metal-organic compounds
Diaqua[N-(5-nitro-2-oxidobenzylidene)glycinato]copper(II) dihydrate
aChemistry Department, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
*Correspondence e-mail: zouyang@zstu.edu.cn
In the title complex, [Cu(C9H6N2O5)(H2O)2]·2H2O, the CuII atom has a square-pyramidal coordination environment with a tridentate N-(5-nitro-2-oxidobenzylidene)glycinate Schiff base ligand and a water molecule in the basal plane. The apical site is occupied by an O atom from another coordinated water molecule. The is stabilized by O—H⋯O hydrogen bonds, building a two-dimensional network parallel to (100).
Related literature
For general background to metabolic reactions requiring pyridoxal-5′-phosphate as a cofactor, see: Bkouche-Waksman et al. (1988); Wetmore et al. (2001); Zabinski & Toney (2001). For related Schiff base complexes, see: Ganguly et al. (2008); Jammi et al. (2008). For a related structure, see: Ueki et al. (1967).
Experimental
Crystal data
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Refinement
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Data collection: SMART (Bruker, 2007); cell SAINT (Bruker, 2007); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and DIAMOND (Brandenburg, 1999).
Supporting information
10.1107/S1600536810010652/hy2290sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536810010652/hy2290Isup2.hkl
The title compound was prepared as follows: Glycine (10 mmol), 5-nitrosalicylaldehyde (10 mmol) and LiOH (20 mmol) were dissolved and refluxed in MeOH/H2O (v/v 1:1). CuCl2.2H2O (10 mmol) was then added to the solution and the resulting solution was adjusted to pH = 9–11. The mixture was stirred at room temperature for 24 h. Violet-blue precipitate that formed was filtered. The filtrate was allowed to evaporate slowly at room temperature. After several days, blue crystals suitable for X-ray diffraction were obtained.
H atoms of water molecules were located in a difference Fourier map and refined with distance restraints of O—H = 0.85 (1) Å, and with Uiso(H) = 1.2Ueq(O). Other H atoms were positioned geometrically and refined using a riding model, with C—H = 0.93 (CH) and 0.97 (CH2) Å and with Uiso(H) = 1.2Ueq(C).
Data collection: SMART (Bruker, 2007); cell
SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and DIAMOND (Brandenburg, 1999).Fig. 1. Molecular structure of the title complex. Displacement ellipsoids are drawn at the 40% probability level. | |
Fig. 2. A view of the hydrogen-bonded (dashed lines) two-dimensional network. |
[Cu(C9H6N2O5)(H2O)2]·2H2O | F(000) = 732 |
Mr = 357.76 | Dx = 1.764 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 1107 reflections |
a = 17.306 (4) Å | θ = 2.2–25.0° |
b = 10.837 (2) Å | µ = 1.67 mm−1 |
c = 7.185 (2) Å | T = 293 K |
β = 91.63 (1)° | Block, blue |
V = 1347.0 (5) Å3 | 0.25 × 0.2 × 0.15 mm |
Z = 4 |
