| Literature DB >> 26594407 |
Elena A Buvaylo1, Olga Yu Vassilyeva1, Brian W Skelton2.
Abstract
The crystal structure of the tetra-nuclear title compound, [Cu4(C12H15NO5)4(H2O)4], has been previously reported by Back, Oliveira, Canabarro & Iglesias [Z. Anorg. Allg. Chem. (2015), 641, 941-947], based on room-temperature data. In the previously published structure, no standard uncertainties are recorded for the deprotonated hy-droxy-methyl group and water mol-ecule O atoms coordinating to the metal atom indicating that they were not refined; furthermore, the H atoms of some OH groups and water mol-ecules have not been positioned accurately. Since the current structure was determined at a lower temperature, all atoms, including the H atoms of these hy-droxy groups and the water mol-ecule, have been determined more accurately resulting in improved standard uncertainties in the bond lengths and angles. Diffraction data were collected at 200 K, rather than the more usual 100 K, due to apparent disordering at lower temperatures. In addition, it is now possible to report intra- and inter-molecular O-H⋯O inter-actions. In the title complex molecule, which has crystallographic -4 symmetry, the Cu(II) ions are coordinated by the tridentate Schiff base ligands and water mol-ecules, forming a tetra-nuclear Cu4O4 cubane-like core. The Cu(II) ion adopts a CuNO5 elongated octa-hedral environment. The coordination environment of Cu(II) at 200 K displays a small contraction of the Cu-N/O bonds, compared with the room-temperature structure. In the crystal lattice, the neutral clusters are linked by inter-molecular O-H⋯O hydrogen bonds into a one-dimensional hydrogen-bonding network propagating along the b axis.Entities:
Keywords: CuII cubane-type complex; Schiff base ligand; crystal structure; hydrogen bonding; o-vanillin; tris(hydroxymethyl)aminomethane
Year: 2015 PMID: 26594407 PMCID: PMC4647398 DOI: 10.1107/S2056989015017314
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The molecular structure of the title complex, showing the atom-numbering scheme. Non-H atoms are shown with displacement ellipsoids at the 50% probability level. H atoms are not shown.
Selected bond lengths ()
| Cu1O1 | 1.912(4) | Cu1O2 | 2.738(5) |
| Cu1O11 | 1.941(4) | Cu1O11i | 1.968(3) |
| Cu1N10 | 1.953(5) | Cu1O11ii | 2.547(4) |
Symmetry codes: (i) ; (ii) .
Hydrogen-bond geometry (, )
|
|
| H |
|
|
|---|---|---|---|---|
| O12H12O12ii | 0.84 | 2.37 | 2.736(12) | 107 |
| O13H13O2iii | 0.84 | 1.91 | 2.700(6) | 156 |
| O2H2 | 0.93(5) | 1.92(4) | 2.791(6) | 155(8) |
| O2H2 | 0.93(5) | 2.23(7) | 2.853(7) | 124(6) |
| O2H2 | 0.96(5) | 1.95(3) | 2.892(7) | 165(6) |
Symmetry codes: (ii) ; (iii) ; (iv) .
Figure 2Part of the crystal structure with intra- and intermolecular hydrogen bonds shown as blue dashed lines. C—H hydrogens have been omitted for clarity.
Experimental details
| Crystal data | |
| Chemical formula | [Cu4(C12H15NO5)4(H2O)4] |
|
| 1339.22 |
| Crystal system, space group | Tetragonal, |
| Temperature (K) | 200 |
|
| 18.7108(3), 15.3800(3) |
|
| 5384.4(2) |
|
| 4 |
| Radiation type | Mo |
| (mm1) | 1.65 |
| Crystal size (mm) | 0.39 0.23 0.17 |
| Data collection | |
| Diffractometer | Oxford Diffraction Xcalibur |
| Absorption correction | Analytical ( |
|
| 0.687, 0.843 |
| No. of measured, independent and observed [ | 25330, 3247, 2942 |
|
| 0.044 |
| (sin /)max (1) | 0.660 |
| Refinement | |
|
| 0.076, 0.195, 1.12 |
| No. of reflections | 3247 |
| No. of parameters | 188 |
| No. of restraints | 4 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| max, min (e 3) | 1.58, 0.98 |
Computer programs: CrysAlis CCD (Agilent, 2013 ▸), SIR92 (Altomare et al., 1994 ▸), SHELXL2014 (Sheldrick, 2015 ▸), DIAMOND (Brandenburg, 1999 ▸) and WinGX (Farrugia, 2012 ▸).
