Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270104010078/na1661sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270104010078/na1661Isup2.hkl |
CCDC reference: 243585
All chemicals were of reagent grade and commercially available from the Beijing Chemical Reagents Company of China; they were used without further purification. Cu(NO3)2·3H2O (0.12 g), 1,10-phenanthroline (0.117 g), 4-aminobenzoic acid (0.034 g) and NaOH (0.02 g) were mixed with water (10 ml) and stirred at room temperature for 30 min. The mixture was then sealed in air and heated at 443 K for 6 d in a 30-ml Teflon-lined autoclave. After cooling, the black crystals of (I) were collected.
The residual electron density has a maximum located 0.85 Å from atom O1W. H atoms attached to C atoms were placed in geometrically idealized positions with Csp2—H = 0.93 Å and constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq(C). The water O atom is on a twofold axis, so one H atom is related to the other by symmetry. A peak was found 0.85 Å from the O atom but it forms an unacceptable angle of 150° with its symmetry relative. On the other hand, the O atom is affected by a rather large Ueq value of 0.380 (14) Å2, indicative of disorder, the probable cause of which is the lack of hydrogen-bonding interactions involving this water molecule, which is simply occluded in a hole of the structure. These are the reasons why the water H atoms were not considered in the present refinement.
Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL/PC (Sheldrick, 1999); software used to prepare material for publication: SHELXTL/PC.
[Cu2(C12H7N2O)2]·H2O | F(000) = 1080 |
Mr = 535.49 | Dx = 1.751 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 1851 reflections |
a = 30.344 (3) Å | θ = 2.2–23.7° |
b = 3.6676 (3) Å | µ = 2.13 mm−1 |
c = 19.1508 (17) Å | T = 293 K |
β = 107.578 (1)° | Plate, black |
V = 2031.7 (3) Å3 | 0.28 × 0.15 × 0.04 mm |
Z = 4 |
Bruker SMART 1K CCD area-detector diffractometer | 1780 independent reflections |
Radiation source: fine-focus sealed tube | 1506 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.033 |
ϕ and ω scans | θmax = 25.0°, θmin = 2.2° |
Absorption correction: multi-scan (SADABS; Sheldrick, 2000) | h = −36→35 |
Tmin = 0.587, Tmax = 0.920 | k = −4→4 |
6470 measured reflections | l = −22→22 |
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)] = 0.061 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.198 | H-atom parameters constrained |
S = 1.14 | w = 1/[σ2(Fo2) + (0.143P)2] where P = (Fo2 + 2Fc2)/3 |
1780 reflections | (Δ/σ)max < 0.001 |
150 parameters | Δρmax = 1.48 e Å−3 |
6 restraints | Δρmin = −0.52 e Å−3 |