Bruker SMART 1000 CCD diffractometer | 2369 independent reflections |
Radiation source: fine-focus sealed tube | 1107 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.122 |
ϕ and ω scans | θmax = 25.0°, θmin = 2.2° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −20→20 |
Tmin = 0.68, Tmax = 0.78 | k = −8→12 |
6554 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)] = 0.045 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.074 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.62 | w = 1/[σ2(Fo2)] where P = (Fo2 + 2Fc2)/3 |
2369 reflections | (Δ/σ)max < 0.001 |
214 parameters | Δρmax = 0.53 e Å−3 |
8 restraints | Δρmin = −0.41 e Å−3 |
[Cu(C9H6N2O5)(H2O)2]·2H2O | V = 1347.0 (5) Å3 |
Mr = 357.76 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 17.306 (4) Å | µ = 1.67 mm−1 |
b = 10.837 (2) Å | T = 293 K |
c = 7.185 (2) Å | 0.25 × 0.2 × 0.15 mm |
β = 91.63 (1)° |
Bruker SMART 1000 CCD diffractometer | 2369 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 1107 reflections with I > 2σ(I) |
Tmin = 0.68, Tmax = 0.78 | Rint = 0.122 |
6554 measured reflections |
R[F2 > 2σ(F2)] = 0.045 | 8 restraints |
wR(F2) = 0.074 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.62 | Δρmax = 0.53 e Å−3 |
2369 reflections | Δρmin = −0.41 e Å−3 |
214 parameters |
x | y | z | Uiso*/Ueq | ||
Cu1 | 0.68418 (3) | 0.93382 (5) | 1.05603 (9) | 0.0332 (2) | |
N1 | 0.7825 (2) | 0.9810 (4) | 0.9699 (6) | 0.0313 (11) | |
N2 | 0.9642 (3) | 0.5241 (5) | 0.7898 (7) | 0.0533 (15) | |
C1 | 0.7707 (3) | 0.7116 (5) | 1.0012 (7) | 0.0262 (13) | |
C2 | 0.7740 (3) | 0.5812 (4) | 0.9948 (7) | 0.0342 (14) | |
H2 | 0.7324 | 0.5352 | 1.0357 | 0.041* | |
C3 | 0.8371 (3) | 0.5222 (5) | 0.9296 (7) | 0.0384 (15) | |
H3 | 0.8381 | 0.4364 | 0.9284 | 0.046* | |
C4 | 0.8991 (3) | 0.5861 (5) | 0.8659 (7) | 0.0362 (14) | |
C5 | 0.8984 (3) | 0.7134 (5) | 0.8696 (7) | 0.0326 (14) | |
H5 | 0.9409 | 0.7572 | 0.8285 | 0.039* | |
C6 | 0.8343 (2) | 0.7767 (4) | 0.9347 (7) | 0.0241 (12) | |
C7 | 0.8375 (2) | 0.9109 (4) | 0.9286 (6) | 0.0319 (14) | |
H7 | 0.8832 | 0.9473 | 0.8917 | 0.038* | |
C8 | 0.7918 (3) | 1.1165 (4) | 0.9543 (8) | 0.0452 (16) | |
H8A | 0.8051 | 1.1380 | 0.8281 | 0.054* | |
H8B | 0.8334 | 1.1440 | 1.0377 | 0.054* | |
C9 | 0.7174 (3) | 1.1797 (5) | 1.0040 (8) | 0.0404 (15) | |
O1 | 0.70921 (17) | 0.7616 (3) | 1.0634 (5) | 0.0314 (9) | |
O2 | 0.71569 (18) | 1.2917 (3) | 0.9976 (5) | 0.0533 (12) | |
O3 | 0.66318 (17) | 1.1087 (3) | 1.0507 (5) | 0.0405 (10) | |
O4 | 0.9629 (2) | 0.4122 (3) | 0.7780 (6) | 0.0807 (16) | |
O5 | 1.0193 (2) | 0.5843 (4) | 0.7388 (6) | 0.0828 (16) | |
O6 | 0.59324 (19) | 0.9035 (4) | 1.2066 (5) | 0.0389 (10) | |
H6A | 0.559 (3) | 0.890 (5) | 1.134 (5) | 0.053* | |
H6B | 0.583 (3) | 0.942 (4) | 1.297 (5) | 0.047* | |
O7 | 0.48642 (17) | 0.8064 (3) | 0.9756 (6) | 0.0466 (11) | |
