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In the title mononuclear complex, [Cu(C13H10ClN2O)(H2O)]­NO3·H2O, the CuII atom is four-coordinated by two N atoms and one O atom of the tridentate Schiff base ligand and one O atom from the coordinated water mol­ecule in a slightly distorted square-planar configuration. The nitrate ion inter­acts with the copper center [Cu1...O3 = 2.579 (4) Å]. In the crystal, the cations, anions and water mol­ecules are linked by O—H...O and O—H...N hydrogen bonds.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536809052350/zq2021sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536809052350/zq2021Isup2.hkl
Contains datablock I

CCDC reference: 766664

Key indicators

  • Single-crystal X-ray study
  • T = 298 K
  • Mean [sigma](C-C) = 0.005 Å
  • R factor = 0.030
  • wR factor = 0.074
  • Data-to-parameter ratio = 12.4

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for O3 PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for N3 PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L= 0.595 44 PLAT042_ALERT_1_C Calc. and Reported MoietyFormula Strings Differ ?
Alert level G PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 1 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 2 O2 -CU1 -N1 -C1 -106.30 0.70 1.555 1.555 1.555 1.555 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 5 O2 -CU1 -N1 -C8 70.30 0.80 1.555 1.555 1.555 1.555 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 7 O1 -CU1 -N2 -C13 -163.30 1.90 1.555 1.555 1.555 1.555 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 10 O1 -CU1 -N2 -C9 12.00 2.00 1.555 1.555 1.555 1.555 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 15 N2 -CU1 -O1 -C3 -19.00 2.00 1.555 1.555 1.555 1.555
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 4 ALERT level C = Check and explain 6 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 2 ALERT type 2 Indicator that the structure model may be wrong or deficient 2 ALERT type 3 Indicator that the structure quality may be low 5 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check

Comment top

Metals ions are vital for living organisms because they are involved in many fundamental biological processes, e.g. copper proteins known to be involved in a crucial role, such as respiration, iron transport, oxidative stress protection, blood clotting and pigmentation (Arnesano et al., 2004). The study of copper compounds is of great interest in various aspects of chemistry (Downing & Urbach, 1969; Ganeshpure et al., 1996; Bosnich, 1968; Costes et al., 1995). The molecular structure of (I) is illustrated in Fig. 1, and selected bond distances and angles are given in Table 1. The CuII atom is four- coordinated by two nitrogen atoms and one oxygen atom of the tridentate Schiff base ligand, and one oxygen atom from the coordinated water molecule, forming a slightly distorted square-planar coordination configuration. The four coordinating atoms around the Cu centre are approximately coplanar. The Cu1—N2 bond [1.982 (2) Å; Table 1] is a little longer than the value [1.977 (4) Å] observed in a similar copper(II) complex (Sun et al., 2005). The Cu1—N1 bond length [1.936 (2) Å] is comparable with the corresponding value [1.934 (4) Å] observed in the same complex mentioned above (Sun et al., 2005). The Cu1—O1 bond length is 1.889 (18) Å. The nitrate ion is in interaction with the copper center [Cu1···O3 = 2.579 (4) Å]. The bond angles around the CuII centre show some deviations from ideal square-planar geometry. The Schiff base ligands from adjacent molecules are almost parallel due to by π-π interactions leading to the formation of two-dimensional parallel layers (Fig.2). The cations, anions and solvent water molecules are linked by O-H···O hydrogen bonds.

Related literature top

For the role of copper proteins in fundamental biological processes, see: Arnesano et al. (2004). For the chemistry of copper compounds, see: Bosnich (1968); Costes et al. (1995); Downing & Urbach (1969); Ganeshpure et al. (1996). For related structures, see: Sun et al. (2005); You et al. (2004). For related literature, see: Mizutani et al. (1999).

Experimental top

2-Aminomethylpyridine (0.1 mmol, 10.8 mg) and 5-chloro-salicylaldehyde (0.1 mmol, 15.6 mg) were dissolved in methanol (10 ml). The mixture was stirred for 1 h to give a clear yellow solution. To this solution was added a water solution (10 ml) of Cu(NO3)2.3H2O (0.1 mmol, 24.2 mg), with stirring. The mixture was stirred for 10 min to give a deep green solution, which was allowed to evaporate slowly in the open at room temperature. After 5 days, deep blue block-shaped crystals suitable for an X-ray diffraction study were formed at the bottom of the vessel.