[Cu2(C12H7N2O)2]·H2O | V = 2031.7 (3) Å3 |
Mr = 535.49 | Z = 4 |
Monoclinic, C2/c | Mo Kα radiation |
a = 30.344 (3) Å | µ = 2.13 mm−1 |
b = 3.6676 (3) Å | T = 293 K |
c = 19.1508 (17) Å | 0.28 × 0.15 × 0.04 mm |
β = 107.578 (1)° |
Bruker SMART 1K CCD area-detector diffractometer | 1780 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2000) | 1506 reflections with I > 2σ(I) |
Tmin = 0.587, Tmax = 0.920 | Rint = 0.033 |
6470 measured reflections |
R[F2 > 2σ(F2)] = 0.061 | 6 restraints |
wR(F2) = 0.198 | H-atom parameters constrained |
S = 1.14 | Δρmax = 1.48 e Å−3 |
1780 reflections | Δρmin = −0.52 e Å−3 |
150 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. |
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. The water molecule in the compound shows positional disorder near the crystallographic symmetry (1 − x, y, 1.5 − z). After refined several cycles, O1w atom was determined by its average between the atom and symmetry correlational atom. The occupation factor of the water O atom is 0.5. |
x | y | z | Uiso*/Ueq | ||
Cu1 | 0.265841 (19) | 0.64296 (15) | 0.95050 (3) | 0.0418 (4) | |
N1 | 0.30823 (14) | 0.5181 (11) | 0.8844 (2) | 0.0410 (9) | |
N2 | 0.32309 (15) | 0.8069 (10) | 1.0168 (2) | 0.0369 (9) | |
O1 | 0.29373 (12) | 1.0007 (10) | 1.10659 (18) | 0.0478 (9) | |
C1 | 0.2991 (2) | 0.3813 (12) | 0.8173 (3) | 0.0497 (14) | |
H1 | 0.2689 | 0.3160 | 0.7923 | 0.060* | |
C2 | 0.3331 (2) | 0.3320 (13) | 0.7830 (3) | 0.0580 (16) | |
H2 | 0.3253 | 0.2424 | 0.7354 | 0.070* | |
C3 | 0.3781 (2) | 0.4158 (14) | 0.8195 (3) | 0.0507 (13) | |
H3 | 0.4010 | 0.3815 | 0.7972 | 0.061* | |
C4 | 0.3894 (2) | 0.5564 (13) | 0.8922 (3) | 0.0460 (12) | |
C5 | 0.35247 (19) | 0.6082 (12) | 0.9209 (3) | 0.0403 (12) | |
C6 | 0.36095 (17) | 0.7600 (13) | 0.9919 (3) | 0.0377 (11) | |
C7 | 0.4347 (2) | 0.6544 (13) | 0.9343 (4) | 0.0531 (15) | |
H7 | 0.4592 | 0.6227 | 0.9153 | 0.064* | |
C8 | 0.44224 (19) | 0.7949 (14) | 1.0025 (3) | 0.0485 (13) | |
H8 | 0.4723 | 0.8526 | 1.0300 | 0.058* | |
C9 | 0.40577 (19) | 0.8568 (11) | 1.0333 (3) | 0.0416 (12) | |
C10 | 0.41170 (18) | 1.0063 (13) | 1.1040 (3) | 0.0449 (12) | |
H10 | 0.4410 | 1.0703 | 1.1338 | 0.054* | |
C11 | 0.37373 (19) | 1.0556 (13) | 1.1283 (3) | 0.0445 (12) | |
H11 | 0.3776 | 1.1576 | 1.1742 | 0.053* | |
C12 | 0.32904 (18) | 0.9533 (13) | 1.0844 (3) | 0.0401 (11) | |
O1W | 0.5000 | 0.451 (8) | 0.7500 | 0.380 (14) |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cu1 | 0.0402 (5) | 0.0510 (5) | 0.0299 (5) | −0.0033 (2) | 0.0044 (3) | −0.0026 (2) |
N1 | 0.046 (2) | 0.038 (2) | 0.029 (2) | −0.0013 (18) | −0.0028 (18) | 0.0011 (17) |