| [Cu4(C12H15NO5)4(H2O)4] | |
| Mo | |
| Tetragonal, | Cell parameters from 7964 reflections |
| Hall symbol: -I 4ad | θ = 2.8–28.9° |
| µ = 1.65 mm−1 | |
| Prism, dark green | |
| 0.39 × 0.23 × 0.17 mm | |
| Oxford Diffraction Xcalibur diffractometer | 3247 independent reflections |
| Radiation source: Enhance (Mo) X-ray Source | 2942 reflections with |
| Graphite monochromator | |
| Detector resolution: 16.0009 pixels mm-1 | θmax = 28.0°, θmin = 2.8° |
| ω scans | |
| Absorption correction: analytical ( | |
| 25330 measured reflections |
| Refinement on | 4 restraints |
| Least-squares matrix: full | Hydrogen site location: mixed |
| H atoms treated by a mixture of independent and constrained refinement | |
| (Δ/σ)max < 0.001 | |
| 3247 reflections | Δρmax = 1.58 e Å−3 |
| 188 parameters | Δρmin = −0.98 e Å−3 |
| 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. Diffraction data were collected at 200 K, rather than the more usual 100 K, due to apparent disordering at lower temperatures. Water molecule hydrogen atoms were refined with geometries restrained to ideal values. |
| Cu1 | 0.47922 (3) | 0.66025 (3) | 0.69100 (4) | 0.0279 (2) | |
| C1 | 0.5392 (3) | 0.5347 (3) | 0.7698 (3) | 0.0355 (11) | |
| O1 | 0.5448 (2) | 0.58332 (19) | 0.7095 (2) | 0.0350 (8) | |
| C2 | 0.4880 (3) | 0.5355 (3) | 0.8386 (4) | 0.0384 (12) | |
| C3 | 0.4858 (4) | 0.4778 (4) | 0.8971 (4) | 0.0533 (16) | |
| H3 | 0.4506 | 0.4777 | 0.9416 | 0.064* | |
| C4 | 0.5322 (5) | 0.4225 (4) | 0.8922 (5) | 0.063 (2) | |
| H4 | 0.5285 | 0.3839 | 0.9322 | 0.076* | |
| C5 | 0.5845 (5) | 0.4218 (3) | 0.8297 (5) | 0.062 (2) | |
| H5 | 0.6179 | 0.3836 | 0.8277 | 0.075* | |
| C6 | 0.5887 (4) | 0.4770 (3) | 0.7690 (4) | 0.0531 (16) | |
| O6 | 0.6377 (4) | 0.4824 (3) | 0.7043 (4) | 0.0781 (18) | |
| C61 | 0.6974 (6) | 0.4339 (5) | 0.7031 (7) | 0.094 (3) | |
| H61A | 0.7184 | 0.4311 | 0.7614 | 0.14* | |
| H61B | 0.7334 | 0.4512 | 0.6619 | 0.14* | |
| H61C | 0.681 | 0.3863 | 0.6852 | 0.14* | |
| C10 | 0.4376 (3) | 0.5937 (4) | 0.8514 (4) | 0.0453 (14) | |
| H10 | 0.4063 | 0.5904 | 0.8999 | 0.054* | |
| N10 | 0.4318 (2) | 0.6488 (3) | 0.8033 (3) | 0.0416 (11) | |
| C101 | 0.3781 (4) | 0.7071 (4) | 0.8247 (4) | 0.0492 (15) | |
| C11 | 0.3629 (3) | 0.7439 (3) | 0.7393 (4) | 0.0384 (12) | |
| H11A | 0.3232 | 0.7186 | 0.7099 | 0.046* | |
| H11B | 0.3468 | 0.7933 | 0.7513 | 0.046* | |
| O11 | 0.42189 (18) | 0.7465 (2) | 0.6827 (2) | 0.0322 (7) | |
| C12 | 0.4105 (5) | 0.7622 (4) | 0.8871 (5) | 0.065 (2) | |
| H12A | 0.4533 | 0.7841 | 0.8601 | 0.078* | |
| H12B | 0.3753 | 0.8006 | 0.8984 | 0.078* | |
| O12 | 0.4299 (3) | 0.7293 (3) | 0.9664 (3) | 0.0827 (18) | |