Refinement top

The hydrogen atoms bound to carbon atoms were placed in geometrical positions and refined using a riding model, with C—H = 0.94 Å and Uiso(H) =1.2Ueq(C). The hydrogens of the water molecules were located in Fourier difference maps and refined with a distance restraint of 0.85 Å.

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title molecule, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level.
[Figure 2] Fig. 2. Crystal packing of the compound (I). Hydrogen bonds are shown as dashed lines.
Aqua[4-chloro-2-(2-pyridylmethyliminomethyl)phenolato]copper(II) nitrate monohydrate top
Crystal data top
[Cu(C13H10ClN2O)(H2O)]NO3·H2OZ = 2
Mr = 407.26F(000) = 414
Triclinic, P1Dx = 1.729 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.892 (2) ÅCell parameters from 13380 reflections
b = 8.9741 (12) Åθ = 1.8–25.0°
c = 11.8929 (15) ŵ = 1.60 mm1
α = 106.841 (2)°T = 298 K
β = 102.198 (1)°Prism, dark blue
γ = 92.897 (1)°0.47 × 0.41 × 0.30 mm
V = 782.3 (2) Å3
Data collection top
Rigaku SCXmini
diffractometer
2714 independent reflections
Radiation source: Rotating Anode2280 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.016
Detector resolution: 8.192 pixels mm-1θmax = 25.0°, θmin = 1.8°
ω scansh = 99
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)
k = 810
Tmin = 0.520, Tmax = 0.645l = 1314
4114 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.030H-atom parameters constrained
wR(F2) = 0.074 w = 1/[σ2(Fo2) + (0.0271P)2 + 0.5072P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.001
2714 reflectionsΔρmax = 0.40 e Å3
218 parametersΔρmin = 0.39 e Å3
1 restraintExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0320 (19)
Crystal data top
[Cu(C13H10ClN2O)(H2O)]NO3·H2Oγ = 92.897 (1)°
Mr = 407.26V = 782.3 (2) Å3
Triclinic, P1Z = 2
a = 7.892 (2) ÅMo Kα radiation
b = 8.9741 (12) ŵ = 1.60 mm1
c = 11.8929 (15) ÅT = 298 K
α = 106.841 (2)°0.47 × 0.41 × 0.30 mm
β = 102.198 (1)°
Data collection top
Rigaku SCXmini
diffractometer
2714 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)
2280 reflections with I > 2σ(I)
Tmin = 0.520, Tmax = 0.645Rint = 0.016
4114 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0301 restraint
wR(F2) = 0.074H-atom parameters constrained
S = 1.06Δρmax = 0.40 e Å3
2714 reflectionsΔρmin = 0.39 e Å3
218 parameters
Special details top