H7A | 0.4407 (11) | 0.834 (3) | 0.966 (7) | 0.053* | |
H7B | 0.481 (2) | 0.729 (3) | 0.982 (7) | 0.053* | |
O8 | 0.6090 (2) | 0.8942 (3) | 0.7687 (6) | 0.0403 (10) | |
H8E | 0.5724 (19) | 0.857 (3) | 0.821 (6) | 0.053* | |
H8D | 0.631 (2) | 0.844 (4) | 0.703 (6) | 0.048* | |
O9 | 0.58080 (19) | 0.0716 (3) | 0.4864 (5) | 0.0438 (10) | |
H9D | 0.621 (2) | 0.105 (4) | 0.486 (7) | 0.053* | |
H9B | 0.576 (2) | 0.026 (4) | 0.580 (4) | 0.053* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cu1 | 0.0270 (3) | 0.0226 (3) | 0.0505 (4) | 0.0012 (3) | 0.0084 (3) | 0.0002 (4) |
N1 | 0.028 (2) | 0.023 (3) | 0.044 (3) | 0.006 (2) | 0.005 (2) | 0.004 (2) |
N2 | 0.039 (3) | 0.058 (4) | 0.064 (4) | 0.024 (3) | 0.009 (3) | 0.000 (3) |
C1 | 0.022 (3) | 0.029 (3) | 0.028 (3) | −0.001 (3) | 0.003 (3) | 0.006 (3) |
C2 | 0.027 (3) | 0.027 (3) | 0.049 (4) | −0.001 (3) | 0.011 (3) | 0.007 (3) |
C3 | 0.045 (4) | 0.035 (3) | 0.036 (4) | 0.004 (3) | 0.008 (3) | 0.003 (3) |
C4 | 0.038 (3) | 0.033 (4) | 0.038 (4) | 0.015 (3) | 0.005 (3) | 0.000 (3) |
C5 | 0.021 (3) | 0.038 (4) | 0.039 (4) | −0.004 (3) | 0.004 (3) | 0.001 (3) |
C6 | 0.023 (3) | 0.022 (3) | 0.027 (3) | 0.001 (2) | 0.000 (3) | −0.002 (3) |
C7 | 0.025 (3) | 0.029 (3) | 0.041 (4) | −0.005 (3) | 0.005 (3) | 0.001 (3) |
C8 | 0.043 (4) | 0.026 (3) | 0.067 (5) | −0.003 (3) | 0.011 (3) | 0.005 (3) |
C9 | 0.038 (4) | 0.033 (4) | 0.051 (4) | 0.000 (3) | 0.005 (3) | −0.010 (3) |
O1 | 0.026 (2) | 0.020 (2) | 0.048 (3) | −0.0014 (15) | 0.0092 (19) | 0.0026 (17) |
O2 | 0.049 (3) | 0.016 (2) | 0.096 (3) | −0.0022 (19) | 0.011 (2) | −0.005 (2) |
O3 | 0.031 (2) | 0.018 (2) | 0.073 (3) | −0.0009 (16) | 0.010 (2) | −0.0023 (19) |
O4 | 0.077 (3) | 0.037 (3) | 0.130 (4) | 0.025 (2) | 0.026 (3) | −0.013 (3) |
O5 | 0.048 (3) | 0.068 (3) | 0.135 (4) | 0.022 (3) | 0.047 (3) | −0.003 (3) |
O6 | 0.037 (2) | 0.036 (3) | 0.044 (3) | 0.0001 (19) | 0.007 (2) | −0.008 (2) |
O7 | 0.027 (2) | 0.035 (2) | 0.079 (3) | −0.0045 (19) | 0.008 (2) | −0.001 (2) |
O8 | 0.039 (2) | 0.029 (2) | 0.053 (3) | 0.0002 (17) | 0.008 (2) | 0.000 (2) |
O9 | 0.045 (2) | 0.032 (2) | 0.056 (3) | −0.004 (2) | 0.010 (2) | 0.001 (2) |
Cu1—N1 | 1.897 (4) | C5—C6 | 1.396 (6) |
Cu1—O1 | 1.916 (3) | C5—H5 | 0.9300 |
Cu1—O3 | 1.930 (3) | C6—C7 | 1.456 (6) |
Cu1—O6 | 1.963 (4) | C7—H7 | 0.9300 |
Cu1—O8 | 2.447 (4) | C8—C9 | 1.511 (6) |
N1—C7 | 1.260 (5) | C8—H8A | 0.9700 |
N1—C8 | 1.481 (5) | C8—H8B | 0.9700 |
N2—O4 | 1.215 (5) | C9—O2 | 1.215 (5) |
N2—O5 | 1.221 (5) | C9—O3 | 1.266 (5) |
N2—C4 | 1.433 (6) | O6—H6B | 0.80 (3) |
C1—O1 | 1.286 (5) | O6—H6A | 0.80 (4) |
C1—C6 | 1.404 (6) | O7—H7A | 0.85 (3) |
C1—C2 | 1.415 (6) | O7—H7B | 0.85 (3) |
C2—C3 | 1.360 (6) | O8—H8D | 0.82 (3) |
C2—H2 | 0.9300 | O8—H8E | 0.85 (4) |
C3—C4 | 1.367 (6) | O9—H9D | 0.78 (3) |
C3—H3 | 0.9300 | O9—H9B | 0.84 (3) |
C4—C5 | 1.380 (6) | ||
N1—Cu1—O1 | 93.87 (15) | C5—C4—N2 | 118.9 (5) |