N2 | 0.043 (2) | 0.038 (2) | 0.027 (2) | −0.0059 (17) | 0.0056 (18) | −0.0007 (16) |
O1 | 0.048 (2) | 0.062 (2) | 0.0305 (18) | −0.0073 (18) | 0.0072 (16) | −0.0097 (17) |
C1 | 0.064 (4) | 0.038 (3) | 0.039 (3) | 0.004 (2) | 0.001 (3) | −0.004 (2) |
C2 | 0.093 (5) | 0.042 (3) | 0.035 (3) | 0.011 (3) | 0.014 (3) | −0.001 (2) |
C3 | 0.069 (4) | 0.049 (3) | 0.036 (3) | 0.012 (3) | 0.018 (3) | 0.002 (2) |
C4 | 0.058 (3) | 0.037 (2) | 0.044 (3) | 0.009 (2) | 0.017 (3) | 0.009 (2) |
C5 | 0.047 (3) | 0.030 (2) | 0.039 (3) | 0.0037 (18) | 0.005 (2) | 0.0071 (18) |
C6 | 0.044 (3) | 0.031 (2) | 0.034 (2) | 0.002 (2) | 0.006 (2) | 0.008 (2) |
C7 | 0.059 (4) | 0.044 (3) | 0.060 (4) | 0.007 (2) | 0.022 (3) | 0.009 (2) |
C8 | 0.042 (3) | 0.049 (3) | 0.049 (3) | −0.003 (2) | 0.005 (2) | 0.005 (2) |
C9 | 0.046 (3) | 0.034 (2) | 0.037 (3) | −0.0016 (19) | 0.002 (2) | 0.0075 (19) |
C10 | 0.046 (3) | 0.043 (3) | 0.038 (3) | −0.008 (2) | 0.000 (2) | 0.006 (2) |
C11 | 0.060 (3) | 0.039 (3) | 0.030 (2) | −0.010 (2) | 0.007 (2) | 0.000 (2) |
C12 | 0.049 (3) | 0.039 (2) | 0.029 (2) | −0.006 (2) | 0.007 (2) | 0.001 (2) |
O1W | 0.380 (14) | 0.380 (14) | 0.380 (14) | 0.000 | 0.114 (4) | 0.000 |
Cu1—O1i | 1.883 (3) | C3—H3 | 0.9300 |
Cu1—N2 | 1.913 (4) | C4—C5 | 1.403 (8) |
Cu1—N1 | 2.109 (4) | C4—C7 | 1.412 (9) |
Cu1—Cu1i | 2.4971 (11) | C5—C6 | 1.419 (7) |
N1—C1 | 1.328 (7) | C6—C9 | 1.397 (7) |
N1—C5 | 1.354 (7) | C7—C8 | 1.358 (8) |
N2—C12 | 1.361 (6) | C7—H7 | 0.9300 |
N2—C6 | 1.382 (7) | C8—C9 | 1.420 (8) |
O1—C12 | 1.279 (6) | C8—H8 | 0.9300 |
O1—Cu1i | 1.883 (3) | C9—C10 | 1.422 (8) |
C1—C2 | 1.393 (9) | C10—C11 | 1.378 (8) |
C1—H1 | 0.9300 | C10—H10 | 0.9300 |
C2—C3 | 1.366 (9) | C11—C12 | 1.414 (7) |
C2—H2 | 0.9300 | C11—H11 | 0.9300 |
C3—C4 | 1.425 (8) | ||
O1i—Cu1—N2 | 173.36 (16) | N1—C5—C4 | 123.4 (5) |
O1i—Cu1—N1 | 104.07 (15) | N1—C5—C6 | 117.0 (5) |
N2—Cu1—N1 | 82.57 (16) | C4—C5—C6 | 119.6 (5) |
O1i—Cu1—Cu1i | 90.38 (11) | N2—C6—C9 | 122.7 (4) |
N2—Cu1—Cu1i | 82.98 (13) | N2—C6—C5 | 116.8 (5) |
N1—Cu1—Cu1i | 165.50 (11) | C9—C6—C5 | 120.5 (5) |
C1—N1—C5 | 118.3 (5) | C8—C7—C4 | 119.9 (6) |
C1—N1—Cu1 | 132.6 (4) | C8—C7—H7 | 120.0 |
C5—N1—Cu1 | 109.1 (3) | C4—C7—H7 | 120.0 |
C12—N2—C6 | 119.5 (4) | C7—C8—C9 | 122.2 (6) |
C12—N2—Cu1 | 126.0 (4) | C7—C8—H8 | 118.9 |
C6—N2—Cu1 | 114.5 (3) | C9—C8—H8 | 118.9 |
C12—O1—Cu1i | 121.5 (3) | C6—C9—C8 | 118.1 (5) |
N1—C1—C2 | 122.6 (6) | C6—C9—C10 | 117.4 (5) |
N1—C1—H1 | 118.7 | C8—C9—C10 | 124.5 (5) |
C2—C1—H1 | 118.7 | C11—C10—C9 | 119.6 (5) |
C3—C2—C1 | 119.7 (5) | C11—C10—H10 | 120.2 |
C3—C2—H2 | 120.2 | C9—C10—H10 | 120.2 |
C1—C2—H2 | 120.2 | C10—C11—C12 | 120.9 (5) |
C2—C3—C4 | 119.5 (5) | C10—C11—H11 | 119.5 |
