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In the title compound, [Cu(C
7H
3N
2O
4)(C
4H
5N
2)(H
2O)], (I), pyridine-2,6-dicarboxylate (pydc
2−), 2-aminopyrimidine and aqua ligands coordinate the Cu
II centre through two N atoms, two carboxylate O atoms and one water O atom, respectively, to give a nominally distorted square-pyramidal coordination geometry, a common arrangement for copper complexes containing the pydc
2− ligand. Because of the presence of Cu
Xbridged contacts (
X = N or O) between adjacent molecules in the crystal structures of (I) and three analogous previously reported compounds, and the corresponding uncertainty about the effective coordination number of the Cu
II centre, density functional theory (DFT) calculations were used to elucidate the degree of covalency in these contacts. The calculated Wiberg and Mayer bond-order indices reveal that the Cu
O contact can be considered as a coordination bond, whereas the amine group forming a Cu
N contact is not an effective participant in the coordination environment.
Supporting information
CCDC reference: 1054348
Crystal data, data collection and structure refinement details are summarized
in Table 1.
S2. Results and discussion
top
Data collection: CrysAlis PRO (Oxford Diffraction, 2010); cell refinement: CrysAlis PRO (Oxford Diffraction, 2010); data reduction: CrysAlis PRO (Oxford Diffraction, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).
(2-Aminopyrimidine-
κN1)aqua(pyridine-2,6-dicarboxylato-
κ3O2,
N,
O6)copper(II)
top
Crystal data top
[Cu(C7H3N2O4)(C4H5N2)(H2O)] | Z = 2 |
Mr = 341.77 | F(000) = 346 |
Triclinic, P1 | Dx = 1.867 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 7.4376 (4) Å | Cell parameters from 4000 reflections |
b = 8.0321 (4) Å | θ = 2.8–28.8° |
c = 11.4220 (6) Å | µ = 1.83 mm−1 |
α = 80.980 (4)° | T = 294 K |
β = 87.261 (4)° | Prism, blue |
γ = 64.488 (5)° | 0.26 × 0.17 × 0.10 mm |
V = 608.05 (5) Å3 | |
Data collection top
Agilent Xcalibur Eos diffractometer | 2797 independent reflections |
Radiation source: Enhance (Mo) X-ray Source | 2377 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.023 |
Detector resolution: 16.1544 pixels mm-1 | θmax = 28.8°, θmin = 2.8° |
ω scans | h = −9→10 |
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010) | k = −10→10 |
Tmin = 0.913, Tmax = 1.000 | l = −15→15 |
8678 measured reflections | |
Refinement top
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)] = 0.031 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.074 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0336P)2 + 0.2457P] where P = (Fo2 + 2Fc2)/3 |
2797 reflections | (Δ/σ)max = 0.001 |
198 parameters | Δρmax = 0.37 e Å−3 |
0 restraints | Δρmin = −0.30 e Å−3 |
Crystal data top
[Cu(C7H3N2O4)(C4H5N2)(H2O)] | γ = 64.488 (5)° |
