
C2—C3—C4—O7 | −176.6 (5) | O4W—Co1—N1—C2 | 94.4 (3) |
C2—C3—C4—N2 | 2.9 (7) | O7—C4—N2—C5 | 175.7 (4) |
O8—C5—N1—C2 | 177.5 (4) | C3—C4—N2—C5 | −3.9 (7) |
N2—C5—N1—C2 | −1.3 (6) | O8—C5—N2—C4 | −175.7 (4) |
O8—C5—N1—Co1 | 3.2 (7) | N1—C5—N2—C4 | 3.2 (7) |
N2—C5—N1—Co1 | −175.6 (3) | O6—C1—O5—Co1 | −175.9 (4) |
C3—C2—N1—C5 | 0.6 (7) | C2—C1—O5—Co1 | 4.5 (6) |
C1—C2—N1—C5 | 179.6 (4) | O3W—Co1—O5—C1 | 172.9 (4) |
C3—C2—N1—Co1 | 175.7 (4) | O1W—Co1—O5—C1 | 84.7 (4) |
C1—C2—N1—Co1 | −5.2 (5) | N1—Co1—O5—C1 | −5.6 (4) |
O5—Co1—N1—C5 | −179.8 (4) | O4W—Co1—O5—C1 | −98.9 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2N···O8i | 0.85 (4) | 1.98 (4) | 2.818 (5) | 168 (5) |
O1W—H2W···O5ii | 0.89 (6) | 1.82 (9) | 2.694 (5) | 166 (10) |
O1W—H1W···O7iii | 0.89 (8) | 1.84 (4) | 2.683 (5) | 157 (9) |
O3W—H5W···O6ii | 0.89 (9) | 1.87 (10) | 2.732 (6) | 164 (11) |
O3W—H6W···O5W | 0.89 (7) | 2.03 (9) | 2.721 (11) | 134 (10) |
O4W—H7W···O7iv | 0.89 (7) | 1.94 (4) | 2.720 (5) | 146 (6) |
O4W—H8W···O6W | 0.89 (5) | 2.14 (5) | 2.862 (11) | 138 (7) |
O2W—H3W···O8 | 0.88 (4) | 1.82 (3) | 2.666 (5) | 157 (7) |
O2W—H4W···O7W | 0.89 (5) | 2.24 (5) | 3.014 (19) | 146 (7) |
O2W—H4W···O4W | 0.89 (5) | 2.43 (7) | 2.994 (6) | 122 (6) |
Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x+3/2, −y+1/2, z−1/2; (iii) x, −y+1, z−1/2; (iv) x, −y+1, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | [Co(C5H2N2O4)(H2O)4]·2.5H2O |
Mr | 330.12 |
Crystal system, space group | Orthorhombic, Pbcn |
Temperature (K) | 293 |
a, b, c (Å) | 20.8700 (19), 17.1153 (16), 7.3375 (7) |
V (Å3) | 2620.9 (4) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 1.36 |
Crystal size (mm) | 0.16 × 0.11 × 0.05 |
Data collection | |
Diffractometer | Bruker SMART CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2001) |
Tmin, Tmax | 0.82, 0.94 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 17563, 2321, 1971 |
Rint | 0.038 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.063, 0.199, 1.12 |
No. of reflections | 2321 |
No. of parameters | 183 |
No. of restraints | 10 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 1.39, −0.71 |
Computer programs: SMART (Bruker, 2001), SAINT (Bruker, 2001), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL/PC (Sheldrick, 1990) and PLATON (Spek, 2003).
