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Acta Crystallogr Sect E Struct Rep Online. 2010 April 1; 66(Pt 4): m455.
Published online 2010 March 27. doi:  10.1107/S1600536810010652
PMCID: PMC2983767

Diaqua­[N-(5-nitro-2-oxidobenzyl­idene)glycinato]copper(II) dihydrate

Abstract

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 crystal structure 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 [triangle]); Wetmore et al. (2001 [triangle]); Zabinski & Toney (2001 [triangle]). For related Schiff base complexes, see: Ganguly et al. (2008 [triangle]); Jammi et al. (2008 [triangle]). For a related structure, see: Ueki et al. (1967 [triangle]).

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Object name is e-66-0m455-scheme1.jpg

Experimental

Crystal data

  • [Cu(C9H6N2O5)(H2O)2]·2H2O
  • M r = 357.76
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0m455-efi1.jpg
  • a = 17.306 (4) Å
  • b = 10.837 (2) Å
  • c = 7.185 (2) Å
  • β = 91.63 (1)°
  • V = 1347.0 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 1.67 mm−1
  • T = 293 K
  • 0.25 × 0.20 × 0.15 mm

Data collection

  • Bruker SMART 1000 CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.68, T max = 0.78
  • 6554 measured reflections
  • 2369 independent reflections
  • 1107 reflections with I > 2σ(I)
  • R int = 0.122

Refinement

  • R[F 2 > 2σ(F 2)] = 0.045
  • wR(F 2) = 0.074
  • S = 0.62
  • 2369 reflections
  • 214 parameters
  • 8 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.53 e Å−3
  • Δρmin = −0.41 e Å−3

Data collection: SMART (Bruker, 2007 [triangle]); cell refinement: SAINT (Bruker, 2007 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and DIAMOND (Brandenburg, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810010652/hy2290sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810010652/hy2290Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

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.

supplementary crystallographic information

Comment

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).

Experimental

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.

Refinement

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).

Figures

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.

Crystal data

[Cu(C9H6N2O5)(H2O)2]·2H2OF(000) = 732
Mr = 357.76Dx = 1.764 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 1107 reflections
a = 17.306 (4) Åθ = 2.2–25.0°
b = 10.837 (2) ŵ = 1.67 mm1
c = 7.185 (2) ÅT = 293 K
β = 91.63 (1)°Block, blue
V = 1347.0 (5) Å30.25 × 0.2 × 0.15 mm
Z = 4

Data collection

Bruker SMART 1000 CCD diffractometer2369 independent reflections
Radiation source: fine-focus sealed tube1107 reflections with I > 2σ(I)
graphiteRint = 0.122
[var phi] and ω scansθmax = 25.0°, θmin = 2.2°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −20→20
Tmin = 0.68, Tmax = 0.78k = −8→12
6554 measured reflectionsl = −8→8

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.045Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.074H atoms treated by a mixture of independent and constrained refinement
S = 0.62w = 1/[σ2(Fo2)] where P = (Fo2 + 2Fc2)/3
2369 reflections(Δ/σ)max < 0.001
214 parametersΔρmax = 0.53 e Å3
8 restraintsΔρmin = −0.41 e Å3