Mr = 341.77 | V = 608.05 (5) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.4376 (4) Å | Mo Kα radiation |
b = 8.0321 (4) Å | µ = 1.83 mm−1 |
c = 11.4220 (6) Å | T = 294 K |
α = 80.980 (4)° | 0.26 × 0.17 × 0.10 mm |
β = 87.261 (4)° | |
Data collection top
Agilent Xcalibur Eos diffractometer | 2797 independent reflections |
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010) | 2377 reflections with I > 2σ(I) |
Tmin = 0.913, Tmax = 1.000 | Rint = 0.023 |
8678 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.031 | 0 restraints |
wR(F2) = 0.074 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | Δρmax = 0.37 e Å−3 |
2797 reflections | Δρmin = −0.30 e Å−3 |
198 parameters | |
Special details top
Experimental. Absorption correction: CrysAlisPro, Agilent Technologies,
Version 1.171.35.4
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm. |
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 | x | y | z | Uiso*/Ueq | |
Cu1 | 0.58382 (4) | 0.63364 (4) | 0.27226 (2) | 0.02800 (10) | |
N1 | 0.4559 (3) | 0.4729 (2) | 0.26850 (16) | 0.0240 (4) | |
O1 | 0.7374 (2) | 0.4895 (2) | 0.14170 (15) | 0.0368 (4) | |
O2 | 0.7335 (3) | 0.2913 (2) | 0.02734 (15) | 0.0379 (4) | |
C1 | 0.6719 (3) | 0.3808 (3) | 0.1090 (2) | 0.0274 (5) | |
C2 | 0.5024 (3) | 0.3669 (3) | 0.18306 (19) | 0.0241 (4) | |
C3 | 0.4001 (4) | 0.2635 (3) | 0.1699 (2) | 0.0328 (5) | |
H3A | 0.4314 | 0.1891 | 0.1104 | 0.039* | |
C4 | 0.2490 (4) | 0.2737 (3) | 0.2479 (2) | 0.0368 (6) | |
H4A | 0.1762 | 0.2065 | 0.2401 | 0.044* | |
C5 | 0.2041 (3) | 0.3827 (3) | 0.3377 (2) | 0.0319 (5) | |
H5A | 0.1036 | 0.3882 | 0.3908 | 0.038* | |
C6 | 0.3134 (3) | 0.4824 (3) | 0.34576 (19) | 0.0235 (4) | |
C7 | 0.2921 (3) | 0.6128 (3) | 0.4336 (2) | 0.0266 (5) | |
O3 | 0.3991 (2) | 0.7031 (2) | 0.40966 (14) | 0.0308 (4) | |
O4 | 0.1818 (2) | 0.6234 (2) | 0.51765 (15) | 0.0377 (4) | |
N11 | 0.7311 (3) | 0.7845 (3) | 0.29023 (16) | 0.0255 (4) | |
N12 | 0.9146 (3) | 0.7348 (3) | 0.1188 (2) | 0.0397 (5) | |
H12A | 1.000 (4) | 0.751 (4) | 0.077 (3) | 0.040 (8)* | |
H12B | 0.868 (4) | 0.659 (4) | 0.105 (3) | 0.050 (8)* | |
C12 | 0.8681 (3) | 0.8129 (3) | 0.2162 (2) | 0.0262 (5) | |
N13 | 0.9603 (3) | 0.9186 (3) | 0.23718 (18) | 0.0321 (4) | |
C14 | 0.9059 (3) | 1.0040 (3) | 0.3312 (2) | 0.0327 (5) | |
H14A | 0.9664 | 1.0790 | 0.3459 | 0.039* | |
C15 | 0.7651 (3) | 0.9885 (3) | 0.4086 (2) | 0.0337 (5) | |
H15A | 0.7270 | 1.0527 | 0.4733 | 0.040* | |
C16 | 0.6844 (3) | 0.8733 (3) | 0.3851 (2) | 0.0312 (5) | |
H16A | 0.5923 | 0.8555 | 0.4374 | 0.037* | |
O1W | 0.3478 (2) | 0.8782 (2) | 0.14239 (15) | 0.0374 (4) | |
H1W | 0.2332 | 0.9035 | 0.1683 | 0.049* | |
H2W | 0.3575 | 0.8362 | 0.0818 | 0.049* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Cu1 | 0.03005 (16) | 0.03724 (17) | 0.02993 (17) | −0.02393 (13) | 0.01428 (11) | −0.01781 (12) |