C2—C3—H3 | 120.3 | C12—C11—H11 | 119.5 |
C4—C3—H3 | 120.3 | O1—C12—N2 | 119.1 (4) |
C5—C4—C7 | 119.7 (5) | O1—C12—C11 | 121.0 (4) |
C5—C4—C3 | 116.4 (5) | N2—C12—C11 | 119.9 (5) |
C7—C4—C3 | 123.8 (5) | ||
O1i—Cu1—N1—C1 | 1.9 (5) | C12—N2—C6—C5 | −179.6 (4) |
N2—Cu1—N1—C1 | −178.0 (5) | Cu1—N2—C6—C5 | 1.6 (5) |
Cu1i—Cu1—N1—C1 | −173.5 (3) | N1—C5—C6—N2 | −1.0 (6) |
O1i—Cu1—N1—C5 | −179.4 (3) | C4—C5—C6—N2 | 179.5 (4) |
N2—Cu1—N1—C5 | 0.7 (3) | N1—C5—C6—C9 | 179.4 (4) |
Cu1i—Cu1—N1—C5 | 5.2 (7) | C4—C5—C6—C9 | −0.1 (7) |
N1—Cu1—N2—C12 | −179.9 (4) | C5—C4—C7—C8 | 0.6 (7) |
Cu1i—Cu1—N2—C12 | 1.2 (4) | C3—C4—C7—C8 | 178.4 (5) |
N1—Cu1—N2—C6 | −1.3 (3) | C4—C7—C8—C9 | −1.5 (8) |
Cu1i—Cu1—N2—C6 | 179.9 (3) | N2—C6—C9—C8 | 179.7 (4) |
C5—N1—C1—C2 | −0.8 (7) | C5—C6—C9—C8 | −0.7 (6) |
Cu1—N1—C1—C2 | 177.8 (3) | N2—C6—C9—C10 | 0.6 (7) |
N1—C1—C2—C3 | 2.0 (8) | C5—C6—C9—C10 | −179.8 (4) |
C1—C2—C3—C4 | −0.6 (7) | C7—C8—C9—C6 | 1.6 (7) |
C2—C3—C4—C5 | −1.6 (7) | C7—C8—C9—C10 | −179.4 (4) |
C2—C3—C4—C7 | −179.4 (5) | C6—C9—C10—C11 | −1.2 (7) |
C1—N1—C5—C4 | −1.7 (7) | C8—C9—C10—C11 | 179.8 (4) |
Cu1—N1—C5—C4 | 179.4 (4) | C9—C10—C11—C12 | 1.2 (7) |
C1—N1—C5—C6 | 178.9 (4) | Cu1i—O1—C12—N2 | 2.3 (7) |
Cu1—N1—C5—C6 | −0.1 (5) | Cu1i—O1—C12—C11 | −178.7 (3) |
C7—C4—C5—N1 | −179.3 (4) | C6—N2—C12—O1 | 179.0 (4) |
C3—C4—C5—N1 | 2.8 (7) | Cu1—N2—C12—O1 | −2.4 (7) |
C7—C4—C5—C6 | 0.2 (7) | C6—N2—C12—C11 | 0.0 (7) |
C3—C4—C5—C6 | −177.7 (4) | Cu1—N2—C12—C11 | 178.6 (3) |
C12—N2—C6—C9 | 0.0 (7) | C10—C11—C12—O1 | −179.6 (5) |
Cu1—N2—C6—C9 | −178.8 (3) | C10—C11—C12—N2 | −0.6 (7) |
Symmetry code: (i) −x+1/2, −y+3/2, −z+2. |
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2···O1ii | 0.93 | 2.52 | 3.448 (7) | 173 |
Symmetry code: (ii) x, −y+1, z−1/2. |
Experimental details
Crystal data | |
Chemical formula | [Cu2(C12H7N2O)2]·H2O |
Mr | 535.49 |
Crystal system, space group | Monoclinic, C2/c |
Temperature (K) | 293 |
a, b, c (Å) | 30.344 (3), 3.6676 (3), 19.1508 (17) |
β (°) | 107.578 (1) |
V (Å3) | 2031.7 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 2.13 |
Crystal size (mm) | 0.28 × 0.15 × 0.04 |
Data collection | |
Diffractometer | Bruker SMART 1K CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2000) |
Tmin, Tmax | 0.587, 0.920 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6470, 1780, 1506 |
Rint | 0.033 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.061, 0.198, 1.14 |
No. of reflections | 1780 |
No. of parameters | 150 |
No. of restraints | 6 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 1.48, −0.52 |
Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL/PC (Sheldrick, 1999), SHELXTL/PC.