N1—Cu1—O3 | 84.20 (15) | C4—C5—C6 | 120.3 (5) |
O1—Cu1—O3 | 177.76 (14) | C4—C5—H5 | 119.8 |
N1—Cu1—O6 | 164.91 (16) | C6—C5—H5 | 119.8 |
O1—Cu1—O6 | 90.32 (15) | C5—C6—C1 | 120.4 (5) |
O3—Cu1—O6 | 91.26 (15) | C5—C6—C7 | 116.8 (4) |
N1—Cu1—O8 | 103.44 (14) | C1—C6—C7 | 122.9 (4) |
O1—Cu1—O8 | 88.09 (13) | N1—C7—C6 | 124.5 (4) |
O3—Cu1—O8 | 93.45 (13) | N1—C7—H7 | 117.7 |
O6—Cu1—O8 | 91.16 (14) | C6—C7—H7 | 117.7 |
C7—N1—C8 | 119.7 (4) | N1—C8—C9 | 109.6 (4) |
C7—N1—Cu1 | 127.2 (3) | N1—C8—H8A | 109.7 |
C8—N1—Cu1 | 113.1 (3) | C9—C8—H8A | 109.7 |
O4—N2—O5 | 121.6 (5) | N1—C8—H8B | 109.7 |
O4—N2—C4 | 118.8 (5) | C9—C8—H8B | 109.7 |
O5—N2—C4 | 119.5 (5) | H8A—C8—H8B | 108.2 |
O1—C1—C6 | 124.8 (5) | O2—C9—O3 | 126.9 (5) |
O1—C1—C2 | 117.9 (4) | O2—C9—C8 | 117.6 (5) |
C6—C1—C2 | 117.3 (5) | O3—C9—C8 | 115.5 (5) |
C3—C2—C1 | 120.9 (5) | C1—O1—Cu1 | 126.1 (3) |
C3—C2—H2 | 119.5 | C9—O3—Cu1 | 117.5 (3) |
C1—C2—H2 | 119.5 | Cu1—O6—H6B | 125 (4) |
C2—C3—C4 | 121.5 (5) | Cu1—O6—H6A | 106 (3) |
C2—C3—H3 | 119.2 | H6B—O6—H6A | 116 (4) |
C4—C3—H3 | 119.2 | H7A—O7—H7B | 105 (3) |
C3—C4—C5 | 119.5 (5) | H8D—O8—H8E | 108 (3) |
C3—C4—N2 | 121.5 (5) | H9D—O9—H9B | 112 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
O6—H6A···O7 | 0.80 (4) | 1.90 (4) | 2.666 (5) | 162 (5) |
O6—H6B···O9i | 0.80 (3) | 1.96 (3) | 2.726 (5) | 162 (5) |
O7—H7A···O3ii | 0.85 (3) | 1.90 (3) | 2.749 (4) | 178 (4) |
O7—H7B···O9iii | 0.85 (3) | 2.03 (4) | 2.814 (5) | 154 (4) |
O8—H8D···O1iv | 0.82 (3) | 2.05 (3) | 2.860 (4) | 167 (5) |
O8—H8E···O7 | 0.85 (4) | 1.96 (4) | 2.792 (5) | 166 (4) |
O9—H9B···O8v | 0.84 (3) | 2.04 (2) | 2.827 (5) | 156 (5) |
O9—H9D···O2iv | 0.78 (3) | 1.99 (3) | 2.764 (5) | 173 (5) |
Symmetry codes: (i) x, y+1, z+1; (ii) −x+1, −y+2, −z+2; (iii) −x+1, y+1/2, −z+3/2; (iv) x, −y+3/2, z−1/2; (v) x, y−1, z. |
Experimental details
Crystal data | |
Chemical formula | [Cu(C9H6N2O5)(H2O)2]·2H2O |
Mr | 357.76 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 293 |
a, b, c (Å) | 17.306 (4), 10.837 (2), 7.185 (2) |
β (°) | 91.63 (1) |
V (Å3) | 1347.0 (5) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 1.67 |
Crystal size (mm) | 0.25 × 0.2 × 0.15 |
Data collection | |
Diffractometer | Bruker SMART 1000 CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1996) |
Tmin, Tmax | 0.68, 0.78 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6554, 2369, 1107 |
Rint | 0.122 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.045, 0.074, 0.62 |
No. of reflections | 2369 |
No. of parameters | 214 |
No. of restraints | 8 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.53, −0.41 |
Computer programs: SMART (Bruker, 2007), SAINT (Bruker, 2007), SHELXTL (Sheldrick, 2008) and DIAMOND (Brandenburg, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
O6—H6A···O7 | 0.80 (4) | 1.90 (4) | 2.666 (5) | 162 (5) |