N1 | 0.0244 (9) | 0.0274 (9) | 0.0243 (9) | −0.0143 (8) | 0.0062 (7) | −0.0074 (8) |
O1 | 0.0409 (9) | 0.0491 (10) | 0.0401 (10) | −0.0335 (8) | 0.0211 (8) | −0.0258 (8) |
O2 | 0.0448 (10) | 0.0495 (10) | 0.0340 (9) | −0.0297 (9) | 0.0193 (8) | −0.0240 (8) |
C1 | 0.0307 (11) | 0.0325 (12) | 0.0255 (11) | −0.0184 (10) | 0.0086 (9) | −0.0106 (9) |
C2 | 0.0266 (10) | 0.0267 (11) | 0.0232 (11) | −0.0147 (9) | 0.0046 (9) | −0.0070 (9) |
C3 | 0.0398 (13) | 0.0354 (13) | 0.0332 (13) | −0.0235 (11) | 0.0070 (10) | −0.0130 (10) |
C4 | 0.0416 (13) | 0.0414 (14) | 0.0445 (15) | −0.0323 (12) | 0.0106 (11) | −0.0138 (12) |
C5 | 0.0305 (12) | 0.0359 (12) | 0.0359 (13) | −0.0207 (10) | 0.0098 (10) | −0.0071 (10) |
C6 | 0.0231 (10) | 0.0258 (10) | 0.0240 (11) | −0.0127 (9) | 0.0062 (8) | −0.0055 (9) |
C7 | 0.0226 (10) | 0.0321 (12) | 0.0272 (12) | −0.0127 (9) | 0.0059 (9) | −0.0090 (9) |
O3 | 0.0326 (8) | 0.0402 (9) | 0.0313 (9) | −0.0235 (7) | 0.0134 (7) | −0.0178 (7) |
O4 | 0.0352 (9) | 0.0501 (10) | 0.0366 (10) | −0.0243 (8) | 0.0192 (8) | −0.0189 (8) |
N11 | 0.0249 (9) | 0.0323 (10) | 0.0262 (10) | −0.0175 (8) | 0.0071 (7) | −0.0106 (8) |
N12 | 0.0474 (13) | 0.0593 (15) | 0.0342 (12) | −0.0409 (12) | 0.0210 (10) | −0.0209 (11) |
C12 | 0.0230 (10) | 0.0312 (11) | 0.0272 (12) | −0.0141 (9) | 0.0032 (9) | −0.0055 (9) |
N13 | 0.0305 (10) | 0.0393 (11) | 0.0361 (11) | −0.0231 (9) | 0.0075 (8) | −0.0101 (9) |
C14 | 0.0315 (12) | 0.0340 (12) | 0.0414 (14) | −0.0205 (10) | 0.0030 (10) | −0.0116 (11) |
C15 | 0.0331 (12) | 0.0389 (13) | 0.0371 (14) | −0.0192 (11) | 0.0064 (10) | −0.0185 (11) |
C16 | 0.0286 (11) | 0.0406 (13) | 0.0317 (13) | −0.0194 (10) | 0.0098 (10) | −0.0145 (10) |
O1W | 0.0408 (9) | 0.0459 (10) | 0.0360 (10) | −0.0260 (8) | 0.0061 (8) | −0.0153 (8) |
Geometric parameters (Å, º) top
Cu1—N1 | 1.9112 (17) | C6—C7 | 1.516 (3) |
Cu1—N11 | 1.9880 (17) | C7—O4 | 1.222 (3) |
Cu1—O3 | 2.0175 (15) | C7—O3 | 1.284 (3) |
Cu1—O1 | 2.0267 (16) | N11—C16 | 1.340 (3) |
Cu1—O1W | 2.3465 (17) | N11—C12 | 1.365 (3) |
N1—C6 | 1.331 (3) | N12—C12 | 1.321 (3) |
N1—C2 | 1.331 (3) | N12—H12A | 0.82 (3) |
O1—C1 | 1.275 (3) | N12—H12B | 0.85 (3) |
O2—C1 | 1.218 (3) | C12—N13 | 1.352 (3) |
C1—C2 | 1.519 (3) | N13—C14 | 1.319 (3) |
C2—C3 | 1.374 (3) | C14—C15 | 1.372 (3) |
C3—C4 | 1.383 (3) | C14—H14A | 0.9300 |
C3—H3A | 0.9300 | C15—C16 | 1.364 (3) |
C4—C5 | 1.388 (3) | C15—H15A | 0.9300 |
C4—H4A | 0.9300 | C16—H16A | 0.9300 |
C5—C6 | 1.379 (3) | O1W—H1W | 0.8368 |
C5—H5A | 0.9300 | O1W—H2W | 0.8029 |
| | | |
N1—Cu1—N11 | 174.43 (8) | N1—C6—C5 | 120.0 (2) |
N1—Cu1—O3 | 80.07 (7) | N1—C6—C7 | 111.80 (17) |
N11—Cu1—O3 | 98.26 (7) | C5—C6—C7 | 128.22 (19) |
N1—Cu1—O1 | 79.79 (7) | O4—C7—O3 | 126.3 (2) |
N11—Cu1—O1 | 101.38 (7) | O4—C7—C6 | 120.16 (19) |