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
Cu10.68418 (3)0.93382 (5)1.05603 (9)0.0332 (2)
N10.7825 (2)0.9810 (4)0.9699 (6)0.0313 (11)
N20.9642 (3)0.5241 (5)0.7898 (7)0.0533 (15)
C10.7707 (3)0.7116 (5)1.0012 (7)0.0262 (13)
C20.7740 (3)0.5812 (4)0.9948 (7)0.0342 (14)
H20.73240.53521.03570.041*
C30.8371 (3)0.5222 (5)0.9296 (7)0.0384 (15)
H30.83810.43640.92840.046*
C40.8991 (3)0.5861 (5)0.8659 (7)0.0362 (14)
C50.8984 (3)0.7134 (5)0.8696 (7)0.0326 (14)
H50.94090.75720.82850.039*
C60.8343 (2)0.7767 (4)0.9347 (7)0.0241 (12)
C70.8375 (2)0.9109 (4)0.9286 (6)0.0319 (14)
H70.88320.94730.89170.038*
C80.7918 (3)1.1165 (4)0.9543 (8)0.0452 (16)
H8A0.80511.13800.82810.054*
H8B0.83341.14401.03770.054*
C90.7174 (3)1.1797 (5)1.0040 (8)0.0404 (15)
O10.70921 (17)0.7616 (3)1.0634 (5)0.0314 (9)
O20.71569 (18)1.2917 (3)0.9976 (5)0.0533 (12)
O30.66318 (17)1.1087 (3)1.0507 (5)0.0405 (10)
O40.9629 (2)0.4122 (3)0.7780 (6)0.0807 (16)
O51.0193 (2)0.5843 (4)0.7388 (6)0.0828 (16)
O60.59324 (19)0.9035 (4)1.2066 (5)0.0389 (10)
H6A0.559 (3)0.890 (5)1.134 (5)0.053*
H6B0.583 (3)0.942 (4)1.297 (5)0.047*
O70.48642 (17)0.8064 (3)0.9756 (6)0.0466 (11)
H7A0.4407 (11)0.834 (3)0.966 (7)0.053*
H7B0.481 (2)0.729 (3)0.982 (7)0.053*
O80.6090 (2)0.8942 (3)0.7687 (6)0.0403 (10)
H8E0.5724 (19)0.857 (3)0.821 (6)0.053*
H8D0.631 (2)0.844 (4)0.703 (6)0.048*
O90.58080 (19)0.0716 (3)0.4864 (5)0.0438 (10)
H9D0.621 (2)0.105 (4)0.486 (7)0.053*
H9B0.576 (2)0.026 (4)0.580 (4)0.053*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cu10.0270 (3)0.0226 (3)0.0505 (4)0.0012 (3)0.0084 (3)0.0002 (4)
N10.028 (2)0.023 (3)0.044 (3)0.006 (2)0.005 (2)0.004 (2)
N20.039 (3)0.058 (4)0.064 (4)0.024 (3)0.009 (3)0.000 (3)
C10.022 (3)0.029 (3)0.028 (3)−0.001 (3)0.003 (3)0.006 (3)
C20.027 (3)0.027 (3)0.049 (4)−0.001 (3)0.011 (3)0.007 (3)
C30.045 (4)0.035 (3)0.036 (4)0.004 (3)0.008 (3)0.003 (3)
C40.038 (3)0.033 (4)0.038 (4)0.015 (3)0.005 (3)0.000 (3)
C50.021 (3)0.038 (4)0.039 (4)−0.004 (3)0.004 (3)0.001 (3)
C60.023 (3)0.022 (3)0.027 (3)0.001 (2)0.000 (3)−0.002 (3)
C70.025 (3)0.029 (3)0.041 (4)−0.005 (3)0.005 (3)0.001 (3)
C80.043 (4)0.026 (3)0.067 (5)−0.003 (3)0.011 (3)0.005 (3)
C90.038 (4)0.033 (4)0.051 (4)0.000 (3)0.005 (3)−0.010 (3)
O10.026 (2)0.020 (2)0.048 (3)−0.0014 (15)0.0092 (19)0.0026 (17)
O20.049 (3)0.016 (2)0.096 (3)−0.0022 (19)0.011 (2)−0.005 (2)
O30.031 (2)0.018 (2)0.073 (3)−0.0009 (16)0.010 (2)−0.0023 (19)
O40.077 (3)0.037 (3)0.130 (4)0.025 (2)0.026 (3)−0.013 (3)
O50.048 (3)0.068 (3)0.135 (4)0.022 (3)0.047 (3)−0.003 (3)
O60.037 (2)0.036 (3)0.044 (3)0.0001 (19)0.007 (2)−0.008 (2)
O70.027 (2)0.035 (2)0.079 (3)−0.0045 (19)0.008 (2)−0.001 (2)
O80.039 (2)0.029 (2)0.053 (3)0.0002 (17)0.008 (2)0.000 (2)
O90.045 (2)0.032 (2)0.056 (3)−0.004 (2)0.010 (2)0.001 (2)

Geometric parameters (Å, °)