O6—H6B···O9i | 0.80 (3) | 1.96 (3) | 2.726 (5) | 162 (5) |
O7—H7A···O3ii | 0.85 (3) | 1.90 (3) | 2.749 (4) | 178 (4) |
O7—H7B···O9iii | 0.85 (3) | 2.03 (4) | 2.814 (5) | 154 (4) |
O8—H8D···O1iv | 0.82 (3) | 2.05 (3) | 2.860 (4) | 167 (5) |
O8—H8E···O7 | 0.85 (4) | 1.96 (4) | 2.792 (5) | 166 (4) |
O9—H9B···O8v | 0.84 (3) | 2.04 (2) | 2.827 (5) | 156 (5) |
O9—H9D···O2iv | 0.78 (3) | 1.99 (3) | 2.764 (5) | 173 (5) |
Symmetry codes: (i) x, y+1, z+1; (ii) −x+1, −y+2, −z+2; (iii) −x+1, y+1/2, −z+3/2; (iv) x, −y+3/2, z−1/2; (v) x, y−1, z. |
Acknowledgements
The authors thank the Natural Science Foundation of Zhejiang Province, China (No. Y4080342) and the Science Foundation of Zhejiang Sci-Tech University (No. 0813622-Y) for financial support.
References
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Metal Schiff-base complexes derived from amino acids (or peptides) play an important role as key compounds for modeling more complicated PLP-amino acid Schiff bases (PLP = pyridoxal-5'-phosphate), as these are key intermediates in a variety of metabolic reactions involving amino acids, such as decarboxylation, transamination, racemization and C—C bond cleavage, which are catalyzed by enzymes that require PLP as a cofactor (Bkouche-Waksman et al., 1988; Wetmore et al., 2001; Zabinski & Toney, 2001). Considerable effort has been devoted to the preparation, structural characterization, appropriate spectroscopy and magnetic studies of Schiff-base complexes derived from salicylaldehyde and amino acids and reduced salicylidene amino acid (Ganguly et al., 2008), but little attention has been given to Schiff bases derived from nitro-substituted salicylaldehyde, and few structurally characterized complexes have been reported (Jammi et al., 2008). Herein, we report the synthesis and structural study of a copper(II) complex with the Schiff base derived from glycine and 5-nitrosalicylaldehyde.
The title complex is characterized by a square-pyramidal CuII coordination with a deprotonated tridentate Schiff base, 5-nitrosalicylideneglycinate, and a water molecule in the basal plane (Fig. 1). The Cu—N bond distance is 1.897 (4) Å. The two Cu—O bonds are 1.916 (3) and 1.930 (3) Å. The apical Cu1—O8 bond length is 2.447 (4) Å, which is little longer than that in the parent compound of this structure type, aqua(N-salicylideneglycinato)copper(II) hemihydrate [2.334 (6) Å] (Ueki et al., 1967). The phenyl ring (C1–C6) and the C1, C6, C7, N1, O1, Cu1 chelating ring are almost coplanar, with a small dihedral angle of 4.3 (4)°. Hydrogen bonds between the coordinated water molecules and the phenol O atoms of symmetry-related complex molecules lead to the formation of zigzag chains along the c axis (Table 1). Hydrogen bonds between the uncoordinated water molecules and carbonylate O atoms link the chains into a two-dimensional layer (Fig. 2).