Cu1—O1i | 1.883 (3) | Cu1—N1 | 2.109 (4) |
Cu1—N2 | 1.913 (4) | Cu1—Cu1i | 2.4971 (11) |
O1i—Cu1—N2 | 173.36 (16) | N2—Cu1—N1 | 82.57 (16) |
O1i—Cu1—N1 | 104.07 (15) |
Symmetry code: (i) −x+1/2, −y+3/2, −z+2. |
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2···O1ii | 0.93 | 2.52 | 3.448 (7) | 172.9 |
Symmetry code: (ii) x, −y+1, z−1/2. |
The copper(II) complex of 1,10-phenanthroline, the first artificial nuclease, has been well investigated over the past two decades. Although [(phen)2Cu]+ or [(phen)2Cu2]+ (phen is 1,10-phenanthroline) are thought to be the active species for DNA cleavage (Sigman et al., 1993; Lu et al., 2003), it is still not known how these complexes bind to DNA. Therefore, investigating the structures of [(phen)2Cu]+ and [(phen)2Cu2]+ would be helpful for understanding the binding mode. Recently, three supramolecular isomers of dinuclear copper(I) 2-hydroxy-1,10-phenanthroline complexes, [Cu2(ophen)2], synthesized from 1,10-phenanthroline (ophen is? Please define) were studied by Zhang Tong et al. (2002). In our experiments, we have obtained a similar complex, the title compound, (I), and we report its crystal structure here. \sch
The geometric parameters of (I) are listed in Table 1 and the molecular conformation is illustrated in Fig. 1. The compound contains a [Cu2(oxo-phen)2] complex and a water molecule. The complex molecule is located on a centre of symmetry and the water molecule on a twofold axis of the space group C2/c. Each Cu+ ion adopts a square-planar geometry, being coordinated by two N atoms from an oxo-phen ligand and one O atom from another oxo-phen ligand, as well as one Cu atom. This structure is not much different from that reported by Zhang Tong et al. (2002). However, all coordination bonds around the Cu atoms [Cu—N 1.913 (4) and 2.110 (4) Å, Cu—O 1.883 (3) Å and Cu—Cu 2.497 (1) Å] are shorter than the corresponding bonds [Cu—N 1.953 (5)–2.274 (6) Å, Cu—O 1.916 (5)–1.923 (5) Å and Cu—Cu 2.661 (2)–2.679 (3) Å] in [Cu2(ophen)2] supramolecular isomers, especially the Cu—Cu distance, which is shorter by 0.164–0.182 Å but much closer to the values observed in mixed-valence Cu+/Cu2+ complexes [Cu—Cu 2.402 (1)–2.443 (2) Å; Zhang Tong et al., 2002; Zhang Tong & Chen, 2002]. Thus the coordination sphere of (I) is tighter and the interaction of both Cu+ ions is stronger.
The hydrogen-bonding geometry in (I) is listed in Table 2 and illustrated in Fig. 2. In the crystal packing, aromatic π–π stacking interactions are present between the ligand rings of the complex packed along y. These can be best described by considering the C6/C9—C12/N2 ring at (x, y, z) and the C4—C9 ring at (x, y − 1, z), with a centroid-centroid distance of 3.587 (7) Å. The weighted least-squares planes through these two rings are very nearly parallel, as the dihedral angle they form is only 0.40 (13)°. The interplanar spacing is 3.28 (5) Å and the centroid shift is 1.45 (11) Å. Along y, the shortest Cu···Cu contact is b = 3.6676 (3) Å. The coordination plane through atoms Cu1/N1/N2/O1 at (x, y, z) and the equivalent atoms at (1/2 − x, 1/2 + y, 3/2 − z) form a dihedral angle of 48.03 (13)°. This is the direction along which the complex molecules are joined via weak C—H···O hydrogen interactions (Table 2), giving rise to a zigzag chain that, together with the π–π stacking and Cu···Cu interactions, generates a supramolecular two-dimensional array extended along the length of the crystal.