Co1—O5 | 2.075 (4) | Co1—O2W | 2.112 (4) |
Co1—O3W | 2.078 (4) | Co1—O4W | 2.123 (4) |
Co1—O1W | 2.086 (4) | ||
O5—Co1—O3W | 96.2 (2) | O3W—Co1—O2W | 92.1 (2) |
O5—Co1—O1W | 91.51 (19) | O1W—Co1—O2W | 89.7 (2) |
O3W—Co1—O1W | 88.13 (17) | N1—Co1—O2W | 93.31 (16) |
O5—Co1—N1 | 78.39 (15) | O5—Co1—O4W | 89.33 (15) |
O1W—Co1—N1 | 90.59 (17) | O3W—Co1—O4W | 88.23 (16) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2N···O8i | 0.85 (4) | 1.98 (4) | 2.818 (5) | 168 (5) |
O1W—H2W···O5ii | 0.89 (6) | 1.82 (9) | 2.694 (5) | 166 (10) |
O1W—H1W···O7iii | 0.89 (8) | 1.84 (4) | 2.683 (5) | 157 (9) |
O3W—H5W···O6ii | 0.89 (9) | 1.87 (10) | 2.732 (6) | 164 (11) |
O3W—H6W···O5W | 0.89 (7) | 2.03 (9) | 2.721 (11) | 134 (10) |
O4W—H7W···O7iv | 0.89 (7) | 1.94 (4) | 2.720 (5) | 146 (6) |
O4W—H8W···O6W | 0.89 (5) | 2.14 (5) | 2.862 (11) | 138 (7) |
O2W—H3W···O8 | 0.88 (4) | 1.82 (3) | 2.666 (5) | 157 (7) |
O2W—H4W···O7W | 0.89 (5) | 2.24 (5) | 3.014 (19) | 146 (7) |
O2W—H4W···O4W | 0.89 (5) | 2.43 (7) | 2.994 (6) | 122 (6) |
Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x+3/2, −y+1/2, z−1/2; (iii) x, −y+1, z−1/2; (iv) x, −y+1, z+1/2. |
Orotic acid (vitamin B13, H3Or) plays a significant role in biosynthesis of pyrimidine nucleosides (Panzeter & Ringer, 1993) and also found in cell and body fluids of many living organisms (Lalioti et al., 1998). Orotic acid is a good organic building block in coordination chemistry and has a multidentate nature. The most potential coordination sites (pH range of 5–9) are the carboxylate oxygen and the adjacent nitrogen atom for the formation of a stable five-membered chelate ring. The crystal structures of nickel(II) orotate pentahydrate (Wysokinski et al., 2002) and the analogous pentahydrate salt of cobalt (Icbudak et al., 2003) were recently reported. In the present study, we are reporting the crystal structure of tetraaqua(orotato)cobalt(II) 2.5 hydrate (I).
The molecular structure of (I) is shown in Fig. 1 and selected geometrical parameters are given in Table 1. Compound (I) comprises of one CoII ion, one orotate ligand, four coordinated water molecule and 2.5 uncoordinated solvent water molecules. The central CoII ion has a distorted octahedral coordination geometry, comprised of atoms N1 and O4 from a doubly deprotonated bidentate orotate ligand and four water (O1W, O2W, O3W and O4W) molecules.
The orotate ligand is essentially planar. The dihedral angle between the pyrimidine ring and the carboxylate group is 0.8 (4)°. The atom N and carboxylate O atom of the orotate ring form a five-membered chelate ring with the CoII ion. The dihedral angle between the five-membered ring and the six-membered pyrimidine ring is 4.3 (1)°. The Co—N distance is 2.104 (4) Å and Co—O distances lie in the range 2.075 (3)–2.123 (4) Å (Table 1).
The structure is stabilized by N—H···O and O—H···O hydrogen bonding. The intramolecular O—H···O hydrogen bond forms an S(6) motif (Bernstein et al., 1995). The intermolecular N—H···O hydrogen bonding leads to the formation of centrosymmetric dimer of R22(8)-type motif. The four water molecules link the carboxylate (O5 & O6) groups and carbonyl (O7 & O8) atoms through intra and intermolecular hydrogen bond interactions (Table. 2). Hydrogen-bonding interactions between the coordinated and uncoordinated water molecules and between the water molecules and the ligand result in a three-dimensional network structure (Fig. 2).
A π-π interaction is observed between the symmetry-related pyrimidine rings (N1/C1/C2/C3/C4/N2/C5). The six-membered ring at (x,y,z) and (x, 1 - y, z + 1/2) are parallel with an interplanar spacing of 3.267 Å; the ring centroid separation is 3.755 (3) Å.