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
xyzUiso*/Ueq
Cu10.19716 (5)0.40689 (4)0.59865 (3)0.03271 (17)
Cl10.01878 (15)0.28462 (12)0.04586 (8)0.0556 (3)
N10.2799 (3)0.5546 (3)0.5259 (2)0.0322 (6)
N20.3181 (3)0.5696 (3)0.7513 (2)0.0329 (6)
N30.4694 (4)0.1517 (4)0.6974 (3)0.0448 (7)
O10.0888 (3)0.2574 (2)0.44856 (19)0.0391 (6)
O20.0886 (3)0.2783 (3)0.6801 (2)0.0380 (6)
H2A0.16810.22700.70490.046*
H2B0.00400.21040.63500.046*
O30.4553 (4)0.2453 (3)0.6385 (3)0.0632 (8)
O40.5942 (5)0.0744 (5)0.6999 (4)0.0921 (12)
O50.3572 (3)0.1310 (3)0.7528 (2)0.0513 (7)
O60.8275 (3)0.0554 (3)0.5520 (2)0.0496 (7)
H6A0.86620.03260.54620.059*
H6B0.75570.06500.59700.059*
C10.2497 (4)0.5376 (4)0.4119 (3)0.0322 (7)
H10.29420.61910.38880.039*
C20.1531 (4)0.4032 (4)0.3176 (3)0.0304 (7)
C30.0765 (4)0.2710 (4)0.3398 (3)0.0323 (7)
C40.0198 (5)0.1487 (4)0.2394 (3)0.0381 (8)
H40.07260.06180.25200.046*
C50.0380 (5)0.1543 (4)0.1237 (3)0.0395 (8)
H50.10280.07220.05890.047*
C60.0411 (5)0.2835 (4)0.1032 (3)0.0375 (8)
C70.1338 (4)0.4054 (4)0.1972 (3)0.0377 (8)
H70.18500.49110.18220.045*
C80.3778 (5)0.7018 (4)0.6111 (3)0.0382 (8)
H8A0.31380.78910.60300.046*
H8B0.49010.71840.59280.046*
C90.4047 (4)0.6945 (4)0.7380 (3)0.0328 (7)
C100.5091 (5)0.8088 (4)0.8357 (3)0.0420 (9)
H100.56970.89270.82430.050*
C110.5229 (5)0.7975 (4)0.9502 (3)0.0455 (9)
H110.59380.87291.01710.055*
C120.4294 (5)0.6720 (4)0.9639 (3)0.0458 (9)
H120.43400.66341.04050.055*
C130.3297 (5)0.5603 (4)0.8633 (3)0.0417 (9)
H130.26820.47550.87300.050*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cu10.0408 (3)0.0262 (2)0.0313 (2)0.00137 (16)0.00910 (17)0.00954 (17)
Cl10.0840 (8)0.0510 (6)0.0315 (5)0.0041 (5)0.0125 (5)0.0137 (4)
N10.0379 (16)0.0245 (14)0.0342 (15)0.0011 (11)0.0080 (12)0.0102 (12)
N20.0406 (16)0.0255 (14)0.0325 (15)0.0042 (12)0.0070 (12)0.0101 (12)
N30.0422 (19)0.0434 (18)0.0477 (19)0.0011 (15)0.0108 (15)0.0134 (15)
O10.0565 (15)0.0288 (12)0.0320 (13)0.0077 (11)0.0110 (11)0.0112 (10)
O20.0428 (14)0.0348 (13)0.0371 (13)0.0023 (10)0.0100 (10)0.0131 (11)
O30.0651 (19)0.0525 (17)0.093 (2)0.0078 (14)0.0379 (17)0.0412 (17)
O40.071 (2)0.121 (3)0.132 (3)0.050 (2)0.055 (2)0.083 (3)
O50.0485 (16)0.0679 (18)0.0474 (15)0.0065 (13)0.0170 (13)0.0288 (14)
O60.0546 (16)0.0384 (14)0.0572 (16)0.0014 (12)0.0160 (13)0.0162 (13)
C10.0331 (18)0.0297 (17)0.0395 (19)0.0029 (14)0.0115 (14)0.0174 (15)
C20.0323 (17)0.0266 (16)0.0342 (17)0.0037 (13)0.0081 (14)0.0119 (14)
C30.0364 (18)0.0289 (17)0.0338 (18)0.0060 (14)0.0105 (14)0.0111 (14)
C40.046 (2)0.0278 (18)0.0387 (19)0.0032 (15)0.0114 (16)0.0083 (15)
C50.044 (2)0.0333 (19)0.0356 (19)0.0023 (16)0.0081 (15)0.0043 (15)
C60.045 (2)0.0371 (19)0.0306 (18)0.0078 (16)0.0102 (15)0.0099 (16)
C70.042 (2)0.0374 (19)0.0407 (19)0.0049 (16)0.0134 (15)0.0194 (16)
C80.045 (2)0.0274 (17)0.0402 (19)0.0051 (15)0.0077 (16)0.0113 (15)
C90.0339 (18)0.0261 (17)0.0377 (18)0.0064 (14)0.0072 (14)0.0091 (15)
C100.043 (2)0.0322 (19)0.046 (2)0.0008 (16)0.0046 (16)0.0095 (17)
C110.051 (2)0.037 (2)0.038 (2)0.0044 (17)0.0016 (17)0.0046 (17)