| H12 | 0.4473 | 0.76 | 1.0001 | 0.124* | |
| C13 | 0.3123 (4) | 0.6764 (4) | 0.8649 (4) | 0.0551 (17) | |
| H13A | 0.3232 | 0.6592 | 0.9243 | 0.066* | |
| H13B | 0.2751 | 0.7139 | 0.8694 | 0.066* | |
| O13 | 0.2862 (3) | 0.6191 (3) | 0.8141 (4) | 0.0724 (16) | |
| H13 | 0.2492 | 0.6023 | 0.8374 | 0.109* | |
| O2 | 0.3560 (3) | 0.5887 (2) | 0.6505 (3) | 0.0497 (10) | |
| H2AO | 0.341 (4) | 0.618 (4) | 0.605 (3) | 0.075* | |
| H2BO | 0.326 (4) | 0.601 (4) | 0.699 (3) | 0.075* |
| Cu1 | 0.0264 (3) | 0.0308 (3) | 0.0265 (3) | −0.0006 (2) | −0.0008 (2) | 0.0045 (2) |
| C1 | 0.044 (3) | 0.030 (2) | 0.033 (3) | −0.003 (2) | −0.013 (2) | 0.0002 (19) |
| O1 | 0.0390 (19) | 0.0342 (18) | 0.0317 (17) | 0.0055 (15) | 0.0023 (15) | 0.0060 (14) |
| C2 | 0.039 (3) | 0.042 (3) | 0.034 (3) | −0.010 (2) | −0.008 (2) | 0.008 (2) |
| C3 | 0.062 (4) | 0.051 (4) | 0.046 (3) | −0.017 (3) | −0.009 (3) | 0.019 (3) |
| C4 | 0.094 (6) | 0.042 (3) | 0.053 (4) | −0.008 (4) | −0.012 (4) | 0.015 (3) |
| C5 | 0.101 (6) | 0.033 (3) | 0.052 (4) | 0.015 (3) | −0.012 (4) | 0.000 (3) |
| C6 | 0.082 (5) | 0.033 (3) | 0.044 (3) | 0.014 (3) | −0.004 (3) | −0.004 (2) |
| O6 | 0.105 (4) | 0.057 (3) | 0.073 (3) | 0.044 (3) | 0.023 (3) | 0.012 (3) |
| C61 | 0.101 (7) | 0.074 (6) | 0.106 (8) | 0.046 (5) | 0.016 (6) | 0.006 (5) |
| C10 | 0.033 (3) | 0.067 (4) | 0.036 (3) | 0.000 (3) | 0.002 (2) | 0.019 (3) |
| N10 | 0.033 (2) | 0.054 (3) | 0.038 (2) | 0.011 (2) | 0.0041 (19) | 0.013 (2) |
| C101 | 0.055 (4) | 0.054 (4) | 0.039 (3) | 0.020 (3) | 0.009 (3) | 0.002 (3) |
| C11 | 0.039 (3) | 0.040 (3) | 0.037 (3) | 0.006 (2) | 0.009 (2) | −0.005 (2) |
| O11 | 0.0298 (17) | 0.0392 (19) | 0.0274 (17) | 0.0051 (14) | −0.0015 (13) | 0.0032 (14) |
| C12 | 0.095 (6) | 0.057 (4) | 0.042 (4) | 0.026 (4) | 0.006 (4) | −0.004 (3) |
| O12 | 0.126 (5) | 0.081 (4) | 0.041 (3) | 0.019 (4) | −0.006 (3) | −0.003 (3) |
| C13 | 0.060 (4) | 0.058 (4) | 0.047 (3) | 0.015 (3) | 0.025 (3) | 0.003 (3) |
| O13 | 0.049 (3) | 0.083 (4) | 0.085 (4) | 0.002 (3) | 0.027 (3) | −0.004 (3) |
| O2 | 0.060 (3) | 0.037 (2) | 0.053 (3) | −0.0002 (19) | 0.005 (2) | −0.0109 (19) |
| Cu1—O1 | 1.912 (4) | C61—H61C | 0.98 |
| Cu1—O11 | 1.941 (4) | C10—N10 | 1.273 (7) |
| Cu1—N10 | 1.953 (5) | C10—H10 | 0.95 |
| Cu1—O2 | 2.738 (5) | N10—C101 | 1.519 (7) |
| Cu1—O11i | 1.968 (3) | C101—C13 | 1.494 (9) |
| Cu1—O11ii | 2.547 (4) | C101—C11 | 1.510 (8) |
| C1—O1 | 1.303 (6) | C101—C12 | 1.533 (11) |
| C1—C6 | 1.422 (8) | C11—O11 | 1.407 (6) |
| C1—C2 | 1.427 (8) | C11—H11A | 0.99 |
| C2—C3 | 1.406 (8) | C11—H11B | 0.99 |
| C2—C10 | 1.455 (9) | O11—Cu1iii | 1.968 (3) |
| C3—C4 | 1.353 (11) | C12—O12 | 1.414 (9) |