Cu1—N11.897 (4)C5—C61.396 (6)
Cu1—O11.916 (3)C5—H50.9300
Cu1—O31.930 (3)C6—C71.456 (6)
Cu1—O61.963 (4)C7—H70.9300
Cu1—O82.447 (4)C8—C91.511 (6)
N1—C71.260 (5)C8—H8A0.9700
N1—C81.481 (5)C8—H8B0.9700
N2—O41.215 (5)C9—O21.215 (5)
N2—O51.221 (5)C9—O31.266 (5)
N2—C41.433 (6)O6—H6B0.80 (3)
C1—O11.286 (5)O6—H6A0.80 (4)
C1—C61.404 (6)O7—H7A0.85 (3)
C1—C21.415 (6)O7—H7B0.85 (3)
C2—C31.360 (6)O8—H8D0.82 (3)
C2—H20.9300O8—H8E0.85 (4)
C3—C41.367 (6)O9—H9D0.78 (3)
C3—H30.9300O9—H9B0.84 (3)
C4—C51.380 (6)
N1—Cu1—O193.87 (15)C5—C4—N2118.9 (5)
N1—Cu1—O384.20 (15)C4—C5—C6120.3 (5)
O1—Cu1—O3177.76 (14)C4—C5—H5119.8
N1—Cu1—O6164.91 (16)C6—C5—H5119.8
O1—Cu1—O690.32 (15)C5—C6—C1120.4 (5)
O3—Cu1—O691.26 (15)C5—C6—C7116.8 (4)
N1—Cu1—O8103.44 (14)C1—C6—C7122.9 (4)
O1—Cu1—O888.09 (13)N1—C7—C6124.5 (4)
O3—Cu1—O893.45 (13)N1—C7—H7117.7
O6—Cu1—O891.16 (14)C6—C7—H7117.7
C7—N1—C8119.7 (4)N1—C8—C9109.6 (4)
C7—N1—Cu1127.2 (3)N1—C8—H8A109.7
C8—N1—Cu1113.1 (3)C9—C8—H8A109.7
O4—N2—O5121.6 (5)N1—C8—H8B109.7
O4—N2—C4118.8 (5)C9—C8—H8B109.7
O5—N2—C4119.5 (5)H8A—C8—H8B108.2
O1—C1—C6124.8 (5)O2—C9—O3126.9 (5)
O1—C1—C2117.9 (4)O2—C9—C8117.6 (5)
C6—C1—C2117.3 (5)O3—C9—C8115.5 (5)
C3—C2—C1120.9 (5)C1—O1—Cu1126.1 (3)
C3—C2—H2119.5C9—O3—Cu1117.5 (3)
C1—C2—H2119.5Cu1—O6—H6B125 (4)
C2—C3—C4121.5 (5)Cu1—O6—H6A106 (3)
C2—C3—H3119.2H6B—O6—H6A116 (4)
C4—C3—H3119.2H7A—O7—H7B105 (3)
C3—C4—C5119.5 (5)H8D—O8—H8E108 (3)
C3—C4—N2121.5 (5)H9D—O9—H9B112 (4)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O6—H6A···O70.80 (4)1.90 (4)2.666 (5)162 (5)
O6—H6B···O9i0.80 (3)1.96 (3)2.726 (5)162 (5)
O7—H7A···O3ii0.85 (3)1.90 (3)2.749 (4)178 (4)
O7—H7B···O9iii0.85 (3)2.03 (4)2.814 (5)154 (4)
O8—H8D···O1iv0.82 (3)2.05 (3)2.860 (4)167 (5)
O8—H8E···O70.85 (4)1.96 (4)2.792 (5)166 (4)
O9—H9B···O8v0.84 (3)2.04 (2)2.827 (5)156 (5)
O9—H9D···O2iv0.78 (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.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HY2290).

References

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  • Ganguly, R., Sreenivasulu, B. & Vittal, J. J. (2008). Coord. Chem. Rev.252, 1027–1050.
  • Jammi, S., Rout, L., Saha, P., Akkilagunta, V. K., Sanyasi, S. & Punniyamurthy, T. (2008). Inorg. Chem.47, 5093–5098. [PubMed]
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  • Ueki, T., Ashida, T., Sasada, Y. & Kakudo, M. (1967). Acta Cryst.22, 870–878.
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