C120.062 (3)0.039 (2)0.0327 (19)0.0069 (18)0.0041 (17)0.0095 (17)
C130.054 (2)0.0351 (19)0.0377 (19)0.0024 (17)0.0105 (17)0.0140 (16)
Geometric parameters (Å, º) top
Cu1—O11.889 (2)C2—C31.421 (4)
Cu1—N11.936 (3)C3—C41.407 (4)
Cu1—O21.975 (2)C4—C51.368 (5)
Cu1—N21.982 (3)C4—H40.9300
Cl1—C61.747 (3)C5—C61.396 (5)
N1—C11.288 (4)C5—H50.9300
N1—C81.469 (4)C6—C71.359 (5)
N2—C131.343 (4)C7—H70.9300
N2—C91.349 (4)C8—C91.500 (4)
N3—O41.233 (4)C8—H8A0.9700
N3—O31.236 (4)C8—H8B0.9700
N3—O51.247 (4)C9—C101.379 (4)
O1—C31.318 (4)C10—C111.376 (5)
O2—H2A0.8500C10—H100.9300
O2—H2B0.8500C11—C121.383 (5)
O6—H6A0.8500C11—H110.9300
O6—H6B0.8499C12—C131.372 (5)
C1—C21.433 (4)C12—H120.9300
C1—H10.9300C13—H130.9300
C2—C71.414 (4)
O1—Cu1—N193.94 (10)C3—C4—H4119.1
O1—Cu1—O288.85 (9)C4—C5—C6119.9 (3)
N1—Cu1—O2171.60 (10)C4—C5—H5120.1
O1—Cu1—N2176.81 (10)C6—C5—H5120.1
N1—Cu1—N282.98 (11)C7—C6—C5120.6 (3)
O2—Cu1—N294.32 (10)C7—C6—Cl1120.8 (3)
C1—N1—C8118.5 (3)C5—C6—Cl1118.5 (3)
C1—N1—Cu1125.9 (2)C6—C7—C2120.6 (3)
C8—N1—Cu1115.6 (2)C6—C7—H7119.7
C13—N2—C9118.7 (3)C2—C7—H7119.7
C13—N2—Cu1125.8 (2)N1—C8—C9109.7 (3)
C9—N2—Cu1115.3 (2)N1—C8—H8A109.7
O4—N3—O3120.0 (3)C9—C8—H8A109.7
O4—N3—O5118.9 (3)N1—C8—H8B109.7
O3—N3—O5121.1 (3)C9—C8—H8B109.7
C3—O1—Cu1127.6 (2)H8A—C8—H8B108.2
Cu1—O2—H2A105.5N2—C9—C10121.7 (3)
Cu1—O2—H2B115.4N2—C9—C8115.8 (3)
H2A—O2—H2B106.1C10—C9—C8122.5 (3)
H6A—O6—H6B107.8C11—C10—C9119.5 (3)
N1—C1—C2125.3 (3)C11—C10—H10120.3
N1—C1—H1117.3C9—C10—H10120.3
C2—C1—H1117.3C10—C11—C12118.7 (3)
C7—C2—C3119.4 (3)C10—C11—H11120.6
C7—C2—C1117.3 (3)C12—C11—H11120.6
C3—C2—C1123.4 (3)C13—C12—C11119.4 (3)
O1—C3—C4118.5 (3)C13—C12—H12120.3
O1—C3—C2123.8 (3)C11—C12—H12120.3
C4—C3—C2117.7 (3)N2—C13—C12122.1 (3)
C5—C4—C3121.8 (3)N2—C13—H13119.0
C5—C4—H4119.1C12—C13—H13119.0
O1—Cu1—N1—C12.8 (3)O1—C3—C4—C5179.8 (3)
O2—Cu1—N1—C1106.3 (7)C2—C3—C4—C51.0 (5)
N2—Cu1—N1—C1178.0 (3)C3—C4—C5—C60.3 (5)
O1—Cu1—N1—C8179.4 (2)C4—C5—C6—C71.1 (5)
O2—Cu1—N1—C870.3 (8)C4—C5—C6—Cl1178.7 (3)
N2—Cu1—N1—C81.4 (2)C5—C6—C7—C20.5 (5)
O1—Cu1—N2—C13163.3 (19)Cl1—C6—C7—C2179.3 (3)
N1—Cu1—N2—C13178.8 (3)C3—C2—C7—C60.8 (5)
O2—Cu1—N2—C139.1 (3)C1—C2—C7—C6178.7 (3)
O1—Cu1—N2—C912 (2)C1—N1—C8—C9177.7 (3)
N1—Cu1—N2—C93.5 (2)Cu1—N1—C8—C95.5 (4)
O2—Cu1—N2—C9175.5 (2)C13—N2—C9—C102.4 (5)
N1—Cu1—O1—C33.4 (3)Cu1—N2—C9—C10173.3 (3)
O2—Cu1—O1—C3168.7 (3)C13—N2—C9—C8176.7 (3)
N2—Cu1—O1—C319 (2)Cu1—N2—C9—C87.6 (4)
C8—N1—C1—C2178.5 (3)N1—C8—C9—N28.4 (4)
Cu1—N1—C1—C22.0 (5)N1—C8—C9—C10172.5 (3)
N1—C1—C2—C7179.8 (3)N2—C9—C10—C111.4 (5)
N1—C1—C2—C30.7 (5)C8—C9—C10—C11177.7 (3)
Cu1—O1—C3—C4176.1 (2)C9—C10—C11—C120.8 (5)
Cu1—O1—C3—C23.1 (5)C10—C11—C12—C131.8 (6)
C7—C2—C3—O1179.3 (3)C9—N2—C13—C121.3 (5)
C1—C2—C3—O11.2 (5)Cu1—N2—C13—C12173.9 (3)
C7—C2—C3—C41.5 (5)C11—C12—C13—N20.8 (6)
C1—C2—C3—C4178.0 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2a···O50.851.832.676 (4)173
O2—H2a···N30.852.523.253 (4)146
O2—H2a···O30.852.573.052 (4)117
O2—H2b···O6i0.851.812.657 (4)174
O6—H6a···O1ii0.852.082.915 (3)166
O6—H6b···O40.851.932.782 (5)177
Symmetry codes: (i) x1, y, z; (ii) x+1, y, z+1.