| C3—H3 | 0.95 | C12—H12A | 0.99 |
| C4—C5 | 1.373 (11) | C12—H12B | 0.99 |
| C4—H4 | 0.95 | O12—H12 | 0.84 |
| C5—C6 | 1.394 (9) | C13—O13 | 1.413 (9) |
| C5—H5 | 0.95 | C13—H13A | 0.99 |
| C6—O6 | 1.356 (9) | C13—H13B | 0.99 |
| O6—C61 | 1.439 (9) | O13—H13 | 0.84 |
| C61—H61A | 0.98 | O2—H2AO | 0.93 (5) |
| C61—H61B | 0.98 | O2—H2BO | 0.96 (5) |
| O1—Cu1—O11 | 171.70 (15) | H61A—C61—H61B | 109.5 |
| O1—Cu1—N10 | 94.41 (17) | O6—C61—H61C | 109.5 |
| O11—Cu1—N10 | 84.16 (17) | H61A—C61—H61C | 109.5 |
| N10—Cu1—O2 | 76.41 (16) | H61B—C61—H61C | 109.5 |
| O11—Cu1—O2 | 85.77 (14) | N10—C10—C2 | 125.6 (5) |
| O1—Cu1—O2 | 101.89 (14) | N10—C10—H10 | 117.2 |
| O1—Cu1—O11i | 94.54 (15) | C2—C10—H10 | 117.2 |
| O11—Cu1—O11i | 88.41 (16) | C10—N10—C101 | 120.8 (5) |
| N10—Cu1—O11i | 166.34 (18) | C10—N10—Cu1 | 124.3 (4) |
| O2—Cu1—O11ii | 159.30 (12) | C101—N10—Cu1 | 114.4 (3) |
| O1—Cu1—O11i | 94.54 (15) | C13—C101—C11 | 112.3 (6) |
| O11—Cu1—O11i | 88.44 (16) | C13—C101—N10 | 111.0 (5) |
| O1—Cu1—O11ii | 93.29 (13) | C11—C101—N10 | 105.3 (4) |
| N10—Cu1—O11ii | 116.70 (16) | C13—C101—C12 | 109.1 (6) |
| O11—Cu1—O11ii | 80.15 (13) | C11—C101—C12 | 108.2 (6) |
| O11i—Cu1—O11ii | 73.02 (12) | N10—C101—C12 | 110.9 (5) |
| O2—Cu1—O11i | 91.64 (15) | O11—C11—C101 | 113.9 (5) |
| O2—Cu1—O11ii | 159.32 (12) | O11—C11—H11A | 108.8 |
| O1—C1—C6 | 118.1 (5) | C101—C11—H11A | 108.8 |
| O1—C1—C2 | 125.1 (5) | O11—C11—H11B | 108.8 |
| C6—C1—C2 | 116.8 (5) | C101—C11—H11B | 108.8 |
| C1—O1—Cu1 | 125.5 (3) | H11A—C11—H11B | 107.7 |
| C3—C2—C1 | 119.2 (6) | C11—O11—Cu1 | 111.4 (3) |
| C3—C2—C10 | 118.0 (6) | C11—O11—Cu1iii | 121.3 (3) |
| C1—C2—C10 | 122.9 (5) | Cu1—O11—Cu1iii | 108.47 (17) |
| C4—C3—C2 | 122.2 (7) | O12—C12—C101 | 110.4 (6) |
| C4—C3—H3 | 118.9 | O12—C12—H12A | 109.6 |
| C2—C3—H3 | 118.9 | C101—C12—H12A | 109.6 |
| C3—C4—C5 | 120.2 (6) | O12—C12—H12B | 109.6 |
| C3—C4—H4 | 119.9 | C101—C12—H12B | 109.6 |
| C5—C4—H4 | 119.9 | H12A—C12—H12B | 108.1 |
| C4—C5—C6 | 120.2 (7) | C12—O12—H12 | 109.5 |
| C4—C5—H5 | 119.9 | O13—C13—C101 | 110.4 (5) |
| C6—C5—H5 | 119.9 | O13—C13—H13A | 109.6 |
| O6—C6—C5 | 125.7 (6) | C101—C13—H13A | 109.6 |
| O6—C6—C1 | 113.0 (5) | O13—C13—H13B | 109.6 |
| C5—C6—C1 | 121.3 (7) | C101—C13—H13B | 109.6 |
| C6—O6—C61 | 119.2 (6) | H13A—C13—H13B | 108.1 |
| O6—C61—H61A | 109.5 | C13—O13—H13 | 109.5 |
| O6—C61—H61B | 109.5 | H2AO—O2—H2BO | 105 (3) |
| H··· | ||||
| O12—H12···O12ii | 0.84 | 2.37 | 2.736 (12) | 107 |
| O13—H13···O2iv | 0.84 | 1.91 | 2.700 (6) | 156 |
| O2—H2 | 0.93 (5) | 1.92 (4) | 2.791 (6) | 155 (8) |
| O2—H2 | 0.93 (5) | 2.23 (7) | 2.853 (7) | 124 (6) |
| O2—H2 | 0.96 (5) | 1.95 (3) | 2.892 (7) | 165 (6) |