O3—Cu1—O1 | 159.40 (6) | O3—C7—C6 | 113.59 (18) |
N1—Cu1—O1W | 93.49 (7) | C7—O3—Cu1 | 115.69 (14) |
N11—Cu1—O1W | 91.85 (7) | C16—N11—C12 | 116.53 (18) |
O3—Cu1—O1W | 91.03 (6) | C16—N11—Cu1 | 115.40 (14) |
O1—Cu1—O1W | 94.48 (7) | C12—N11—Cu1 | 128.03 (15) |
C6—N1—C2 | 122.75 (18) | C12—N12—H12A | 117.5 (19) |
C6—N1—Cu1 | 118.48 (14) | C12—N12—H12B | 121 (2) |
C2—N1—Cu1 | 118.55 (14) | H12A—N12—H12B | 121 (3) |
C1—O1—Cu1 | 115.47 (14) | N12—C12—N13 | 117.5 (2) |
O2—C1—O1 | 126.1 (2) | N12—C12—N11 | 119.3 (2) |
O2—C1—C2 | 119.90 (19) | N13—C12—N11 | 123.2 (2) |
O1—C1—C2 | 113.96 (18) | C14—N13—C12 | 117.3 (2) |
N1—C2—C3 | 120.5 (2) | N13—C14—C15 | 123.6 (2) |
N1—C2—C1 | 111.58 (17) | N13—C14—H14A | 118.2 |
C3—C2—C1 | 127.9 (2) | C15—C14—H14A | 118.2 |
C2—C3—C4 | 117.8 (2) | C16—C15—C14 | 116.0 (2) |
C2—C3—H3A | 121.1 | C16—C15—H15A | 122.0 |
C4—C3—H3A | 121.1 | C14—C15—H15A | 122.0 |
C3—C4—C5 | 121.1 (2) | N11—C16—C15 | 123.3 (2) |
C3—C4—H4A | 119.4 | N11—C16—H16A | 118.4 |
C5—C4—H4A | 119.4 | C15—C16—H16A | 118.4 |
C6—C5—C4 | 117.9 (2) | Cu1—O1W—H1W | 109.7 |
C6—C5—H5A | 121.1 | Cu1—O1W—H2W | 104.5 |
C4—C5—H5A | 121.1 | H1W—O1W—H2W | 108.5 |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N12—H12A···O2i | 0.82 (3) | 2.19 (3) | 2.984 (3) | 164 (3) |
N12—H12B···O1 | 0.85 (3) | 1.98 (3) | 2.780 (3) | 157 (3) |
O1W—H1W···N13ii | 0.84 | 2.10 | 2.931 (2) | 170 |
O1W—H2W···O2iii | 0.80 | 2.03 | 2.761 (2) | 150 |
Symmetry codes: (i) −x+2, −y+1, −z; (ii) x−1, y, z; (iii) −x+1, −y+1, −z. |
Experimental details
Crystal data |
Chemical formula | [Cu(C7H3N2O4)(C4H5N2)(H2O)] |
Mr | 341.77 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 294 |
a, b, c (Å) | 7.4376 (4), 8.0321 (4), 11.4220 (6) |
α, β, γ (°) | 80.980 (4), 87.261 (4), 64.488 (5) |
V (Å3) | 608.05 (5) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 1.83 |
Crystal size (mm) | 0.26 × 0.17 × 0.10 |
|
Data collection |
Diffractometer | Agilent Xcalibur Eos diffractometer |
Absorption correction | Multi-scan (CrysAlis PRO; Oxford Diffraction, 2010) |
Tmin, Tmax | 0.913, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8678, 2797, 2377 |
Rint | 0.023 |
(sin θ/λ)max (Å−1) | 0.679 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.031, 0.074, 1.06 |
No. of reflections | 2797 |
No. of parameters | 198 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.37, −0.30 |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N12—H12A···O2i | 0.82 (3) | 2.19 (3) | 2.984 (3) | 164 (3) |
N12—H12B···O1 | 0.85 (3) | 1.98 (3) | 2.780 (3) | 157 (3) |
O1W—H1W···N13ii | 0.84 | 2.10 | 2.931 (2) | 170.4 |
O1W—H2W···O2iii | 0.80 | 2.03 | 2.761 (2) | 150.4 |
Symmetry codes: (i) −x+2, −y+1, −z; (ii) x−1, y, z; (iii) −x+1, −y+1, −z. |
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