Experimental details

Crystal data
Chemical formula[Cu(C13H10ClN2O)(H2O)]NO3·H2O
Mr407.26
Crystal system, space groupTriclinic, P1
Temperature (K)298
a, b, c (Å)7.892 (2), 8.9741 (12), 11.8929 (15)
α, β, γ (°)106.841 (2), 102.198 (1), 92.897 (1)
V3)782.3 (2)
Z2
Radiation typeMo Kα
µ (mm1)1.60
Crystal size (mm)0.47 × 0.41 × 0.30
Data collection
DiffractometerRigaku SCXmini
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku, 2005)
Tmin, Tmax0.520, 0.645
No. of measured, independent and
observed [I > 2σ(I)] reflections
4114, 2714, 2280
Rint0.016
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.030, 0.074, 1.06
No. of reflections2714
No. of parameters218
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.40, 0.39

Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Selected geometric parameters (Å, º) top
Cu1—O11.889 (2)Cu1—O21.975 (2)
Cu1—N11.936 (3)Cu1—N21.982 (3)
O1—Cu1—N193.94 (10)O1—Cu1—N2176.81 (10)
O1—Cu1—O288.85 (9)N1—Cu1—N282.98 (11)
N1—Cu1—O2171.60 (10)O2—Cu1—N294.32 (10)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2a···O50.851.8292.676 (4)173.17
O2—H2a···N30.852.5173.253 (4)145.46
O2—H2a···O30.852.573.052 (4)117.12
O2—H2b···O6i0.851.8112.657 (4)173.63
O6—H6a···O1ii0.852.0832.915 (3)165.91
O6—H6b···O40.851.9342.782 (5)176.61
Symmetry codes: (i) x1, y, z; (ii) x+1, y, z+1.
 

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